0s autopkgtest [08:21:52]: starting date and time: 2024-05-24 08:21:52+0000
  0s autopkgtest [08:21:52]: git checkout: d60bd36 autopkgtest-build-lxd: Add missing remote prefix in get_boot_id().
  0s autopkgtest [08:21:52]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7n6d0e2n/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:r-cran-ggplot2 --apt-upgrade r-cran-matrixstats --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-cran-ggplot2/3.5.1+dfsg-1 -- lxd -r lxd-armhf-10.44.124.113 lxd-armhf-10.44.124.113:autopkgtest/ubuntu/oracular/armhf
 49s autopkgtest [08:22:41]: testbed dpkg architecture: armhf
 52s autopkgtest [08:22:44]: testbed apt version: 2.7.14build2
 52s autopkgtest [08:22:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 54s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [73.9 kB]
 54s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [1964 B]
 55s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [53.5 kB]
 55s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [497 kB]
 55s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [3388 B]
 55s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf Packages [112 kB]
 55s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf Packages [432 kB]
 55s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf Packages [1968 B]
 55s Fetched 1176 kB in 1s (946 kB/s)
 55s Reading package lists...
 79s tee: /proc/self/fd/2: Permission denied
107s Hit:1 http://ftpmaster.internal/ubuntu oracular InRelease
107s Hit:2 http://ftpmaster.internal/ubuntu oracular-updates InRelease
107s Hit:3 http://ftpmaster.internal/ubuntu oracular-security InRelease
107s Hit:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease
110s Reading package lists...
110s Reading package lists...
111s Building dependency tree...
111s Reading state information...
112s Calculating upgrade...
113s The following package was automatically installed and is no longer required:
113s   libatm1t64
113s Use 'apt autoremove' to remove it.
113s The following NEW packages will be installed:
113s   python3-jaraco.context python3-jaraco.functools
113s The following packages will be upgraded:
113s   apparmor apport apport-core-dump-handler apt apt-utils bash-completion curl
113s   dhcpcd-base dpkg dpkg-dev dracut-install eatmydata fwupd gcc-14-base
113s   gir1.2-girepository-2.0 gir1.2-glib-2.0 groff-base initramfs-tools
113s   initramfs-tools-bin initramfs-tools-core iproute2 klibc-utils less libacl1
113s   libapparmor1 libapt-pkg6.0t64 libbpf1 libbsd0 libc-bin libc6 libcap-ng0
113s   libcurl3t64-gnutls libcurl4t64 libdpkg-perl libeatmydata1 libelf1t64
113s   libevent-core-2.1-7t64 libexpat1 libfwupd2 libgcc-s1 libgcrypt20
113s   libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgnutls30t64
113s   libgpg-error-l10n libgpg-error0 libklibc liblocale-gettext-perl liblz4-1
113s   libnss3 libnvme1t64 libpam-modules libpam-modules-bin libpam-runtime
113s   libpam0g libperl5.38t64 libslang2 libsqlite3-0 libstdc++6 libtirpc-common
113s   libtirpc3t64 libuv1t64 libxcb1 locales man-db pastebinit perl perl-base
113s   perl-modules-5.38 python-apt-common python-babel-localedata python3-apport
113s   python3-apt python3-babel python3-blinker python3-httplib2 python3-jinja2
113s   python3-keyring python3-problem-report python3-pyparsing python3-six rsync
113s   tzdata ubuntu-pro-client ubuntu-pro-client-l10n vim-common vim-tiny xxd
114s 89 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
114s Need to get 48.8 MB of archives.
114s After this operation, 267 kB of additional disk space will be used.
114s Get:1 http://ftpmaster.internal/ubuntu oracular/main armhf gcc-14-base armhf 14.1.0-1ubuntu1 [48.4 kB]
114s Get:2 http://ftpmaster.internal/ubuntu oracular/main armhf libgcc-s1 armhf 14.1.0-1ubuntu1 [41.5 kB]
114s Get:3 http://ftpmaster.internal/ubuntu oracular/main armhf libstdc++6 armhf 14.1.0-1ubuntu1 [714 kB]
114s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf libc6 armhf 2.39-0ubuntu8.1 [2828 kB]
114s Get:5 http://ftpmaster.internal/ubuntu oracular/main armhf libgpg-error-l10n all 1.49-2 [8228 B]
114s Get:6 http://ftpmaster.internal/ubuntu oracular/main armhf libgpg-error0 armhf 1.49-2 [62.7 kB]
114s Get:7 http://ftpmaster.internal/ubuntu oracular/main armhf libgcrypt20 armhf 1.10.3-3 [454 kB]
114s Get:8 http://ftpmaster.internal/ubuntu oracular/main armhf liblz4-1 armhf 1.9.4-2 [58.0 kB]
114s Get:9 http://ftpmaster.internal/ubuntu oracular/main armhf libapt-pkg6.0t64 armhf 2.9.3 [1013 kB]
114s Get:10 http://ftpmaster.internal/ubuntu oracular/main armhf dpkg armhf 1.22.6ubuntu10 [1230 kB]
114s Get:11 http://ftpmaster.internal/ubuntu oracular/main armhf libperl5.38t64 armhf 5.38.2-4 [4102 kB]
115s Get:12 http://ftpmaster.internal/ubuntu oracular/main armhf perl armhf 5.38.2-4 [231 kB]
115s Get:13 http://ftpmaster.internal/ubuntu oracular/main armhf perl-base armhf 5.38.2-4 [1671 kB]
115s Get:14 http://ftpmaster.internal/ubuntu oracular/main armhf perl-modules-5.38 all 5.38.2-4 [3110 kB]
115s Get:15 http://ftpmaster.internal/ubuntu oracular/main armhf libc-bin armhf 2.39-0ubuntu8.1 [530 kB]
115s Get:16 http://ftpmaster.internal/ubuntu oracular/main armhf apt armhf 2.9.3 [1397 kB]
115s Get:17 http://ftpmaster.internal/ubuntu oracular/main armhf apt-utils armhf 2.9.3 [217 kB]
115s Get:18 http://ftpmaster.internal/ubuntu oracular/main armhf libgnutls30t64 armhf 3.8.5-2ubuntu1 [958 kB]
115s Get:19 http://ftpmaster.internal/ubuntu oracular/main armhf libpam0g armhf 1.5.3-7ubuntu1 [62.3 kB]
115s Get:20 http://ftpmaster.internal/ubuntu oracular/main armhf libpam-modules-bin armhf 1.5.3-7ubuntu1 [47.0 kB]
115s Get:21 http://ftpmaster.internal/ubuntu oracular/main armhf libpam-modules armhf 1.5.3-7ubuntu1 [266 kB]
115s Get:22 http://ftpmaster.internal/ubuntu oracular/main armhf liblocale-gettext-perl armhf 1.07-7 [14.8 kB]
115s Get:23 http://ftpmaster.internal/ubuntu oracular/main armhf libacl1 armhf 2.3.2-2 [15.1 kB]
115s Get:24 http://ftpmaster.internal/ubuntu oracular/main armhf rsync armhf 3.3.0-1 [414 kB]
115s Get:25 http://ftpmaster.internal/ubuntu oracular/main armhf python-apt-common all 2.9.0 [20.1 kB]
115s Get:26 http://ftpmaster.internal/ubuntu oracular/main armhf python3-apt armhf 2.9.0 [162 kB]
115s Get:27 http://ftpmaster.internal/ubuntu oracular/main armhf python3-pyparsing all 3.1.2-1 [86.4 kB]
115s Get:28 http://ftpmaster.internal/ubuntu oracular/main armhf python3-httplib2 all 0.22.0-1 [30.4 kB]
115s Get:29 http://ftpmaster.internal/ubuntu oracular/main armhf python3-problem-report all 2.28.1-0ubuntu4 [23.9 kB]
115s Get:30 http://ftpmaster.internal/ubuntu oracular/main armhf python3-apport all 2.28.1-0ubuntu4 [92.1 kB]
115s Get:31 http://ftpmaster.internal/ubuntu oracular/main armhf gir1.2-girepository-2.0 armhf 1.80.1-3 [24.7 kB]
115s Get:32 http://ftpmaster.internal/ubuntu oracular/main armhf gir1.2-glib-2.0 armhf 2.80.2-1ubuntu1 [182 kB]
115s Get:33 http://ftpmaster.internal/ubuntu oracular/main armhf libglib2.0-0t64 armhf 2.80.2-1ubuntu1 [1421 kB]
115s Get:34 http://ftpmaster.internal/ubuntu oracular/main armhf libgirepository-1.0-1 armhf 1.80.1-3 [107 kB]
115s Get:35 http://ftpmaster.internal/ubuntu oracular/main armhf apport-core-dump-handler all 2.28.1-0ubuntu4 [16.9 kB]
115s Get:36 http://ftpmaster.internal/ubuntu oracular/main armhf apport all 2.28.1-0ubuntu4 [83.4 kB]
115s Get:37 http://ftpmaster.internal/ubuntu oracular/main armhf libcap-ng0 armhf 0.8.5-1 [13.6 kB]
115s Get:38 http://ftpmaster.internal/ubuntu oracular/main armhf libpam-runtime all 1.5.3-7ubuntu1 [40.8 kB]
115s Get:39 http://ftpmaster.internal/ubuntu oracular/main armhf dhcpcd-base armhf 1:10.0.6-5 [186 kB]
115s Get:40 http://ftpmaster.internal/ubuntu oracular/main armhf libelf1t64 armhf 0.191-1 [49.8 kB]
115s Get:41 http://ftpmaster.internal/ubuntu oracular/main armhf libbpf1 armhf 1:1.4.1-1 [151 kB]
115s Get:42 http://ftpmaster.internal/ubuntu oracular/main armhf libtirpc-common all 1.3.4+ds-1.3 [8106 B]
115s Get:43 http://ftpmaster.internal/ubuntu oracular/main armhf libtirpc3t64 armhf 1.3.4+ds-1.3 [73.3 kB]
115s Get:44 http://ftpmaster.internal/ubuntu oracular/main armhf iproute2 armhf 6.9.0-1 [1083 kB]
115s Get:45 http://ftpmaster.internal/ubuntu oracular/main armhf less armhf 590-2ubuntu2.1 [131 kB]
115s Get:46 http://ftpmaster.internal/ubuntu oracular/main armhf libapparmor1 armhf 4.0.1-0ubuntu1 [45.5 kB]
115s Get:47 http://ftpmaster.internal/ubuntu oracular/main armhf libbsd0 armhf 0.12.2-1 [36.5 kB]
115s Get:48 http://ftpmaster.internal/ubuntu oracular/main armhf libexpat1 armhf 2.6.2-1 [65.9 kB]
115s Get:49 http://ftpmaster.internal/ubuntu oracular/main armhf libglib2.0-data all 2.80.2-1ubuntu1 [49.3 kB]
115s Get:50 http://ftpmaster.internal/ubuntu oracular/main armhf libslang2 armhf 2.3.3-5 [478 kB]
115s Get:51 http://ftpmaster.internal/ubuntu oracular/main armhf libsqlite3-0 armhf 3.45.3-1 [601 kB]
115s Get:52 http://ftpmaster.internal/ubuntu oracular/main armhf locales all 2.39-0ubuntu8.1 [4234 kB]
115s Get:53 http://ftpmaster.internal/ubuntu oracular/main armhf tzdata all 2024a-4ubuntu1 [274 kB]
115s Get:54 http://ftpmaster.internal/ubuntu oracular/main armhf ubuntu-pro-client-l10n armhf 32.1 [19.4 kB]
115s Get:55 http://ftpmaster.internal/ubuntu oracular/main armhf ubuntu-pro-client armhf 32.1 [230 kB]
115s Get:56 http://ftpmaster.internal/ubuntu oracular/main armhf vim-tiny armhf 2:9.1.0377-1ubuntu1 [670 kB]
115s Get:57 http://ftpmaster.internal/ubuntu oracular/main armhf vim-common all 2:9.1.0377-1ubuntu1 [385 kB]
115s Get:58 http://ftpmaster.internal/ubuntu oracular/main armhf xxd armhf 2:9.1.0377-1ubuntu1 [63.0 kB]
115s Get:59 http://ftpmaster.internal/ubuntu oracular/main armhf apparmor armhf 4.0.1-0ubuntu1 [565 kB]
115s Get:60 http://ftpmaster.internal/ubuntu oracular/main armhf bash-completion all 1:2.14.0-1 [206 kB]
115s Get:61 http://ftpmaster.internal/ubuntu oracular/main armhf groff-base armhf 1.23.0-4 [946 kB]
115s Get:62 http://ftpmaster.internal/ubuntu oracular/main armhf libuv1t64 armhf 1.48.0-4 [83.2 kB]
116s Get:63 http://ftpmaster.internal/ubuntu oracular/main armhf libxcb1 armhf 1.17.0-2 [46.3 kB]
116s Get:64 http://ftpmaster.internal/ubuntu oracular/main armhf man-db armhf 2.12.1-1 [1201 kB]
116s Get:65 http://ftpmaster.internal/ubuntu oracular/main armhf curl armhf 8.5.0-2ubuntu10.1 [219 kB]
116s Get:66 http://ftpmaster.internal/ubuntu oracular/main armhf libcurl4t64 armhf 8.5.0-2ubuntu10.1 [296 kB]
116s Get:67 http://ftpmaster.internal/ubuntu oracular/main armhf dpkg-dev all 1.22.6ubuntu10 [1074 kB]
116s Get:68 http://ftpmaster.internal/ubuntu oracular/main armhf libdpkg-perl all 1.22.6ubuntu10 [269 kB]
116s Get:69 http://ftpmaster.internal/ubuntu oracular/main armhf dracut-install armhf 060+5-8ubuntu1 [34.3 kB]
116s Get:70 http://ftpmaster.internal/ubuntu oracular/main armhf libeatmydata1 armhf 131-2 [7106 B]
116s Get:71 http://ftpmaster.internal/ubuntu oracular/main armhf eatmydata all 131-2 [5576 B]
116s Get:72 http://ftpmaster.internal/ubuntu oracular/main armhf libcurl3t64-gnutls armhf 8.5.0-2ubuntu10.1 [290 kB]
116s Get:73 http://ftpmaster.internal/ubuntu oracular/main armhf libfwupd2 armhf 1.9.20-1 [126 kB]
116s Get:74 http://ftpmaster.internal/ubuntu oracular/main armhf fwupd armhf 1.9.20-1 [4368 kB]
116s Get:75 http://ftpmaster.internal/ubuntu oracular/main armhf initramfs-tools all 0.142ubuntu27 [7898 B]
116s Get:76 http://ftpmaster.internal/ubuntu oracular/main armhf initramfs-tools-core all 0.142ubuntu27 [49.5 kB]
116s Get:77 http://ftpmaster.internal/ubuntu oracular/main armhf initramfs-tools-bin armhf 0.142ubuntu27 [20.9 kB]
116s Get:78 http://ftpmaster.internal/ubuntu oracular/main armhf klibc-utils armhf 2.0.13-4ubuntu1 [93.8 kB]
116s Get:79 http://ftpmaster.internal/ubuntu oracular/main armhf libklibc armhf 2.0.13-4ubuntu1 [45.0 kB]
116s Get:80 http://ftpmaster.internal/ubuntu oracular/main armhf libevent-core-2.1-7t64 armhf 2.1.12-stable-10 [82.5 kB]
116s Get:81 http://ftpmaster.internal/ubuntu oracular/main armhf libnss3 armhf 2:3.100-1 [1331 kB]
116s Get:82 http://ftpmaster.internal/ubuntu oracular/main armhf libnvme1t64 armhf 1.9-1 [69.9 kB]
116s Get:83 http://ftpmaster.internal/ubuntu oracular/main armhf pastebinit all 1.7.0-1 [14.9 kB]
116s Get:84 http://ftpmaster.internal/ubuntu oracular/main armhf python3-babel all 2.14.0-1 [96.4 kB]
116s Get:85 http://ftpmaster.internal/ubuntu oracular/main armhf python-babel-localedata all 2.14.0-1 [6385 kB]
116s Get:86 http://ftpmaster.internal/ubuntu oracular/main armhf python3-blinker all 1.8.2-1 [11.4 kB]
116s Get:87 http://ftpmaster.internal/ubuntu oracular/main armhf python3-jaraco.context all 4.3.0-1 [6994 B]
116s Get:88 http://ftpmaster.internal/ubuntu oracular/main armhf python3-jaraco.functools all 4.0.0-1 [10.7 kB]
116s Get:89 http://ftpmaster.internal/ubuntu oracular/main armhf python3-jinja2 all 3.1.3-1 [107 kB]
116s Get:90 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-keyring all 25.2.1-1 [39.9 kB]
116s Get:91 http://ftpmaster.internal/ubuntu oracular/main armhf python3-six all 1.16.0-6 [13.0 kB]
117s Preconfiguring packages ...
118s Fetched 48.8 MB in 3s (19.0 MB/s)
118s (Reading database ... 
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118s Preparing to unpack .../gcc-14-base_14.1.0-1ubuntu1_armhf.deb ...
118s Unpacking gcc-14-base:armhf (14.1.0-1ubuntu1) over (14-20240412-0ubuntu1) ...
118s Setting up gcc-14-base:armhf (14.1.0-1ubuntu1) ...
118s (Reading database ... 
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118s Preparing to unpack .../libgcc-s1_14.1.0-1ubuntu1_armhf.deb ...
118s Unpacking libgcc-s1:armhf (14.1.0-1ubuntu1) over (14-20240412-0ubuntu1) ...
118s Setting up libgcc-s1:armhf (14.1.0-1ubuntu1) ...
119s (Reading database ... 
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119s Preparing to unpack .../libstdc++6_14.1.0-1ubuntu1_armhf.deb ...
119s Unpacking libstdc++6:armhf (14.1.0-1ubuntu1) over (14-20240412-0ubuntu1) ...
119s Setting up libstdc++6:armhf (14.1.0-1ubuntu1) ...
119s (Reading database ... 
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119s Preparing to unpack .../libc6_2.39-0ubuntu8.1_armhf.deb ...
119s Unpacking libc6:armhf (2.39-0ubuntu8.1) over (2.39-0ubuntu8) ...
120s Setting up libc6:armhf (2.39-0ubuntu8.1) ...
121s (Reading database ... 
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121s Preparing to unpack .../libgpg-error-l10n_1.49-2_all.deb ...
121s Unpacking libgpg-error-l10n (1.49-2) over (1.47-3build2) ...
121s Preparing to unpack .../libgpg-error0_1.49-2_armhf.deb ...
121s Unpacking libgpg-error0:armhf (1.49-2) over (1.47-3build2) ...
121s Setting up libgpg-error0:armhf (1.49-2) ...
121s (Reading database ... 
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121s Preparing to unpack .../libgcrypt20_1.10.3-3_armhf.deb ...
121s Unpacking libgcrypt20:armhf (1.10.3-3) over (1.10.3-2build1) ...
121s Setting up libgcrypt20:armhf (1.10.3-3) ...
121s (Reading database ... 
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121s Preparing to unpack .../liblz4-1_1.9.4-2_armhf.deb ...
121s Unpacking liblz4-1:armhf (1.9.4-2) over (1.9.4-1build1) ...
121s Setting up liblz4-1:armhf (1.9.4-2) ...
121s (Reading database ... 
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121s Preparing to unpack .../libapt-pkg6.0t64_2.9.3_armhf.deb ...
121s Unpacking libapt-pkg6.0t64:armhf (2.9.3) over (2.7.14build2) ...
122s Setting up libapt-pkg6.0t64:armhf (2.9.3) ...
122s (Reading database ... 
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122s Preparing to unpack .../dpkg_1.22.6ubuntu10_armhf.deb ...
122s Unpacking dpkg (1.22.6ubuntu10) over (1.22.6ubuntu6) ...
122s Setting up dpkg (1.22.6ubuntu10) ...
123s (Reading database ... 
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147s Setting up libexpat1:armhf (2.6.2-1) ...
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147s Setting up libxcb1:armhf (1.17.0-2) ...
147s Setting up apt-utils (2.9.3) ...
147s Setting up python3-jaraco.functools (4.0.0-1) ...
147s Setting up python3-jaraco.context (4.3.0-1) ...
148s Setting up libcurl4t64:armhf (8.5.0-2ubuntu10.1) ...
148s Setting up python3-problem-report (2.28.1-0ubuntu4) ...
148s Setting up libtirpc-common (1.3.4+ds-1.3) ...
148s Setting up libsqlite3-0:armhf (3.45.3-1) ...
148s Setting up libuv1t64:armhf (1.48.0-4) ...
148s Setting up libcurl3t64-gnutls:armhf (8.5.0-2ubuntu10.1) ...
148s Setting up less (590-2ubuntu2.1) ...
148s Setting up pastebinit (1.7.0-1) ...
148s Setting up libnss3:armhf (2:3.100-1) ...
148s Setting up locales (2.39-0ubuntu8.1) ...
149s Generating locales (this might take a while)...
155s   en_US.UTF-8... done
155s Generation complete.
155s Setting up xxd (2:9.1.0377-1ubuntu1) ...
155s Setting up libelf1t64:armhf (0.191-1) ...
155s Setting up python-babel-localedata (2.14.0-1) ...
155s Setting up tzdata (2024a-4ubuntu1) ...
155s 
155s Current default time zone: 'Etc/UTC'
155s Local time is now:      Fri May 24 08:24:27 UTC 2024.
155s Universal Time is now:  Fri May 24 08:24:27 UTC 2024.
155s Run 'dpkg-reconfigure tzdata' if you wish to change it.
155s 
155s Setting up python3-six (1.16.0-6) ...
156s Setting up apparmor (4.0.1-0ubuntu1) ...
156s Installing new version of config file /etc/apparmor.d/abstractions/authentication ...
156s Installing new version of config file /etc/apparmor.d/abstractions/samba ...
156s Installing new version of config file /etc/apparmor.d/firefox ...
156s apparmor_parser: Unable to replace "lsb_release".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
156s 
156s apparmor_parser: Unable to replace "kmod".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
156s 
156s apparmor_parser: Unable to replace "nvidia_modprobe".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
156s 
158s Reloading AppArmor profiles 
158s /sbin/apparmor_parser: Unable to replace "1password".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "Discord".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "MongoDB Compass".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "balena-etcher".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "brave".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "buildah".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "busybox".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "cam".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "ch-checkns".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "ch-run".  /sbin/apparmor_parser: Unable to replace "vscode".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "chrome".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "crun".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "devhelp".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "element-desktop".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "epiphany".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "evolution".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "firefox".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "flatpak".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "foliate".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "bwrap".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "geary".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "github-desktop".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "goldendict".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "ipa_verify".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "kchmviewer".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "keybase".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "libcamerify".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "linux-sandbox".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "lc-compliance".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "loupe".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "lxc-create".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "lxc-destroy".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "lxc-stop".  /sbin/apparmor_parser: Unable to replace "lxc-execute".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "lxc-usernsexec".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "mmdebstrap".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "msedge".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "nautilus".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "notepadqq".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "lxc-unshare".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "obsidian".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "lxc-attach".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "opam".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "opera".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "pageedit".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "qcam".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "privacybrowser".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "qutebrowser".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "qmapshack".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "rpm".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "runc".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "rssguard".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "sbuild".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "polypane".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "podman".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "sbuild-abort".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "sbuild-adduser".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "rootlesskit".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "sbuild-clean".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "sbuild-createchroot".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "sbuild-destroychroot".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "plasmashell".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "sbuild-distupgrade".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "sbuild-shell".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "sbuild-apt".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "sbuild-unhold".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "sbuild-update".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "sbuild-upgrade".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "scide".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "sbuild-checkpackages".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "sbuild-hold".  /sbin/apparmor_parser: Unable to replace "signal-desktop".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "steam".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "stress-ng".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "slack".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "thunderbird".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "toybox".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "systemd-coredump".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "surfshark".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "trinity".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "slirp4netns".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "tup".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "tuxedo-control-center".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "unprivileged_userns".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "lsb_release".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "kmod".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "nvidia_modprobe".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "userbindmount".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "uwsgi-core".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "vdens".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "virtiofsd".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "vivaldi-bin".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "vpnns".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "wike".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "wpcom".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "unix-chkpwd".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_apt_news".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "/usr/bin/man".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "/usr/lib/NetworkManager/nm-dhcp-client.action".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "rsyslogd".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
158s /sbin/apparmor_parser: Unable to replace "tcpdump".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
158s 
159s /sbin/apparmor_parser: Unable to replace "transmission-cli".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
159s 
159s Error: At least one profile failed to load
159s Setting up libklibc:armhf (2.0.13-4ubuntu1) ...
159s Setting up python3-jinja2 (3.1.3-1) ...
160s Setting up libglib2.0-0t64:armhf (2.80.2-1ubuntu1) ...
160s No schema files found: doing nothing.
160s Setting up libglib2.0-data (2.80.2-1ubuntu1) ...
160s Setting up vim-common (2:9.1.0377-1ubuntu1) ...
160s Setting up libslang2:armhf (2.3.3-5) ...
160s Setting up python3-pyparsing (3.1.2-1) ...
160s Setting up libnvme1t64 (1.9-1) ...
160s Setting up bash-completion (1:2.14.0-1) ...
160s Installing new version of config file /etc/profile.d/bash_completion.sh ...
160s Setting up perl-modules-5.38 (5.38.2-4) ...
160s Setting up dhcpcd-base (1:10.0.6-5) ...
160s Setting up gir1.2-glib-2.0:armhf (2.80.2-1ubuntu1) ...
160s Setting up python-apt-common (2.9.0) ...
160s Setting up dracut-install (060+5-8ubuntu1) ...
160s Setting up groff-base (1.23.0-4) ...
160s Setting up libeatmydata1:armhf (131-2) ...
160s Setting up python3-keyring (25.2.1-1) ...
161s Setting up python3-httplib2 (0.22.0-1) ...
161s Setting up libgirepository-1.0-1:armhf (1.80.1-3) ...
161s Setting up libevent-core-2.1-7t64:armhf (2.1.12-stable-10) ...
161s Setting up curl (8.5.0-2ubuntu10.1) ...
161s Setting up libperl5.38t64:armhf (5.38.2-4) ...
161s Setting up klibc-utils (2.0.13-4ubuntu1) ...
161s Setting up libbsd0:armhf (0.12.2-1) ...
161s Setting up libgpg-error-l10n (1.49-2) ...
161s Setting up liblocale-gettext-perl (1.07-7) ...
161s Setting up libbpf1:armhf (1:1.4.1-1) ...
161s Setting up rsync (3.3.0-1) ...
162s rsync.service is a disabled or a static unit not running, not starting it.
162s Setting up initramfs-tools-bin (0.142ubuntu27) ...
162s Setting up python3-blinker (1.8.2-1) ...
163s Setting up eatmydata (131-2) ...
163s Setting up libtirpc3t64:armhf (1.3.4+ds-1.3) ...
163s Setting up python3-babel (2.14.0-1) ...
163s Setting up python3-apt (2.9.0) ...
164s Setting up iproute2 (6.9.0-1) ...
164s Removing obsolete conffile /etc/iproute2/group ...
164s Removing obsolete conffile /etc/iproute2/rt_realms ...
164s Removing obsolete conffile /etc/iproute2/rt_scopes ...
164s Removing obsolete conffile /etc/iproute2/rt_tables ...
164s Removing obsolete conffile /etc/iproute2/rt_tables.d/README ...
164s Removing obsolete conffile /etc/iproute2/rt_protos.d/README ...
164s Removing obsolete conffile /etc/iproute2/rt_protos ...
164s Removing obsolete conffile /etc/iproute2/rt_dsfield ...
164s Removing obsolete conffile /etc/iproute2/nl_protos ...
164s Removing obsolete conffile /etc/iproute2/ematch_map ...
164s Removing obsolete conffile /etc/iproute2/bpf_pinning ...
164s Setting up libfwupd2:armhf (1.9.20-1) ...
164s Setting up vim-tiny (2:9.1.0377-1ubuntu1) ...
164s Setting up man-db (2.12.1-1) ...
164s Updating database of manual pages ...
167s apparmor_parser: Unable to replace "/usr/bin/man".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
167s 
168s man-db.service is a disabled or a static unit not running, not starting it.
168s Setting up python3-apport (2.28.1-0ubuntu4) ...
168s Setting up perl (5.38.2-4) ...
168s Setting up gir1.2-girepository-2.0:armhf (1.80.1-3) ...
168s Setting up libdpkg-perl (1.22.6ubuntu10) ...
168s Setting up initramfs-tools-core (0.142ubuntu27) ...
168s Setting up ubuntu-pro-client (32.1) ...
168s Installing new version of config file /etc/apparmor.d/ubuntu_pro_apt_news ...
169s apparmor_parser: Unable to replace "ubuntu_pro_apt_news".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
169s 
170s apparmor_parser: Unable to replace "apt_methods".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
170s 
170s apparmor_parser: Unable to replace "ubuntu_pro_esm_cache".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
170s 
172s Setting up fwupd (1.9.20-1) ...
173s fwupd-offline-update.service is a disabled or a static unit not running, not starting it.
173s fwupd-refresh.service is a disabled or a static unit not running, not starting it.
174s fwupd.service is a disabled or a static unit not running, not starting it.
174s Setting up ubuntu-pro-client-l10n (32.1) ...
174s Setting up initramfs-tools (0.142ubuntu27) ...
174s update-initramfs: deferring update (trigger activated)
174s Setting up dpkg-dev (1.22.6ubuntu10) ...
174s Setting up apport-core-dump-handler (2.28.1-0ubuntu4) ...
175s Setting up apport (2.28.1-0ubuntu4) ...
175s Installing new version of config file /etc/apport/crashdb.conf ...
177s apport-autoreport.service is a disabled or a static unit not running, not starting it.
177s Processing triggers for dbus (1.14.10-4ubuntu4) ...
177s Processing triggers for libc-bin (2.39-0ubuntu8.1) ...
177s Processing triggers for initramfs-tools (0.142ubuntu27) ...
179s Reading package lists...
180s Building dependency tree...
180s Reading state information...
181s The following packages will be REMOVED:
181s   libatm1t64*
182s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded.
182s After this operation, 94.2 kB disk space will be freed.
182s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 58570 files and directories currently installed.)
182s Removing libatm1t64:armhf (1:2.5.1-5.1build1) ...
182s Processing triggers for libc-bin (2.39-0ubuntu8.1) ...
185s autopkgtest [08:24:57]: rebooting testbed after setup commands that affected boot
231s autopkgtest [08:25:43]: testbed running kernel: Linux 5.4.0-174-generic #193-Ubuntu SMP Thu Mar 7 15:13:37 UTC 2024
262s autopkgtest [08:26:14]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-matrixstats
274s Get:1 http://ftpmaster.internal/ubuntu oracular/universe r-cran-matrixstats 1.2.0-1 (dsc) [2230 B]
274s Get:2 http://ftpmaster.internal/ubuntu oracular/universe r-cran-matrixstats 1.2.0-1 (tar) [211 kB]
274s Get:3 http://ftpmaster.internal/ubuntu oracular/universe r-cran-matrixstats 1.2.0-1 (diff) [4752 B]
274s gpgv: Signature made Mon Jan  8 21:38:59 2024 UTC
274s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
274s gpgv:                issuer "tille@debian.org"
274s gpgv: Can't check signature: No public key
274s dpkg-source: warning: cannot verify inline signature for ./r-cran-matrixstats_1.2.0-1.dsc: no acceptable signature found
274s autopkgtest [08:26:26]: testing package r-cran-matrixstats version 1.2.0-1
276s autopkgtest [08:26:28]: build not needed
284s autopkgtest [08:26:36]: test run-unit-test: preparing testbed
294s Reading package lists...
295s Building dependency tree...
295s Reading state information...
296s Starting pkgProblemResolver with broken count: 0
296s Starting 2 pkgProblemResolver with broken count: 0
296s Done
297s The following additional packages will be installed:
297s   fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
297s   fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1
297s   libdeflate0 libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3
297s   libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap
297s   libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax
297s   liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
297s   libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6
297s   libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0
297s   libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css r-base-core
297s   r-cran-base64enc r-cran-cli r-cran-colorspace r-cran-commonmark
297s   r-cran-digest r-cran-evaluate r-cran-fansi r-cran-farver r-cran-ggplot2
297s   r-cran-glue r-cran-gtable r-cran-highr r-cran-isoband r-cran-knitr
297s   r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-magrittr
297s   r-cran-markdown r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-mgcv
297s   r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-r.cache
297s   r-cran-r.devices r-cran-r.methodss3 r-cran-r.oo r-cran-r.rsp r-cran-r.utils
297s   r-cran-r6 r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-tibble
297s   r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr r-cran-xfun
297s   r-cran-yaml tcl tcl8.6 unzip x11-common xdg-utils zip
297s Suggested packages:
297s   fonts-mathjax-extras fonts-stix libjs-mathjax-doc tk8.6 libjs-html5shiv
297s   elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-kernsmooth
297s   r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs
297s   r-cran-dplyr r-cran-png r-cran-jpeg r-cran-rmarkdown r-cran-viridis
297s   r-cran-covr r-cran-magick r-cran-sf r-cran-bit64 r-cran-dbi
297s   r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-stringi
297s   r-cran-survival r-cran-units r-cran-vdiffr r-cran-testthat r-cran-cairo
297s   r-cran-codetools r-cran-bench r-cran-blob r-cran-brio r-cran-callr
297s   r-cran-crayon r-cran-here r-cran-hms r-cran-htmltools r-cran-pkgbuild
297s   r-cran-pkgload r-cran-purrr r-cran-tidyr tcl-tclreadline
297s Recommended packages:
297s   javascript-common r-recommended r-base-dev r-doc-html r-cran-callr
297s   r-cran-covr r-cran-crayon r-cran-htmltools r-cran-htmlwidgets r-cran-mockery
297s   r-cran-processx r-cran-ps r-cran-rmarkdown r-cran-rprojroot
297s   r-cran-rstudioapi r-cran-testthat r-cran-whoami r-cran-curl r-cran-xml2
297s   r-cran-unitizer r-cran-dplyr r-cran-hexbin r-cran-hmisc r-cran-mapproj
297s   r-cran-maps r-cran-multcomp r-cran-profvis r-cran-quantreg r-cran-ragg
297s   r-cran-rpart r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-dbi
297s   r-cran-rsqlite r-cran-waldo r-cran-testit r-cran-bslib r-cran-codetools
297s   r-cran-formatr r-cran-gridsvg r-cran-jpeg r-cran-magick r-cran-png
297s   r-cran-reticulate r-cran-rgl r-cran-sass r-cran-tikzdevice r-cran-tinytex
297s   r-cran-webshot node-highlight.js r-cran-lintr r-cran-tidyverse r-cran-rcurl
297s   r-cran-lubridate libjs-remark-slide r-cran-fs r-cran-usethis r-cran-bit64
297s   r-cran-dichromat r-cran-hms r-cran-stringi r-cran-data.table r-cran-mockr
297s   r-cran-formattable r-cran-generics r-cran-pkgdown r-cran-zeallot r-cran-mime
297s   r-cran-remotes r-cran-renv r-cran-jsonlite r-cran-runit
297s   libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils
297s   x11-xserver-utils
297s The following NEW packages will be installed:
297s   autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core
297s   fonts-dejavu-mono fonts-glyphicons-halflings fonts-mathjax libblas3
297s   libcairo2 libdatrie1 libdeflate0 libfontconfig1 libfreetype6 libgfortran5
297s   libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8
297s   libjpeg8 libjs-bootstrap libjs-highlight.js libjs-jquery
297s   libjs-jquery-datatables libjs-mathjax liblapack3 liblerc4 libpango-1.0-0
297s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0
297s   libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6
297s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64
297s   node-normalize.css r-base-core r-cran-base64enc r-cran-cli r-cran-colorspace
297s   r-cran-commonmark r-cran-digest r-cran-evaluate r-cran-fansi r-cran-farver
297s   r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-highr r-cran-isoband
297s   r-cran-knitr r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-magrittr
297s   r-cran-markdown r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-mgcv
297s   r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-r.cache
297s   r-cran-r.devices r-cran-r.methodss3 r-cran-r.oo r-cran-r.rsp r-cran-r.utils
297s   r-cran-r6 r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-tibble
297s   r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr r-cran-xfun
297s   r-cran-yaml tcl tcl8.6 unzip x11-common xdg-utils zip
297s 0 upgraded, 100 newly installed, 0 to remove and 0 not upgraded.
297s Need to get 82.3 MB/82.3 MB of archives.
297s After this operation, 175 MB of additional disk space will be used.
297s Get:1 /tmp/autopkgtest.nMUE6C/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [760 B]
298s Get:2 http://ftpmaster.internal/ubuntu oracular/main armhf libfreetype6 armhf 2.13.2+dfsg-1build3 [331 kB]
298s Get:3 http://ftpmaster.internal/ubuntu oracular/main armhf fonts-dejavu-mono all 2.37-8 [502 kB]
298s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf fonts-dejavu-core all 2.37-8 [835 kB]
298s Get:5 http://ftpmaster.internal/ubuntu oracular/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB]
298s Get:6 http://ftpmaster.internal/ubuntu oracular/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB]
298s Get:7 http://ftpmaster.internal/ubuntu oracular/main armhf fontconfig armhf 2.15.0-1.1ubuntu2 [189 kB]
298s Get:8 http://ftpmaster.internal/ubuntu oracular/universe armhf fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB]
298s Get:9 http://ftpmaster.internal/ubuntu oracular/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
298s Get:10 http://ftpmaster.internal/ubuntu oracular/main armhf libblas3 armhf 3.12.0-3build1 [123 kB]
298s Get:11 http://ftpmaster.internal/ubuntu oracular/main armhf libpixman-1-0 armhf 0.42.2-1build1 [193 kB]
298s Get:12 http://ftpmaster.internal/ubuntu oracular/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB]
298s Get:13 http://ftpmaster.internal/ubuntu oracular/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B]
298s Get:14 http://ftpmaster.internal/ubuntu oracular/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB]
298s Get:15 http://ftpmaster.internal/ubuntu oracular/main armhf libcairo2 armhf 1.18.0-3build1 [482 kB]
298s Get:16 http://ftpmaster.internal/ubuntu oracular/main armhf libdatrie1 armhf 0.2.13-3build1 [15.7 kB]
298s Get:17 http://ftpmaster.internal/ubuntu oracular/main armhf libdeflate0 armhf 1.20-1 [38.3 kB]
298s Get:18 http://ftpmaster.internal/ubuntu oracular/main armhf libgfortran5 armhf 14.1.0-1ubuntu1 [311 kB]
298s Get:19 http://ftpmaster.internal/ubuntu oracular/main armhf libgomp1 armhf 14.1.0-1ubuntu1 [125 kB]
298s Get:20 http://ftpmaster.internal/ubuntu oracular/main armhf libgraphite2-3 armhf 1.3.14-2build1 [64.6 kB]
298s Get:21 http://ftpmaster.internal/ubuntu oracular/main armhf libharfbuzz0b armhf 8.3.0-2build2 [446 kB]
298s Get:22 http://ftpmaster.internal/ubuntu oracular/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB]
298s Get:23 http://ftpmaster.internal/ubuntu oracular/main armhf libice6 armhf 2:1.0.10-1build3 [35.4 kB]
298s Get:24 http://ftpmaster.internal/ubuntu oracular/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu2 [125 kB]
298s Get:25 http://ftpmaster.internal/ubuntu oracular/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B]
298s Get:26 http://ftpmaster.internal/ubuntu oracular/universe armhf libjs-bootstrap all 3.4.1+dfsg-3 [129 kB]
298s Get:27 http://ftpmaster.internal/ubuntu oracular/universe armhf libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB]
298s Get:28 http://ftpmaster.internal/ubuntu oracular/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
299s Get:29 http://ftpmaster.internal/ubuntu oracular/universe armhf libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB]
299s Get:30 http://ftpmaster.internal/ubuntu oracular/main armhf liblapack3 armhf 3.12.0-3build1 [2085 kB]
299s Get:31 http://ftpmaster.internal/ubuntu oracular/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu2 [151 kB]
299s Get:32 http://ftpmaster.internal/ubuntu oracular/main armhf libthai-data all 0.1.29-2build1 [158 kB]
299s Get:33 http://ftpmaster.internal/ubuntu oracular/main armhf libthai0 armhf 0.1.29-2build1 [15.2 kB]
299s Get:34 http://ftpmaster.internal/ubuntu oracular/main armhf libpango-1.0-0 armhf 1.52.2+ds-1 [209 kB]
299s Get:35 http://ftpmaster.internal/ubuntu oracular/main armhf libpangoft2-1.0-0 armhf 1.52.2+ds-1 [36.4 kB]
299s Get:36 http://ftpmaster.internal/ubuntu oracular/main armhf libpangocairo-1.0-0 armhf 1.52.2+ds-1 [24.9 kB]
299s Get:37 http://ftpmaster.internal/ubuntu oracular/main armhf libpaper1 armhf 1.1.29build1 [12.6 kB]
299s Get:38 http://ftpmaster.internal/ubuntu oracular/main armhf libpaper-utils armhf 1.1.29build1 [8184 B]
299s Get:39 http://ftpmaster.internal/ubuntu oracular/main armhf libsharpyuv0 armhf 1.4.0-0.1 [16.3 kB]
299s Get:40 http://ftpmaster.internal/ubuntu oracular/main armhf libsm6 armhf 2:1.2.3-1build3 [14.1 kB]
299s Get:41 http://ftpmaster.internal/ubuntu oracular/main armhf libtcl8.6 armhf 8.6.14+dfsg-1build1 [903 kB]
299s Get:42 http://ftpmaster.internal/ubuntu oracular/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB]
299s Get:43 http://ftpmaster.internal/ubuntu oracular/main armhf libwebp7 armhf 1.4.0-0.1 [184 kB]
299s Get:44 http://ftpmaster.internal/ubuntu oracular/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu2 [178 kB]
299s Get:45 http://ftpmaster.internal/ubuntu oracular/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB]
299s Get:46 http://ftpmaster.internal/ubuntu oracular/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B]
299s Get:47 http://ftpmaster.internal/ubuntu oracular/main armhf libtk8.6 armhf 8.6.14-1build1 [681 kB]
299s Get:48 http://ftpmaster.internal/ubuntu oracular/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB]
299s Get:49 http://ftpmaster.internal/ubuntu oracular/universe armhf node-normalize.css all 8.0.1-5 [10.8 kB]
299s Get:50 http://ftpmaster.internal/ubuntu oracular/main armhf zip armhf 3.0-13build1 [163 kB]
299s Get:51 http://ftpmaster.internal/ubuntu oracular/main armhf unzip armhf 6.0-28ubuntu4 [163 kB]
299s Get:52 http://ftpmaster.internal/ubuntu oracular/main armhf xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB]
299s Get:53 http://ftpmaster.internal/ubuntu oracular/universe armhf r-base-core armhf 4.4.0-2 [28.1 MB]
300s Get:54 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-base64enc armhf 0.1-3-3 [27.3 kB]
300s Get:55 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-cli armhf 3.6.2-1 [1363 kB]
300s Get:56 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-colorspace armhf 2.1-0+dfsg-1 [1538 kB]
300s Get:57 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-commonmark armhf 1.9.1-1 [110 kB]
300s Get:58 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-digest armhf 0.6.35-1 [202 kB]
300s Get:59 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-evaluate all 0.23-1 [90.2 kB]
300s Get:60 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-fansi armhf 1.0.5-1 [611 kB]
300s Get:61 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-farver armhf 2.1.1-2 [1353 kB]
300s Get:62 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-glue armhf 1.7.0-1 [153 kB]
300s Get:63 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-rlang armhf 1.1.3-1 [1658 kB]
300s Get:64 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
300s Get:65 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-gtable all 0.3.4+dfsg-1 [191 kB]
300s Get:66 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-isoband armhf 0.2.7-1 [1477 kB]
300s Get:67 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-mass armhf 7.3-60.0.1-1 [1118 kB]
300s Get:68 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-lattice armhf 0.22-6-1 [1363 kB]
300s Get:69 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-nlme armhf 3.1.164-1build1 [2248 kB]
300s Get:70 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-matrix armhf 1.6-5-1 [3762 kB]
301s Get:71 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-mgcv armhf 1.9-1-1 [3205 kB]
301s Get:72 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-labeling all 0.4.3-1 [62.1 kB]
301s Get:73 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-munsell all 0.5.0-2build1 [208 kB]
301s Get:74 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-r6 all 2.5.1-1 [99.0 kB]
301s Get:75 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB]
301s Get:76 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-viridislite all 0.4.2-2 [1088 kB]
301s Get:77 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-scales all 1.3.0-1 [603 kB]
301s Get:78 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-magrittr armhf 2.0.3-1 [154 kB]
301s Get:79 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-utf8 armhf 1.2.4-1 [136 kB]
301s Get:80 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-vctrs armhf 0.6.5-1 [1310 kB]
301s Get:81 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-pillar all 1.9.0+dfsg-1 [464 kB]
301s Get:82 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB]
301s Get:83 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-tibble armhf 3.2.1+dfsg-2 [415 kB]
301s Get:84 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-withr all 2.5.0-1 [225 kB]
301s Get:85 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB]
301s Get:86 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-xfun armhf 0.44+dfsg-1 [517 kB]
301s Get:87 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-highr all 0.10+dfsg-2 [38.5 kB]
301s Get:88 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-yaml armhf 2.3.8-2 [100 kB]
301s Get:89 http://ftpmaster.internal/ubuntu oracular/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
301s Get:90 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-knitr all 1.46+dfsg-1 [911 kB]
301s Get:91 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-markdown all 1.12+dfsg-2 [179 kB]
301s Get:92 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-matrixstats armhf 1.2.0-1 [478 kB]
301s Get:93 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-r.methodss3 all 1.8.2-1 [84.0 kB]
301s Get:94 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-r.oo all 1.26.0-1 [955 kB]
301s Get:95 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-r.utils all 2.12.3-1 [1386 kB]
301s Get:96 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-r.cache all 0.16.0-1 [113 kB]
301s Get:97 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-r.devices all 2.17.2+ds-1 [398 kB]
301s Get:98 http://ftpmaster.internal/ubuntu oracular/main armhf tcl8.6 armhf 8.6.14+dfsg-1build1 [14.6 kB]
301s Get:99 http://ftpmaster.internal/ubuntu oracular/main armhf tcl armhf 8.6.14build1 [4124 B]
301s Get:100 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-r.rsp all 0.46.0+ds-1 [1412 kB]
303s Preconfiguring packages ...
303s Fetched 82.3 MB in 4s (20.7 MB/s)
303s Selecting previously unselected package libfreetype6:armhf.
303s (Reading database ... 
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(Reading database ... 58565 files and directories currently installed.)
303s Preparing to unpack .../00-libfreetype6_2.13.2+dfsg-1build3_armhf.deb ...
303s Unpacking libfreetype6:armhf (2.13.2+dfsg-1build3) ...
303s Selecting previously unselected package fonts-dejavu-mono.
303s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ...
303s Unpacking fonts-dejavu-mono (2.37-8) ...
303s Selecting previously unselected package fonts-dejavu-core.
303s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ...
303s Unpacking fonts-dejavu-core (2.37-8) ...
303s Selecting previously unselected package fontconfig-config.
303s Preparing to unpack .../03-fontconfig-config_2.15.0-1.1ubuntu2_armhf.deb ...
304s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
304s Selecting previously unselected package libfontconfig1:armhf.
304s Preparing to unpack .../04-libfontconfig1_2.15.0-1.1ubuntu2_armhf.deb ...
304s Unpacking libfontconfig1:armhf (2.15.0-1.1ubuntu2) ...
304s Selecting previously unselected package fontconfig.
304s Preparing to unpack .../05-fontconfig_2.15.0-1.1ubuntu2_armhf.deb ...
304s Unpacking fontconfig (2.15.0-1.1ubuntu2) ...
304s Selecting previously unselected package fonts-glyphicons-halflings.
304s Preparing to unpack .../06-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ...
304s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ...
304s Selecting previously unselected package fonts-mathjax.
304s Preparing to unpack .../07-fonts-mathjax_2.7.9+dfsg-1_all.deb ...
304s Unpacking fonts-mathjax (2.7.9+dfsg-1) ...
304s Selecting previously unselected package libblas3:armhf.
304s Preparing to unpack .../08-libblas3_3.12.0-3build1_armhf.deb ...
304s Unpacking libblas3:armhf (3.12.0-3build1) ...
304s Selecting previously unselected package libpixman-1-0:armhf.
304s Preparing to unpack .../09-libpixman-1-0_0.42.2-1build1_armhf.deb ...
304s Unpacking libpixman-1-0:armhf (0.42.2-1build1) ...
305s Selecting previously unselected package libxcb-render0:armhf.
305s Preparing to unpack .../10-libxcb-render0_1.17.0-2_armhf.deb ...
305s Unpacking libxcb-render0:armhf (1.17.0-2) ...
305s Selecting previously unselected package libxcb-shm0:armhf.
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306s Selecting previously unselected package liblapack3:armhf.
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306s Selecting previously unselected package libthai-data.
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306s Selecting previously unselected package libpango-1.0-0:armhf.
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306s Selecting previously unselected package libpangocairo-1.0-0:armhf.
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307s Selecting previously unselected package libpaper1:armhf.
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307s Selecting previously unselected package libsharpyuv0:armhf.
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307s Selecting previously unselected package libjbig0:armhf.
307s Preparing to unpack .../40-libjbig0_2.1-6.1ubuntu2_armhf.deb ...
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307s Selecting previously unselected package libwebp7:armhf.
307s Preparing to unpack .../41-libwebp7_1.4.0-0.1_armhf.deb ...
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307s Selecting previously unselected package libtiff6:armhf.
307s Preparing to unpack .../42-libtiff6_4.5.1+git230720-4ubuntu2_armhf.deb ...
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307s Selecting previously unselected package libxft2:armhf.
307s Preparing to unpack .../43-libxft2_2.3.6-1build1_armhf.deb ...
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307s Selecting previously unselected package libxss1:armhf.
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307s Selecting previously unselected package libtk8.6:armhf.
307s Preparing to unpack .../45-libtk8.6_8.6.14-1build1_armhf.deb ...
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307s Selecting previously unselected package libxt6t64:armhf.
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308s Selecting previously unselected package node-normalize.css.
308s Preparing to unpack .../47-node-normalize.css_8.0.1-5_all.deb ...
308s Unpacking node-normalize.css (8.0.1-5) ...
308s Selecting previously unselected package zip.
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308s Unpacking zip (3.0-13build1) ...
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308s Preparing to unpack .../49-unzip_6.0-28ubuntu4_armhf.deb ...
308s Unpacking unzip (6.0-28ubuntu4) ...
308s Selecting previously unselected package xdg-utils.
308s Preparing to unpack .../50-xdg-utils_1.1.3-4.1ubuntu3_all.deb ...
308s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ...
308s Selecting previously unselected package r-base-core.
308s Preparing to unpack .../51-r-base-core_4.4.0-2_armhf.deb ...
308s Unpacking r-base-core (4.4.0-2) ...
309s Selecting previously unselected package r-cran-base64enc.
309s Preparing to unpack .../52-r-cran-base64enc_0.1-3-3_armhf.deb ...
309s Unpacking r-cran-base64enc (0.1-3-3) ...
309s Selecting previously unselected package r-cran-cli.
309s Preparing to unpack .../53-r-cran-cli_3.6.2-1_armhf.deb ...
309s Unpacking r-cran-cli (3.6.2-1) ...
309s Selecting previously unselected package r-cran-colorspace.
309s Preparing to unpack .../54-r-cran-colorspace_2.1-0+dfsg-1_armhf.deb ...
309s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ...
309s Selecting previously unselected package r-cran-commonmark.
309s Preparing to unpack .../55-r-cran-commonmark_1.9.1-1_armhf.deb ...
309s Unpacking r-cran-commonmark (1.9.1-1) ...
309s Selecting previously unselected package r-cran-digest.
309s Preparing to unpack .../56-r-cran-digest_0.6.35-1_armhf.deb ...
309s Unpacking r-cran-digest (0.6.35-1) ...
309s Selecting previously unselected package r-cran-evaluate.
309s Preparing to unpack .../57-r-cran-evaluate_0.23-1_all.deb ...
309s Unpacking r-cran-evaluate (0.23-1) ...
309s Selecting previously unselected package r-cran-fansi.
309s Preparing to unpack .../58-r-cran-fansi_1.0.5-1_armhf.deb ...
309s Unpacking r-cran-fansi (1.0.5-1) ...
309s Selecting previously unselected package r-cran-farver.
309s Preparing to unpack .../59-r-cran-farver_2.1.1-2_armhf.deb ...
309s Unpacking r-cran-farver (2.1.1-2) ...
310s Selecting previously unselected package r-cran-glue.
310s Preparing to unpack .../60-r-cran-glue_1.7.0-1_armhf.deb ...
310s Unpacking r-cran-glue (1.7.0-1) ...
310s Selecting previously unselected package r-cran-rlang.
310s Preparing to unpack .../61-r-cran-rlang_1.1.3-1_armhf.deb ...
310s Unpacking r-cran-rlang (1.1.3-1) ...
310s Selecting previously unselected package r-cran-lifecycle.
310s Preparing to unpack .../62-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ...
310s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ...
310s Selecting previously unselected package r-cran-gtable.
310s Preparing to unpack .../63-r-cran-gtable_0.3.4+dfsg-1_all.deb ...
310s Unpacking r-cran-gtable (0.3.4+dfsg-1) ...
310s Selecting previously unselected package r-cran-isoband.
310s Preparing to unpack .../64-r-cran-isoband_0.2.7-1_armhf.deb ...
310s Unpacking r-cran-isoband (0.2.7-1) ...
310s Selecting previously unselected package r-cran-mass.
310s Preparing to unpack .../65-r-cran-mass_7.3-60.0.1-1_armhf.deb ...
310s Unpacking r-cran-mass (7.3-60.0.1-1) ...
310s Selecting previously unselected package r-cran-lattice.
310s Preparing to unpack .../66-r-cran-lattice_0.22-6-1_armhf.deb ...
310s Unpacking r-cran-lattice (0.22-6-1) ...
310s Selecting previously unselected package r-cran-nlme.
310s Preparing to unpack .../67-r-cran-nlme_3.1.164-1build1_armhf.deb ...
310s Unpacking r-cran-nlme (3.1.164-1build1) ...
310s Selecting previously unselected package r-cran-matrix.
310s Preparing to unpack .../68-r-cran-matrix_1.6-5-1_armhf.deb ...
310s Unpacking r-cran-matrix (1.6-5-1) ...
311s Selecting previously unselected package r-cran-mgcv.
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311s Unpacking r-cran-mgcv (1.9-1-1) ...
311s Selecting previously unselected package r-cran-labeling.
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311s Selecting previously unselected package r-cran-munsell.
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311s Unpacking r-cran-munsell (0.5.0-2build1) ...
311s Selecting previously unselected package r-cran-r6.
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311s Selecting previously unselected package r-cran-rcolorbrewer.
311s Preparing to unpack .../73-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ...
311s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ...
311s Selecting previously unselected package r-cran-viridislite.
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311s Unpacking r-cran-viridislite (0.4.2-2) ...
311s Selecting previously unselected package r-cran-scales.
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311s Selecting previously unselected package r-cran-magrittr.
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311s Selecting previously unselected package r-cran-utf8.
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311s Selecting previously unselected package r-cran-vctrs.
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311s Selecting previously unselected package r-cran-pillar.
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312s Selecting previously unselected package r-cran-pkgconfig.
312s Preparing to unpack .../80-r-cran-pkgconfig_2.0.3-2build1_all.deb ...
312s Unpacking r-cran-pkgconfig (2.0.3-2build1) ...
312s Selecting previously unselected package r-cran-tibble.
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312s Unpacking r-cran-tibble (3.2.1+dfsg-2) ...
312s Selecting previously unselected package r-cran-withr.
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312s Selecting previously unselected package r-cran-ggplot2.
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312s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ...
312s Selecting previously unselected package r-cran-xfun.
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312s Selecting previously unselected package r-cran-highr.
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312s Selecting previously unselected package r-cran-yaml.
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313s Selecting previously unselected package libjs-mathjax.
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313s Unpacking libjs-mathjax (2.7.9+dfsg-1) ...
314s Selecting previously unselected package r-cran-knitr.
314s Preparing to unpack .../88-r-cran-knitr_1.46+dfsg-1_all.deb ...
314s Unpacking r-cran-knitr (1.46+dfsg-1) ...
314s Selecting previously unselected package r-cran-markdown.
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315s Unpacking r-cran-markdown (1.12+dfsg-2) ...
315s Selecting previously unselected package r-cran-matrixstats.
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315s Unpacking r-cran-matrixstats (1.2.0-1) ...
315s Selecting previously unselected package r-cran-r.methodss3.
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315s Unpacking r-cran-r.methodss3 (1.8.2-1) ...
315s Selecting previously unselected package r-cran-r.oo.
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315s Unpacking r-cran-r.oo (1.26.0-1) ...
315s Selecting previously unselected package r-cran-r.utils.
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315s Selecting previously unselected package r-cran-r.cache.
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315s Unpacking r-cran-r.cache (0.16.0-1) ...
315s Selecting previously unselected package r-cran-r.devices.
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315s Selecting previously unselected package tcl8.6.
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315s Unpacking tcl (8.6.14build1) ...
315s Selecting previously unselected package r-cran-r.rsp.
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315s Unpacking r-cran-r.rsp (0.46.0+ds-1) ...
316s Selecting previously unselected package autopkgtest-satdep.
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316s Setting up libgraphite2-3:armhf (1.3.14-2build1) ...
316s Setting up libpixman-1-0:armhf (0.42.2-1build1) ...
316s Setting up libsharpyuv0:armhf (1.4.0-0.1) ...
316s Setting up libpaper1:armhf (1.1.29build1) ...
316s 
316s Creating config file /etc/papersize with new version
316s Setting up fonts-mathjax (2.7.9+dfsg-1) ...
316s Setting up liblerc4:armhf (4.0.0+ds-4ubuntu2) ...
316s Setting up libjs-mathjax (2.7.9+dfsg-1) ...
316s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ...
316s Setting up libdatrie1:armhf (0.2.13-3build1) ...
316s Setting up libxcb-render0:armhf (1.17.0-2) ...
316s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ...
316s Setting up unzip (6.0-28ubuntu4) ...
316s Setting up x11-common (1:7.7+23ubuntu3) ...
317s Setting up libdeflate0:armhf (1.20-1) ...
317s Setting up libxcb-shm0:armhf (1.17.0-2) ...
317s Setting up libpaper-utils (1.1.29build1) ...
317s Setting up libgomp1:armhf (14.1.0-1ubuntu1) ...
317s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ...
317s Setting up zip (3.0-13build1) ...
317s Setting up libblas3:armhf (3.12.0-3build1) ...
317s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
317s Setting up libfreetype6:armhf (2.13.2+dfsg-1build3) ...
317s Setting up fonts-dejavu-mono (2.37-8) ...
317s Setting up libtcl8.6:armhf (8.6.14+dfsg-1build1) ...
317s Setting up fonts-dejavu-core (2.37-8) ...
317s Setting up libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ...
317s Setting up libgfortran5:armhf (14.1.0-1ubuntu1) ...
317s Setting up libwebp7:armhf (1.4.0-0.1) ...
317s Setting up libjs-highlight.js (9.18.5+dfsg1-2) ...
317s Setting up libharfbuzz0b:armhf (8.3.0-2build2) ...
317s Setting up libthai-data (0.1.29-2build1) ...
317s Setting up libxss1:armhf (1:1.2.3-1build3) ...
317s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
317s Setting up node-normalize.css (8.0.1-5) ...
317s Setting up xdg-utils (1.1.3-4.1ubuntu3) ...
317s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
317s Setting up libjs-bootstrap (3.4.1+dfsg-3) ...
317s Setting up libjpeg8:armhf (8c-2ubuntu11) ...
317s Setting up libice6:armhf (2:1.0.10-1build3) ...
317s Setting up tcl8.6 (8.6.14+dfsg-1build1) ...
317s Setting up liblapack3:armhf (3.12.0-3build1) ...
317s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
317s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
317s Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ...
317s Setting up libthai0:armhf (0.1.29-2build1) ...
317s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu2) ...
317s Setting up tcl (8.6.14build1) ...
317s Setting up libfontconfig1:armhf (2.15.0-1.1ubuntu2) ...
317s Setting up libsm6:armhf (2:1.2.3-1build3) ...
317s Setting up fontconfig (2.15.0-1.1ubuntu2) ...
320s Regenerating fonts cache... done.
320s Setting up libxft2:armhf (2.3.6-1build1) ...
320s Setting up libtk8.6:armhf (8.6.14-1build1) ...
320s Setting up libpango-1.0-0:armhf (1.52.2+ds-1) ...
320s Setting up libcairo2:armhf (1.18.0-3build1) ...
320s Setting up libxt6t64:armhf (1:1.2.1-1.2build1) ...
320s Setting up libpangoft2-1.0-0:armhf (1.52.2+ds-1) ...
320s Setting up libpangocairo-1.0-0:armhf (1.52.2+ds-1) ...
320s Setting up r-base-core (4.4.0-2) ...
320s 
320s Creating config file /etc/R/Renviron with new version
320s Setting up r-cran-labeling (0.4.3-1) ...
320s Setting up r-cran-lattice (0.22-6-1) ...
320s Setting up r-cran-nlme (3.1.164-1build1) ...
320s Setting up r-cran-farver (2.1.1-2) ...
320s Setting up r-cran-viridislite (0.4.2-2) ...
320s Setting up r-cran-commonmark (1.9.1-1) ...
320s Setting up r-cran-r6 (2.5.1-1) ...
320s Setting up r-cran-magrittr (2.0.3-1) ...
320s Setting up r-cran-rlang (1.1.3-1) ...
320s Setting up r-cran-matrixstats (1.2.0-1) ...
320s Setting up r-cran-xfun (0.44+dfsg-1) ...
320s Setting up r-cran-withr (2.5.0-1) ...
320s Setting up r-cran-base64enc (0.1-3-3) ...
320s Setting up r-cran-digest (0.6.35-1) ...
320s Setting up r-cran-yaml (2.3.8-2) ...
320s Setting up r-cran-evaluate (0.23-1) ...
320s Setting up r-cran-highr (0.10+dfsg-2) ...
320s Setting up r-cran-fansi (1.0.5-1) ...
320s Setting up r-cran-mass (7.3-60.0.1-1) ...
320s Setting up r-cran-glue (1.7.0-1) ...
320s Setting up r-cran-cli (3.6.2-1) ...
320s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
320s Setting up r-cran-r.methodss3 (1.8.2-1) ...
320s Setting up r-cran-pkgconfig (2.0.3-2build1) ...
320s Setting up r-cran-utf8 (1.2.4-1) ...
320s Setting up r-cran-colorspace (2.1-0+dfsg-1) ...
320s Setting up r-cran-markdown (1.12+dfsg-2) ...
320s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ...
320s Setting up r-cran-isoband (0.2.7-1) ...
320s Setting up r-cran-gtable (0.3.4+dfsg-1) ...
320s Setting up r-cran-matrix (1.6-5-1) ...
320s Setting up r-cran-knitr (1.46+dfsg-1) ...
320s Setting up r-cran-mgcv (1.9-1-1) ...
320s Setting up r-cran-vctrs (0.6.5-1) ...
320s Setting up r-cran-pillar (1.9.0+dfsg-1) ...
320s Setting up r-cran-munsell (0.5.0-2build1) ...
320s Setting up r-cran-tibble (3.2.1+dfsg-2) ...
320s Setting up r-cran-r.oo (1.26.0-1) ...
320s Setting up r-cran-scales (1.3.0-1) ...
320s Setting up r-cran-r.utils (2.12.3-1) ...
320s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ...
320s Setting up r-cran-r.devices (2.17.2+ds-1) ...
320s Setting up r-cran-r.cache (0.16.0-1) ...
320s Setting up r-cran-r.rsp (0.46.0+ds-1) ...
320s Setting up autopkgtest-satdep (0) ...
320s Processing triggers for man-db (2.12.1-1) ...
321s Processing triggers for install-info (7.1-3build2) ...
321s Processing triggers for libc-bin (2.39-0ubuntu8.1) ...
350s (Reading database ... 69797 files and directories currently installed.)
350s Removing autopkgtest-satdep (0) ...
357s autopkgtest [08:27:48]: test run-unit-test: [-----------------------
359s 
359s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
359s Copyright (C) 2024 The R Foundation for Statistical Computing
359s Platform: arm-unknown-linux-gnueabihf (32-bit)
359s 
359s R is free software and comes with ABSOLUTELY NO WARRANTY.
359s You are welcome to redistribute it under certain conditions.
359s Type 'license()' or 'licence()' for distribution details.
359s 
359s R is a collaborative project with many contributors.
359s Type 'contributors()' for more information and
359s 'citation()' on how to cite R or R packages in publications.
359s 
359s Type 'demo()' for some demos, 'help()' for on-line help, or
359s 'help.start()' for an HTML browser interface to help.
359s Type 'q()' to quit R.
359s 
360s > library("matrixStats")
360s > 
360s > allocArray_R <- function(nrow, ncol, value = NA) {
360s +   array(data = value, dim = dim)
360s + }
360s > 
360s > values <- list(
360s +   -1L, 0L, +1L, NA_integer_, .Machine$integer.max,
360s +   -1, 0, +1, NA_real_, NaN, -Inf, +Inf,
360s +   .Machine$double.xmin, .Machine$double.xmax,
360s +   .Machine$double.eps, .Machine$double.neg.eps,
360s +   FALSE, TRUE, NA
360s + )
360s > 
360s > dim <- c(2L, 4L, 3L)
360s > for (value in values) {
360s +   x0 <- allocArray_R(dim, value = value)
360s +   x <- allocArray(dim, value = value)
360s +   if (!identical(x, x0)) {
360s +     str(list(dim = dim, value = value, x = x, x0 = x0))
360s +     stopifnot(identical(x, x0))
360s +   }
360s + }
360s > 
360s 
360s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
360s Copyright (C) 2024 The R Foundation for Statistical Computing
360s Platform: arm-unknown-linux-gnueabihf (32-bit)
360s 
360s R is free software and comes with ABSOLUTELY NO WARRANTY.
360s You are welcome to redistribute it under certain conditions.
360s Type 'license()' or 'licence()' for distribution details.
360s 
360s R is a collaborative project with many contributors.
360s Type 'contributors()' for more information and
360s 'citation()' on how to cite R or R packages in publications.
360s 
360s Type 'demo()' for some demos, 'help()' for on-line help, or
360s 'help.start()' for an HTML browser interface to help.
360s Type 'q()' to quit R.
360s 
360s > library("matrixStats")
360s > 
360s > allocMatrix_R <- function(nrow, ncol, value = NA) {
360s +   matrix(data = value, nrow = nrow, ncol = ncol)
360s + }
360s > 
360s > values <- list(
360s +   -1L, 0L, +1L, NA_integer_, .Machine$integer.max,
360s +   -1, 0, +1, NA_real_, NaN, -Inf, +Inf,
360s +   .Machine$double.xmin, .Machine$double.xmax,
360s +   .Machine$double.eps, .Machine$double.neg.eps,
360s +   FALSE, TRUE, NA
360s + )
360s > 
360s > nrow <- 2L
360s > ncol <- 3L
360s > for (value in values) {
360s +   x0 <- allocMatrix_R(nrow, ncol, value = value)
360s +   x <- allocMatrix(nrow, ncol, value = value)
360s +   if (!identical(x, x0)) {
360s +     str(list(nrow = nrow, ncol = ncol, value = value, x = x, x0 = x0))
360s +     stopifnot(identical(x, x0))
360s +   }
360s + }
360s > 
361s 
361s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
361s Copyright (C) 2024 The R Foundation for Statistical Computing
361s Platform: arm-unknown-linux-gnueabihf (32-bit)
361s 
361s R is free software and comes with ABSOLUTELY NO WARRANTY.
361s You are welcome to redistribute it under certain conditions.
361s Type 'license()' or 'licence()' for distribution details.
361s 
361s R is a collaborative project with many contributors.
361s Type 'contributors()' for more information and
361s 'citation()' on how to cite R or R packages in publications.
361s 
361s Type 'demo()' for some demos, 'help()' for on-line help, or
361s 'help.start()' for an HTML browser interface to help.
361s Type 'q()' to quit R.
361s 
361s > library("matrixStats")
361s > 
361s > allocVector_R <- function(length, value = NA) {
361s +   x <- vector(mode = typeof(value), length = length)
361s +   if (!is.finite(value) || value != 0) x[] <- value
361s +   x
361s + }
361s > 
361s > values <- list(
361s +   -1L, 0L, +1L, NA_integer_, .Machine$integer.max,
361s +   -1, 0, +1, NA_real_, NaN, -Inf, +Inf,
361s +   .Machine$double.xmin, .Machine$double.xmax,
361s +   .Machine$double.eps, .Machine$double.neg.eps,
361s +   FALSE, TRUE, NA
361s + )
361s > 
361s > n <- 10L
361s > for (value in values) {
361s +   x0 <- allocVector_R(n, value = value)
361s +   x <- allocVector(n, value = value)
361s +   if (!identical(x, x0)) {
361s +     str(list(n = n, value = value, x = x, x0 = x0))
361s +     stopifnot(identical(x, x0))
361s +   }
361s + }
361s > 
361s 
361s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
361s Copyright (C) 2024 The R Foundation for Statistical Computing
361s Platform: arm-unknown-linux-gnueabihf (32-bit)
361s 
361s R is free software and comes with ABSOLUTELY NO WARRANTY.
361s You are welcome to redistribute it under certain conditions.
361s Type 'license()' or 'licence()' for distribution details.
361s 
361s R is a collaborative project with many contributors.
361s Type 'contributors()' for more information and
361s 'citation()' on how to cite R or R packages in publications.
361s 
361s Type 'demo()' for some demos, 'help()' for on-line help, or
361s 'help.start()' for an HTML browser interface to help.
361s Type 'q()' to quit R.
361s 
362s > library("matrixStats")
362s > 
362s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
362s > # Setup
362s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
362s > data <- data.frame(
362s +   logical   = c(TRUE, FALSE, TRUE),
362s +   integer   = 1:3,
362s +   double    = seq(from = 1.0, to = 3.0, by = 1.0),
362s +   complex   = seq(from = 1.0, to = 3.0, by = 1.0) + 1.0i,
362s +   character = letters[1:3],
362s +   stringsAsFactors = FALSE
362s + )
362s > 
362s > modes <- names(data)
362s > 
362s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
362s > # Special cases
362s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
362s > cat("NULL...\n")
362s NULL...
362s > stopifnot(identical(anyMissing(NULL), FALSE))
362s > cat("NULL...done\n")
362s NULL...done
362s > 
362s > cat("raw...\n")
362s raw...
362s > stopifnot(identical(anyMissing(as.raw(0:2)), FALSE))
362s > cat("raw...done\n")
362s raw...done
362s > 
362s > cat("list(NULL)...\n")
362s list(NULL)...
362s > stopifnot(identical(anyMissing(list(NULL)), FALSE))
362s > cat("list(NULL)...done\n")
362s list(NULL)...done
362s > 
362s > 
362s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
362s > # Scalars, vectors, and matrices of various modes
362s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
362s > for (mode in modes) {
362s +   cat(sprintf("Mode: %s...\n", mode))
362s +   values <- data[[mode]]
362s + 
362s +   # Scalars
362s +   cat(" scalar\n")
362s +   x <- values[1L]
362s +   print(x)
362s +   stopifnot(identical(anyMissing(x), FALSE))
362s +   is.na(x) <- TRUE
362s +   print(x)
362s +   stopifnot(identical(anyMissing(x), TRUE))
362s + 
362s +   # Vectors
362s +   cat(" vector\n")
362s +   x <- values
362s +   print(x)
362s +   stopifnot(identical(anyMissing(x), FALSE))
362s +   is.na(x)[2L] <- TRUE
362s +   print(x)
362s +   stopifnot(identical(anyMissing(x), TRUE))
362s + 
362s +   # Matrices
362s +   cat(" matrix\n")
362s +   x <- matrix(c(values, values), ncol = 2L)
362s +   print(x)
362s +   stopifnot(identical(anyMissing(x), FALSE))
362s +   is.na(x)[2L] <- TRUE
362s +   print(x)
362s +   stopifnot(identical(anyMissing(x), TRUE))
362s + 
362s +   cat(sprintf("Mode: %s...done\n", mode))
362s + } # for (mode ...)
362s Mode: logical...
362s  scalar
362s [1] TRUE
362s [1] NA
362s  vector
362s [1]  TRUE FALSE  TRUE
362s [1] TRUE   NA TRUE
362s  matrix
362s       [,1]  [,2]
362s [1,]  TRUE  TRUE
362s [2,] FALSE FALSE
362s [3,]  TRUE  TRUE
362s      [,1]  [,2]
362s [1,] TRUE  TRUE
362s [2,]   NA FALSE
362s [3,] TRUE  TRUE
362s Mode: logical...done
362s Mode: integer...
362s  scalar
362s [1] 1
362s [1] NA
362s  vector
362s [1] 1 2 3
362s [1]  1 NA  3
362s  matrix
362s      [,1] [,2]
362s [1,]    1    1
362s [2,]    2    2
362s [3,]    3    3
362s      [,1] [,2]
362s [1,]    1    1
362s [2,]   NA    2
362s [3,]    3    3
362s Mode: integer...done
362s Mode: double...
362s  scalar
362s [1] 1
362s [1] NA
362s  vector
362s [1] 1 2 3
362s [1]  1 NA  3
362s  matrix
362s      [,1] [,2]
362s [1,]    1    1
362s [2,]    2    2
362s [3,]    3    3
362s      [,1] [,2]
362s [1,]    1    1
362s [2,]   NA    2
362s [3,]    3    3
362s Mode: double...done
362s Mode: complex...
362s  scalar
362s [1] 1+1i
362s [1] NA
362s  vector
362s [1] 1+1i 2+1i 3+1i
362s [1] 1+1i   NA 3+1i
362s  matrix
362s      [,1] [,2]
362s [1,] 1+1i 1+1i
362s [2,] 2+1i 2+1i
362s [3,] 3+1i 3+1i
362s      [,1] [,2]
362s [1,] 1+1i 1+1i
362s [2,]   NA 2+1i
362s [3,] 3+1i 3+1i
362s Mode: complex...done
362s Mode: character...
362s  scalar
362s [1] "a"
362s [1] NA
362s  vector
362s [1] "a" "b" "c"
362s [1] "a" NA  "c"
362s  matrix
362s      [,1] [,2]
362s [1,] "a"  "a" 
362s [2,] "b"  "b" 
362s [3,] "c"  "c" 
362s      [,1] [,2]
362s [1,] "a"  "a" 
362s [2,] NA   "b" 
362s [3,] "c"  "c" 
362s Mode: character...done
362s > 
362s > 
362s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
362s > # Data frames
362s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
362s > cat("data.frame...\n")
362s data.frame...
362s > x <- data
362s > stopifnot(identical(anyMissing(x), FALSE))
362s > for (mode in modes) {
362s +   x <- data
362s +   is.na(x[[mode]])[2L] <- TRUE
362s +   print(x)
362s +   stopifnot(identical(anyMissing(x), TRUE))
362s + } # for (mode ...)
362s   logical integer double complex character
362s 1    TRUE       1      1    1+1i         a
362s 2      NA       2      2    2+1i         b
362s 3    TRUE       3      3    3+1i         c
362s   logical integer double complex character
362s 1    TRUE       1      1    1+1i         a
362s 2   FALSE      NA      2    2+1i         b
362s 3    TRUE       3      3    3+1i         c
362s   logical integer double complex character
362s 1    TRUE       1      1    1+1i         a
362s 2   FALSE       2     NA    2+1i         b
362s 3    TRUE       3      3    3+1i         c
362s   logical integer double complex character
362s 1    TRUE       1      1    1+1i         a
362s 2   FALSE       2      2      NA         b
362s 3    TRUE       3      3    3+1i         c
362s   logical integer double complex character
362s 1    TRUE       1      1    1+1i         a
362s 2   FALSE       2      2    2+1i      <NA>
362s 3    TRUE       3      3    3+1i         c
362s > cat("data.frame...done\n")
362s data.frame...done
362s > 
362s > 
362s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
362s > # Lists
362s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
362s > cat("list...\n")
362s list...
362s > x <- as.list(data)
362s > stopifnot(identical(anyMissing(x), FALSE))
362s > for (mode in modes) {
362s +   x <- as.list(data)
362s +   is.na(x[[mode]])[2L] <- TRUE
362s +   print(x)
362s +   stopifnot(identical(anyMissing(x), TRUE))
362s + } # for (mode ...)
362s $logical
362s [1] TRUE   NA TRUE
362s 
362s $integer
362s [1] 1 2 3
362s 
362s $double
362s [1] 1 2 3
362s 
362s $complex
362s [1] 1+1i 2+1i 3+1i
362s 
362s $character
362s [1] "a" "b" "c"
362s 
362s $logical
362s [1]  TRUE FALSE  TRUE
362s 
362s $integer
362s [1]  1 NA  3
362s 
362s $double
362s [1] 1 2 3
362s 
362s $complex
362s [1] 1+1i 2+1i 3+1i
362s 
362s $character
362s [1] "a" "b" "c"
362s 
362s $logical
362s [1]  TRUE FALSE  TRUE
362s 
362s $integer
362s [1] 1 2 3
362s 
362s $double
362s [1]  1 NA  3
362s 
362s $complex
362s [1] 1+1i 2+1i 3+1i
362s 
362s $character
362s [1] "a" "b" "c"
362s 
362s $logical
362s [1]  TRUE FALSE  TRUE
362s 
362s $integer
362s [1] 1 2 3
362s 
362s $double
362s [1] 1 2 3
362s 
362s $complex
362s [1] 1+1i   NA 3+1i
362s 
362s $character
362s [1] "a" "b" "c"
362s 
362s $logical
362s [1]  TRUE FALSE  TRUE
362s 
362s $integer
362s [1] 1 2 3
362s 
362s $double
362s [1] 1 2 3
362s 
362s $complex
362s [1] 1+1i 2+1i 3+1i
362s 
362s $character
362s [1] "a" NA  "c"
362s 
362s > cat("list...done\n")
362s list...done
362s > 
362s 
362s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
362s Copyright (C) 2024 The R Foundation for Statistical Computing
362s Platform: arm-unknown-linux-gnueabihf (32-bit)
362s 
362s R is free software and comes with ABSOLUTELY NO WARRANTY.
362s You are welcome to redistribute it under certain conditions.
362s Type 'license()' or 'licence()' for distribution details.
362s 
362s R is a collaborative project with many contributors.
362s Type 'contributors()' for more information and
362s 'citation()' on how to cite R or R packages in publications.
362s 
362s Type 'demo()' for some demos, 'help()' for on-line help, or
362s 'help.start()' for an HTML browser interface to help.
362s Type 'q()' to quit R.
362s 
362s > library("matrixStats")
362s > 
362s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
362s > # Subsetted tests
362s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
362s > source("utils/validateIndicesFramework.R")
362s > x <- runif(4, min = -3, max = 3)
362s > x[2] <- NA
362s > for (mode in c("integer", "numeric")) {
362s +   storage.mode(x) <- mode
362s +   for (idxs in index_cases) {
362s +     validateIndicesTestVector(x, idxs,
362s +                               ftest = anyMissing, fsure = function(x, ...) {
362s +         anyValue(x, value = NA)
362s +     })
362s +   }
362s + }
362s > 
363s 
363s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
363s Copyright (C) 2024 The R Foundation for Statistical Computing
363s Platform: arm-unknown-linux-gnueabihf (32-bit)
363s 
363s R is free software and comes with ABSOLUTELY NO WARRANTY.
363s You are welcome to redistribute it under certain conditions.
363s Type 'license()' or 'licence()' for distribution details.
363s 
363s R is a collaborative project with many contributors.
363s Type 'contributors()' for more information and
363s 'citation()' on how to cite R or R packages in publications.
363s 
363s Type 'demo()' for some demos, 'help()' for on-line help, or
363s 'help.start()' for an HTML browser interface to help.
363s Type 'q()' to quit R.
363s 
363s > ## 1. Don't test with valgrind
363s > ## 2. Test only R (>= 3.0.2) because of that's what knitr requires
363s > if  (getRversion() >= "3.0.2" && Sys.getenv("_R_CHECK_USE_VALGRIND_") == "") {
363s + 
363s + ## 3. Make sure all suggested packages are installed / can be loaded
363s + pkgs <- c("base64enc", "ggplot2", "knitr", "markdown", "microbenchmark",
363s +           "R.devices", "R.rsp")
363s + if (all(unlist(lapply(pkgs, FUN = requireNamespace)))) {
363s +   html <- matrixStats:::benchmark("binCounts")
363s +   print(html)
363s + }
363s + 
363s + rm(list = "pkgs")
363s + 
363s + }
363s Loading required namespace: base64enc
363s Loading required namespace: ggplot2
364s Loading required namespace: knitr
364s Loading required namespace: markdown
364s Loading required namespace: microbenchmark
364s Failed with error:  ‘there is no package called ‘microbenchmark’’
364s Loading required namespace: R.devices
365s Loading required namespace: R.rsp
365s > 
365s 
365s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
365s Copyright (C) 2024 The R Foundation for Statistical Computing
365s Platform: arm-unknown-linux-gnueabihf (32-bit)
365s 
365s R is free software and comes with ABSOLUTELY NO WARRANTY.
365s You are welcome to redistribute it under certain conditions.
365s Type 'license()' or 'licence()' for distribution details.
365s 
365s R is a collaborative project with many contributors.
365s Type 'contributors()' for more information and
365s 'citation()' on how to cite R or R packages in publications.
365s 
365s Type 'demo()' for some demos, 'help()' for on-line help, or
365s 'help.start()' for an HTML browser interface to help.
365s Type 'q()' to quit R.
365s 
365s > library("matrixStats")
365s > library("stats")
365s > 
365s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
365s > # Local functions
365s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
365s > binCounts_hist <- function(x, bx, right = FALSE, ...) {
365s +   n0 <- graphics::hist(x, breaks = bx, right = right,
365s +                        include.lowest = TRUE, plot = FALSE)$counts
365s + }
365s > 
365s > 
365s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
365s > # Non-sorted and sorted positions
365s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
365s > nx <- 1000L  # Number of data points
365s > nb <- 200L   # Number of bins
365s > 
365s > # Uniformely distributed bins
365s > bx <- seq(from = 0, to = 1, length.out = nb + 1L)
365s > bx <- c(-1, bx, 2)
365s > 
365s > # Sample data points
365s > set.seed(0xBEEF)
365s > x <- runif(nx, min = 0, max = 1)
365s > 
365s > for (kk in 1:2) {
365s +   n0 <- binCounts_hist(x, bx = bx)
365s +   n1 <- binCounts(x, bx = bx)
365s +   # Sanity check
365s +   stopifnot(identical(n1, n0))
365s + 
365s +   # Check reversed
365s +   n1r <- rev(binCounts(-x, bx = rev(-bx), right = TRUE))
365s +   stopifnot(identical(n1r, n1))
365s + 
365s +   # Retry with a sorted vector
365s +   x <- sort(x)
365s + } # for (kk in 1:2)
366s > 
366s > 
366s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
366s > # Missing values
366s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
366s > x <- 1:40
366s > x[20] <- NA_integer_
366s > nx <- length(x)
366s > 
366s > # Bins
366s > bx <- c(0.5, 50.5, 100.5, 150.5, 200.5)
366s > 
366s > y_smooth0 <- binCounts_hist(x, bx = bx)
366s > y_smooth <- binCounts(x, bx = bx)
366s > # Sanity check
366s > stopifnot(all.equal(y_smooth, y_smooth0))
366s > 
366s > 
366s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
366s > # Border cases
366s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
366s > x <- 1:10
366s > bx <- min(x) - c(10, 1)
366s > y_smooth <- binCounts(x, bx = bx)
366s > stopifnot(all.equal(y_smooth, 0L))
366s > bx <- range(x)
366s > y_smooth <- binCounts(x, bx = bx)
366s > stopifnot(all.equal(y_smooth, length(x) - 1L))
366s > bx <- max(x) + c(1, 10)
366s > y_smooth <- binCounts(x, bx = bx)
366s > stopifnot(all.equal(y_smooth, 0L))
366s > 
366s > # Every second empty
366s > x <- 1:10
366s > bx <- rep(x, each = 2L)
366s > y_smooth <- binCounts(x, bx = bx)
366s > stopifnot(all.equal(y_smooth, rep(c(0L, 1L), length.out = length(bx) - 1L)))
366s > ## NOTE: binCounts_hist() does not give the same last bin count
366s > 
366s > 
366s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
366s > # Exception handling
366s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
366s > # Zero bin bounderies (invalid bin definition)
366s > bx <- double(0L)
366s > res <- try(y_smooth <- binCounts(1:10, bx = bx), silent = TRUE)
366s > stopifnot(inherits(res, "try-error"))
366s > 
366s > # One bin boundery (invalid bin definition)
366s > bx <- double(1L)
366s > res <- try(y_smooth <- binCounts(1:10, bx = bx), silent = TRUE)
366s > stopifnot(inherits(res, "try-error"))
366s > 
366s 
366s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
366s Copyright (C) 2024 The R Foundation for Statistical Computing
366s Platform: arm-unknown-linux-gnueabihf (32-bit)
366s 
366s R is free software and comes with ABSOLUTELY NO WARRANTY.
366s You are welcome to redistribute it under certain conditions.
366s Type 'license()' or 'licence()' for distribution details.
366s 
366s R is a collaborative project with many contributors.
366s Type 'contributors()' for more information and
366s 'citation()' on how to cite R or R packages in publications.
366s 
366s Type 'demo()' for some demos, 'help()' for on-line help, or
366s 'help.start()' for an HTML browser interface to help.
366s Type 'q()' to quit R.
366s 
366s > library("matrixStats")
366s > 
366s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
366s > # Local functions
366s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
366s > binCounts_hist <- function(x, bx, right = FALSE, ...) {
366s +   n0 <- graphics::hist(x, breaks = bx, right = right,
366s +                        include.lowest = TRUE, plot = FALSE)$counts
366s + }
366s > 
366s > 
366s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
366s > # Subsetted tests
366s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
366s > source("utils/validateIndicesFramework.R")
366s > x <- runif(6, min = -6, max = 6)
366s > storage.mode(x) <- "integer"
366s > bx <- c(-6, 0, 3, 4, 10)
366s > for (idxs in index_cases) {
366s +   validateIndicesTestVector(x, idxs,
366s +                             ftest = binCounts, fsure = binCounts_hist,
366s +                             bx = bx, right = FALSE)
366s +   validateIndicesTestVector(x, idxs,
366s +                             ftest = binCounts, fsure = binCounts_hist,
366s +                             bx = bx, right = TRUE)
366s + }
366s > 
366s 
366s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
366s Copyright (C) 2024 The R Foundation for Statistical Computing
366s Platform: arm-unknown-linux-gnueabihf (32-bit)
366s 
366s R is free software and comes with ABSOLUTELY NO WARRANTY.
366s You are welcome to redistribute it under certain conditions.
366s Type 'license()' or 'licence()' for distribution details.
366s 
366s R is a collaborative project with many contributors.
366s Type 'contributors()' for more information and
366s 'citation()' on how to cite R or R packages in publications.
366s 
366s Type 'demo()' for some demos, 'help()' for on-line help, or
366s 'help.start()' for an HTML browser interface to help.
366s Type 'q()' to quit R.
366s 
367s > library("matrixStats")
367s > library("stats")
367s > 
367s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
367s > # Naive R implementation of binMeans()
367s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
367s > binMeans0 <- function(y, x, bx, na.rm = TRUE, count = TRUE, right = FALSE) {
367s +   n_smooth <- length(bx) - 1L
367s +   res <- double(n_smooth)
367s +   counts <- rep(NaN, times = n_smooth)
367s + 
367s +   if (na.rm) {
367s +     keep <- !is.na(x) & !is.na(y)
367s +     x <- x[keep]
367s +     y <- y[keep]
367s +   }
367s + 
367s +   # For each bin...
367s +   for (kk in seq_len(n_smooth)) {
367s +     if (right) {
367s +       idxs <- which(bx[kk] <  x & x <= bx[kk + 1L])
367s +     } else {
367s +       idxs <- which(bx[kk] <= x & x <  bx[kk + 1L])
367s +     }
367s +     y_kk <- y[idxs]
367s +     res[kk] <- mean(y_kk)
367s +     counts[kk] <- length(idxs)
367s +   } # for (kk ...)
367s + 
367s +   if (count) attr(res, "count") <- counts
367s +   res
367s + }
367s > 
367s > 
367s > 
367s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
367s > # Case #1
367s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
367s > x <- 1:100
367s > nx <- length(x)
367s > y <- double(nx)
367s > y[1:25] <- 5
367s > y[51:75] <- -5
367s > y <- y + rnorm(nx)
367s > 
367s > # Bins
367s > bx <- c(0.5, 25.5, 50.5, 75.5, 100.5)
367s > 
367s > y_smooth0 <- binMeans0(y, x = x, bx = bx)
367s > y_smooth <- binMeans(y, x = x, bx = bx)
367s > n_smooth <- binCounts(x, bx = bx)
367s > # Sanity check
367s > stopifnot(all.equal(y_smooth, y_smooth0))
367s > stopifnot(all.equal(attr(y_smooth, "count"), n_smooth))
367s > 
367s > y_smooth0r <- rev(binMeans0(y, x = -x, bx = rev(-bx),
367s +                             count = FALSE, right = TRUE))
367s > y_smoothr <- rev(binMeans(y, x = -x, bx = rev(-bx),
367s +                           count = FALSE, right = TRUE))
367s > # Sanity check
367s > stopifnot(all.equal(y_smooth0r, y_smooth0, check.attributes = FALSE))
367s > stopifnot(all.equal(y_smoothr, y_smooth0r))
367s > 
367s > 
367s > # Integer input
367s > y <- as.integer(y)
367s > y_smooth0 <- binMeans0(y, x = x, bx = bx)
367s > y_smooth <- binMeans(y, x = x, bx = bx)
367s > n_smooth <- binCounts(x, bx = bx)
367s > # Sanity check
367s > stopifnot(is.integer(y),
367s +           all.equal(y_smooth, y_smooth0),
367s +           all.equal(attr(y_smooth, "count"), n_smooth))
367s > 
367s > # Logical input
367s > y <- as.logical(y)
367s > y_smooth0 <- binMeans0(y, x = x, bx = bx)
367s > y_smooth <- binMeans(y, x = x, bx = bx)
367s > n_smooth <- binCounts(x, bx = bx)
367s > # Sanity check
367s > stopifnot(is.logical(y),
367s +           all.equal(y_smooth, y_smooth0),
367s +           all.equal(attr(y_smooth, "count"), n_smooth))
367s > 
367s > 
367s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
367s > # Case #2
367s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
367s > nx <- 1e3
367s > x <- runif(nx)
367s > y <- runif(nx)
367s > 
367s > nb <- 10
367s > bx <- do.call(seq, c(as.list(range(x)), length.out = nb))
367s > bx1 <- c(bx[-1], bx[nb] + 1)
367s > 
367s > y_smooth0 <- binMeans0(y, x = x, bx = bx1)
367s > y_smooth <- binMeans(y, x = x, bx = bx1)
367s > n_smooth <- binCounts(x, bx = bx1)
367s > y_smoothr <- rev(binMeans(y, x = -x, bx = rev(-bx1), right = TRUE))
367s > 
367s > # Sanity check
367s > stopifnot(all.equal(y_smooth, y_smooth0))
367s > stopifnot(all.equal(attr(y_smooth, "count"), n_smooth))
367s > stopifnot(all.equal(y_smoothr, y_smooth, check.attributes = FALSE))
367s > 
367s > 
367s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
367s > # Empty bins
367s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
367s > x <- c(6:8, 16:19)
367s > nx <- length(x)
367s > y <- runif(nx)
367s > bx <- c(0, 5, 10, 15, 20, 25)
367s > y_smooth0 <- binMeans0(y, x = x, bx = bx)
367s > y_smooth <- binMeans(y, x = x, bx = bx)
367s > n_smooth <- binCounts(x, bx = bx)
367s > stopifnot(all.equal(attr(y_smooth, "count"), n_smooth))
367s > stopifnot(all.equal(y_smooth, y_smooth0))
367s > 
367s > 
367s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
367s > # Missing values
367s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
367s > x <- 1:100
367s > x[50] <- NA_integer_
367s > nx <- length(x)
367s > y <- double(nx)
367s > y[1:25] <- 5
367s > y[51:75] <- -5
367s > y[82:92] <- NA_real_
367s > y <- y + rnorm(nx)
367s > 
367s > # Bins
367s > bx <- c(0.5, 25.5, 75.5, 82.5, 100.5)
367s > 
367s > y_smooth0 <- binMeans0(y, x = x, bx = bx)
367s > y_smooth <- binMeans(y, x = x, bx = bx)
367s > # Sanity check
367s > stopifnot(all.equal(y_smooth, y_smooth0))
367s > 
367s > 
367s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
367s > # Exception handling
367s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
367s > # Zero bin bounderies (invalid bin definition)
367s > bx <- double(0L)
367s > res <- try(y_smooth <- binMeans(x = 1:5, y = 1:5, bx = bx), silent = TRUE)
367s > stopifnot(inherits(res, "try-error"))
367s > 
367s > # One bin boundery (invalid bin definition)
367s > bx <- double(1L)
367s > res <- try(y_smooth <- binMeans(x = 1:5, y = 1:5, bx = bx), silent = TRUE)
367s > stopifnot(inherits(res, "try-error"))
367s > 
367s 
367s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
367s Copyright (C) 2024 The R Foundation for Statistical Computing
367s Platform: arm-unknown-linux-gnueabihf (32-bit)
367s 
367s R is free software and comes with ABSOLUTELY NO WARRANTY.
367s You are welcome to redistribute it under certain conditions.
367s Type 'license()' or 'licence()' for distribution details.
367s 
367s R is a collaborative project with many contributors.
367s Type 'contributors()' for more information and
367s 'citation()' on how to cite R or R packages in publications.
367s 
367s Type 'demo()' for some demos, 'help()' for on-line help, or
367s 'help.start()' for an HTML browser interface to help.
367s Type 'q()' to quit R.
367s 
367s > library("matrixStats")
367s > 
367s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
367s > # Naive R implementation of binMeans()
367s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
367s > binMeans0 <- function(y, x, bx, na.rm = TRUE, count = TRUE, right = FALSE) {
367s +   n_smooth <- length(bx) - 1L
367s +   res <- double(n_smooth)
367s +   counts <- rep(NaN, times = n_smooth)
367s + 
367s +   if (na.rm) {
367s +     keep <- !is.na(x) & !is.na(y)
367s +     x <- x[keep]
367s +     y <- y[keep]
367s +   }
367s + 
367s +   # For each bin...
367s +   for (kk in seq_len(n_smooth)) {
367s +     if (right) {
367s +       idxs <- which(bx[kk] <  x & x <= bx[kk + 1L])
367s +     } else {
367s +       idxs <- which(bx[kk] <= x & x <  bx[kk + 1L])
367s +     }
367s +     y_kk <- y[idxs]
367s +     res[kk] <- mean(y_kk)
367s +     counts[kk] <- length(idxs)
367s +   } # for (kk ...)
367s + 
367s +   if (count) attr(res, "count") <- counts
367s +   res
367s + }
367s > 
367s > 
367s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
367s > # Subsetted tests
367s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
367s > source("utils/validateIndicesFramework.R")
367s > y <- runif(6, min = -6, max = 6)
367s > x <- runif(6, min = -6, max = 6)
367s > storage.mode(x) <- "integer"
367s > bx <- c(-6, 0, 3, 4, 10)
367s > for (idxs in index_cases) {
367s +   for (na.rm in c(TRUE, FALSE)) {
367s +     validateIndicesTestVector_w(y, x, idxs,
367s +                                 ftest = binMeans, fsure = binMeans0,
367s +                                 bx = bx, na.rm = na.rm,
367s +                                 count = TRUE, right = FALSE)
367s +     validateIndicesTestVector_w(y, x, idxs,
367s +                                 ftest = binMeans, fsure = binMeans0,
367s +                                 bx = bx, na.rm = na.rm,
367s +                                 count = TRUE, right = TRUE)
367s +   }
367s + }
368s > 
368s 
368s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
368s Copyright (C) 2024 The R Foundation for Statistical Computing
368s Platform: arm-unknown-linux-gnueabihf (32-bit)
368s 
368s R is free software and comes with ABSOLUTELY NO WARRANTY.
368s You are welcome to redistribute it under certain conditions.
368s Type 'license()' or 'licence()' for distribution details.
368s 
368s R is a collaborative project with many contributors.
368s Type 'contributors()' for more information and
368s 'citation()' on how to cite R or R packages in publications.
368s 
368s Type 'demo()' for some demos, 'help()' for on-line help, or
368s 'help.start()' for an HTML browser interface to help.
368s Type 'q()' to quit R.
368s 
368s > library("matrixStats")
368s > 
368s > count_R <- function(x, value = TRUE, na.rm = FALSE, ...) {
368s +   if (is.na(value)) {
368s +     counts <- sum(is.na(x))
368s +   } else {
368s +     counts <- sum(x == value, na.rm = na.rm)
368s +   }
368s +   as.integer(counts)
368s + }
368s > 
368s > 
368s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
368s > # Data type: integer and numeric
368s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
368s > for (mode in c("integer", "double")) {
368s +   x <- runif(20 * 5, min = -3, max = 3)
368s +   x[sample.int(length(x), size = 7)] <- 0
368s +   storage.mode(x) <- mode
368s + 
368s +   for (na.rm in c(FALSE, TRUE)) {
368s +     # Count zeros
368s +     n0 <- count_R(x, value = 0, na.rm = na.rm)
368s +     n1 <- count(x, value = 0, na.rm = na.rm)
368s +     stopifnot(identical(n1, n0))
368s +     all <- allValue(x, value = 0, na.rm = na.rm)
368s +     any <- anyValue(x, value = 0, na.rm = na.rm)
368s + 
368s +     # Count NAs
368s +     n0 <- count_R(x, value = NA, na.rm = na.rm)
368s +     n1 <- count(x, value = NA, na.rm = na.rm)
368s +     stopifnot(identical(n1, n0))
368s +     all <- allValue(x, value = NA, na.rm = na.rm)
368s +     any <- anyValue(x, value = NA, na.rm = na.rm)
368s + 
368s +     if (mode == "integer") {
368s +       ux <- unique(as.vector(x))
368s +       n0 <- n1 <- integer(length(x))
368s +       for (value in ux) {
368s +         n0 <- n0 + count_R(x, value = value, na.rm = na.rm)
368s +         n1 <- n1 + count(x, value = value, na.rm = na.rm)
368s +         stopifnot(identical(n1, n0))
368s +       }
368s +       stopifnot(all(n0 == ncol(x)))
368s +     } # if (mode == "integer")
368s + 
368s +   } # for (na.rm ...)
368s + } # for (mode ...)
368s > 
368s > # All NAs
368s > na_list <- list(NA_integer_, NA_real_, NaN)
368s > for (na_value in na_list) {
368s +   x <- rep(na_value, times = 10L)
368s +   for (na.rm in c(FALSE, TRUE)) {
368s +     n0 <- count_R(x, na.rm = na.rm)
368s +     n1 <- count(x, na.rm = na.rm)
368s +     stopifnot(identical(n1, n0))
368s + 
368s +     # Count NAs
368s +     n0 <- count_R(x, value = NA, na.rm = na.rm)
368s +     n1 <- count(x, value = NA, na.rm = na.rm)
368s +     stopifnot(identical(n1, n0))
368s +     any <- anyValue(x, value = NA, na.rm = na.rm)
368s +     all <- allValue(x, value = NA, na.rm = na.rm)
368s +     stopifnot(any)
368s +     stopifnot(all)
368s +   }
368s + } # for (na_value ...)
368s > 
368s > 
368s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
368s > # Data type: logical
368s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
368s > x <- logical(length = 10L)
368s > x[3:7] <- TRUE
368s > 
368s > # Row/column counts
368s > for (na.rm in c(FALSE, TRUE)) {
368s +   n0 <- count_R(x, na.rm = na.rm)
368s +   n1 <- count(x, na.rm = na.rm)
368s +   stopifnot(identical(n1, n0))
368s + 
368s +   n_true <- count(x, value = TRUE, na.rm = na.rm)
368s +   n_false <- count(x, value = FALSE, na.rm = na.rm)
368s +   stopifnot(n_true + n_false == ncol(x))
368s + 
368s +   # Count NAs
368s +   n0 <- count_R(x, value = NA, na.rm = na.rm)
368s +   n1 <- count(x, value = NA, na.rm = na.rm)
368s +   stopifnot(identical(n1, n0))
368s + }
368s > 
368s 
368s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
368s Copyright (C) 2024 The R Foundation for Statistical Computing
368s Platform: arm-unknown-linux-gnueabihf (32-bit)
368s 
368s R is free software and comes with ABSOLUTELY NO WARRANTY.
368s You are welcome to redistribute it under certain conditions.
368s Type 'license()' or 'licence()' for distribution details.
368s 
368s R is a collaborative project with many contributors.
368s Type 'contributors()' for more information and
368s 'citation()' on how to cite R or R packages in publications.
368s 
368s Type 'demo()' for some demos, 'help()' for on-line help, or
368s 'help.start()' for an HTML browser interface to help.
368s Type 'q()' to quit R.
368s 
369s > library("matrixStats")
369s > 
369s > count_R <- function(x, value = TRUE, na.rm = FALSE, ...) {
369s +   if (is.na(value)) {
369s +     counts <- sum(is.na(x))
369s +   } else {
369s +     counts <- sum(x == value, na.rm = na.rm)
369s +   }
369s +   as.integer(counts)
369s + }
369s > 
369s > 
369s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
369s > # Subsetted tests
369s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
369s > source("utils/validateIndicesFramework.R")
369s > x <- runif(6, min = -3, max = 3)
369s > storage.mode(x) <- "integer"
369s > for (idxs in index_cases) {
369s +   validateIndicesTestVector(x, idxs,
369s +                             ftest = count, fsure = count_R,
369s +                             value = 0, na.rm = TRUE)
369s +   validateIndicesTestVector(x, idxs,
369s +                             ftest = count, fsure = count_R,
369s +                             value = 0, na.rm = FALSE)
369s +   validateIndicesTestVector(x, idxs,
369s +                             ftest = count, fsure = count_R,
369s +                             value = NA_integer_)
369s + }
369s > 
369s 
369s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
369s Copyright (C) 2024 The R Foundation for Statistical Computing
369s Platform: arm-unknown-linux-gnueabihf (32-bit)
369s 
369s R is free software and comes with ABSOLUTELY NO WARRANTY.
369s You are welcome to redistribute it under certain conditions.
369s Type 'license()' or 'licence()' for distribution details.
369s 
369s R is a collaborative project with many contributors.
369s Type 'contributors()' for more information and
369s 'citation()' on how to cite R or R packages in publications.
369s 
369s Type 'demo()' for some demos, 'help()' for on-line help, or
369s 'help.start()' for an HTML browser interface to help.
369s Type 'q()' to quit R.
369s 
369s > library("matrixStats")
369s > 
369s > diff2_R <- function(..., useNames = NA){
369s +   res <- diff(...)
369s +   if (is.na(useNames) || !useNames) names(res) <- NULL
369s +   res
369s + }
369s > 
369s > set.seed(0x42)
369s > 
369s > for (mode in c("integer", "double")) {
369s +   x <- rnorm(10, sd = 5)
369s +   storage.mode(x) <- mode
369s +   str(x)
369s + 
369s +   for (has_na in c(FALSE, TRUE)) {
369s +     for (setNames in c(TRUE, FALSE)) {
369s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
369s +         if (has_na) {
369s +           x[sample(1:10, size = 3)] <- NA
369s +         }
369s +         if (setNames) {
369s +           names(x) <- LETTERS[1:10]
369s +         }
369s +         for (l in 1:3) {
369s +           for (d in 1:4) {
369s +             cat(sprintf("%s: NAs = %s, lag = %d, differences = %d, setNames = %d, useNames = %d\n",
369s +                         mode, has_na, l, d, setNames, useNames))
369s +             y0 <- diff2_R(x, lag = l, differences = d, useNames = useNames)
369s +             str(y0)
369s +             y1 <- diff2(x, lag = l, differences = d, useNames = useNames)
369s +             str(y1)
369s +             stopifnot(identical(y1, y0))
369s +           }
369s +         }  
369s +       }
369s +     }
369s +   } # for (has_na ...)
369s + }
369s  int [1:10] 11 1 2 0 -1 -3 -3 6 0 0
369s integer: NAs = FALSE, lag = 1, differences = 1, setNames = 1, useNames = 1
369s  Named int [1:9] -10 1 -2 -1 -2 0 9 -6 0
369s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
369s  Named int [1:9] -10 1 -2 -1 -2 0 9 -6 0
369s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
369s integer: NAs = FALSE, lag = 1, differences = 2, setNames = 1, useNames = 1
369s  Named int [1:8] 11 -3 1 -1 2 9 -15 6
369s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
369s  Named int [1:8] 11 -3 1 -1 2 9 -15 6
369s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
369s integer: NAs = FALSE, lag = 1, differences = 3, setNames = 1, useNames = 1
369s  Named int [1:7] -14 4 -2 3 7 -24 21
369s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
369s  Named int [1:7] -14 4 -2 3 7 -24 21
369s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
369s integer: NAs = FALSE, lag = 1, differences = 4, setNames = 1, useNames = 1
369s  Named int [1:6] 18 -6 5 4 -31 45
369s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
369s  Named int [1:6] 18 -6 5 4 -31 45
369s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
369s integer: NAs = FALSE, lag = 2, differences = 1, setNames = 1, useNames = 1
369s  Named int [1:8] -9 -1 -3 -3 -2 9 3 -6
369s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
369s  Named int [1:8] -9 -1 -3 -3 -2 9 3 -6
369s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
369s integer: NAs = FALSE, lag = 2, differences = 2, setNames = 1, useNames = 1
369s  Named int [1:6] 6 -2 1 12 5 -15
369s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
369s  Named int [1:6] 6 -2 1 12 5 -15
369s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
369s integer: NAs = FALSE, lag = 2, differences = 3, setNames = 1, useNames = 1
369s  Named int [1:4] -5 14 4 -27
369s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
369s  Named int [1:4] -5 14 4 -27
369s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
369s integer: NAs = FALSE, lag = 2, differences = 4, setNames = 1, useNames = 1
369s  Named int [1:2] 9 -41
369s  - attr(*, "names")= chr [1:2] "I" "J"
369s  Named int [1:2] 9 -41
369s  - attr(*, "names")= chr [1:2] "I" "J"
369s integer: NAs = FALSE, lag = 3, differences = 1, setNames = 1, useNames = 1
369s  Named int [1:7] -11 -2 -5 -3 7 3 3
369s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
369s  Named int [1:7] -11 -2 -5 -3 7 3 3
369s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
369s integer: NAs = FALSE, lag = 3, differences = 2, setNames = 1, useNames = 1
369s  Named int [1:4] 8 9 8 6
369s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
369s  Named int [1:4] 8 9 8 6
369s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
369s integer: NAs = FALSE, lag = 3, differences = 3, setNames = 1, useNames = 1
369s  Named int -2
369s  - attr(*, "names")= chr "J"
369s  Named int -2
369s  - attr(*, "names")= chr "J"
369s integer: NAs = FALSE, lag = 3, differences = 4, setNames = 1, useNames = 1
369s  Named int(0) 
369s  - attr(*, "names")= chr(0) 
369s  Named int(0) 
369s  - attr(*, "names")= chr(0) 
369s integer: NAs = FALSE, lag = 1, differences = 1, setNames = 1, useNames = 0
369s  int [1:9] -10 1 -2 -1 -2 0 9 -6 0
369s  int [1:9] -10 1 -2 -1 -2 0 9 -6 0
369s integer: NAs = FALSE, lag = 1, differences = 2, setNames = 1, useNames = 0
369s  int [1:8] 11 -3 1 -1 2 9 -15 6
369s  int [1:8] 11 -3 1 -1 2 9 -15 6
369s integer: NAs = FALSE, lag = 1, differences = 3, setNames = 1, useNames = 0
369s  int [1:7] -14 4 -2 3 7 -24 21
369s  int [1:7] -14 4 -2 3 7 -24 21
369s integer: NAs = FALSE, lag = 1, differences = 4, setNames = 1, useNames = 0
369s  int [1:6] 18 -6 5 4 -31 45
369s  int [1:6] 18 -6 5 4 -31 45
369s integer: NAs = FALSE, lag = 2, differences = 1, setNames = 1, useNames = 0
369s  int [1:8] -9 -1 -3 -3 -2 9 3 -6
369s  int [1:8] -9 -1 -3 -3 -2 9 3 -6
369s integer: NAs = FALSE, lag = 2, differences = 2, setNames = 1, useNames = 0
369s  int [1:6] 6 -2 1 12 5 -15
369s  int [1:6] 6 -2 1 12 5 -15
369s integer: NAs = FALSE, lag = 2, differences = 3, setNames = 1, useNames = 0
369s  int [1:4] -5 14 4 -27
369s  int [1:4] -5 14 4 -27
369s integer: NAs = FALSE, lag = 2, differences = 4, setNames = 1, useNames = 0
369s  int [1:2] 9 -41
369s  int [1:2] 9 -41
369s integer: NAs = FALSE, lag = 3, differences = 1, setNames = 1, useNames = 0
369s  int [1:7] -11 -2 -5 -3 7 3 3
369s  int [1:7] -11 -2 -5 -3 7 3 3
369s integer: NAs = FALSE, lag = 3, differences = 2, setNames = 1, useNames = 0
369s  int [1:4] 8 9 8 6
369s  int [1:4] 8 9 8 6
369s integer: NAs = FALSE, lag = 3, differences = 3, setNames = 1, useNames = 0
369s  int -2
369s  int -2
369s integer: NAs = FALSE, lag = 3, differences = 4, setNames = 1, useNames = 0
369s  int(0) 
369s  int(0) 
369s integer: NAs = FALSE, lag = 1, differences = 1, setNames = 0, useNames = 1
369s  Named int [1:9] -10 1 -2 -1 -2 0 9 -6 0
369s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
369s  Named int [1:9] -10 1 -2 -1 -2 0 9 -6 0
369s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
369s integer: NAs = FALSE, lag = 1, differences = 2, setNames = 0, useNames = 1
369s  Named int [1:8] 11 -3 1 -1 2 9 -15 6
369s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
369s  Named int [1:8] 11 -3 1 -1 2 9 -15 6
369s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
369s integer: NAs = FALSE, lag = 1, differences = 3, setNames = 0, useNames = 1
369s  Named int [1:7] -14 4 -2 3 7 -24 21
369s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
369s  Named int [1:7] -14 4 -2 3 7 -24 21
369s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
369s integer: NAs = FALSE, lag = 1, differences = 4, setNames = 0, useNames = 1
369s  Named int [1:6] 18 -6 5 4 -31 45
369s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
369s  Named int [1:6] 18 -6 5 4 -31 45
369s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
369s integer: NAs = FALSE, lag = 2, differences = 1, setNames = 0, useNames = 1
369s  Named int [1:8] -9 -1 -3 -3 -2 9 3 -6
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s  Named int [1:8] -9 -1 -3 -3 -2 9 3 -6
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s integer: NAs = FALSE, lag = 2, differences = 2, setNames = 0, useNames = 1
370s  Named int [1:6] 6 -2 1 12 5 -15
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s  Named int [1:6] 6 -2 1 12 5 -15
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s integer: NAs = FALSE, lag = 2, differences = 3, setNames = 0, useNames = 1
370s  Named int [1:4] -5 14 4 -27
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s  Named int [1:4] -5 14 4 -27
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s integer: NAs = FALSE, lag = 2, differences = 4, setNames = 0, useNames = 1
370s  Named int [1:2] 9 -41
370s  - attr(*, "names")= chr [1:2] "I" "J"
370s  Named int [1:2] 9 -41
370s  - attr(*, "names")= chr [1:2] "I" "J"
370s integer: NAs = FALSE, lag = 3, differences = 1, setNames = 0, useNames = 1
370s  Named int [1:7] -11 -2 -5 -3 7 3 3
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s  Named int [1:7] -11 -2 -5 -3 7 3 3
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s integer: NAs = FALSE, lag = 3, differences = 2, setNames = 0, useNames = 1
370s  Named int [1:4] 8 9 8 6
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s  Named int [1:4] 8 9 8 6
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s integer: NAs = FALSE, lag = 3, differences = 3, setNames = 0, useNames = 1
370s  Named int -2
370s  - attr(*, "names")= chr "J"
370s  Named int -2
370s  - attr(*, "names")= chr "J"
370s integer: NAs = FALSE, lag = 3, differences = 4, setNames = 0, useNames = 1
370s  Named int(0) 
370s  - attr(*, "names")= chr(0) 
370s  Named int(0) 
370s  - attr(*, "names")= chr(0) 
370s integer: NAs = FALSE, lag = 1, differences = 1, setNames = 0, useNames = 0
370s  int [1:9] -10 1 -2 -1 -2 0 9 -6 0
370s  int [1:9] -10 1 -2 -1 -2 0 9 -6 0
370s integer: NAs = FALSE, lag = 1, differences = 2, setNames = 0, useNames = 0
370s  int [1:8] 11 -3 1 -1 2 9 -15 6
370s  int [1:8] 11 -3 1 -1 2 9 -15 6
370s integer: NAs = FALSE, lag = 1, differences = 3, setNames = 0, useNames = 0
370s  int [1:7] -14 4 -2 3 7 -24 21
370s  int [1:7] -14 4 -2 3 7 -24 21
370s integer: NAs = FALSE, lag = 1, differences = 4, setNames = 0, useNames = 0
370s  int [1:6] 18 -6 5 4 -31 45
370s  int [1:6] 18 -6 5 4 -31 45
370s integer: NAs = FALSE, lag = 2, differences = 1, setNames = 0, useNames = 0
370s  int [1:8] -9 -1 -3 -3 -2 9 3 -6
370s  int [1:8] -9 -1 -3 -3 -2 9 3 -6
370s integer: NAs = FALSE, lag = 2, differences = 2, setNames = 0, useNames = 0
370s  int [1:6] 6 -2 1 12 5 -15
370s  int [1:6] 6 -2 1 12 5 -15
370s integer: NAs = FALSE, lag = 2, differences = 3, setNames = 0, useNames = 0
370s  int [1:4] -5 14 4 -27
370s  int [1:4] -5 14 4 -27
370s integer: NAs = FALSE, lag = 2, differences = 4, setNames = 0, useNames = 0
370s  int [1:2] 9 -41
370s  int [1:2] 9 -41
370s integer: NAs = FALSE, lag = 3, differences = 1, setNames = 0, useNames = 0
370s  int [1:7] -11 -2 -5 -3 7 3 3
370s  int [1:7] -11 -2 -5 -3 7 3 3
370s integer: NAs = FALSE, lag = 3, differences = 2, setNames = 0, useNames = 0
370s  int [1:4] 8 9 8 6
370s  int [1:4] 8 9 8 6
370s integer: NAs = FALSE, lag = 3, differences = 3, setNames = 0, useNames = 0
370s  int -2
370s  int -2
370s integer: NAs = FALSE, lag = 3, differences = 4, setNames = 0, useNames = 0
370s  int(0) 
370s  int(0) 
370s integer: NAs = TRUE, lag = 1, differences = 1, setNames = 1, useNames = 1
370s  Named int [1:9] NA NA NA NA NA 0 9 -6 0
370s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
370s  Named int [1:9] NA NA NA NA NA 0 9 -6 0
370s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
370s integer: NAs = TRUE, lag = 1, differences = 2, setNames = 1, useNames = 1
370s  Named int [1:8] NA NA NA NA NA 9 -15 6
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s  Named int [1:8] NA NA NA NA NA 9 -15 6
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s integer: NAs = TRUE, lag = 1, differences = 3, setNames = 1, useNames = 1
370s  Named int [1:7] NA NA NA NA NA -24 21
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s  Named int [1:7] NA NA NA NA NA -24 21
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s integer: NAs = TRUE, lag = 1, differences = 4, setNames = 1, useNames = 1
370s  Named int [1:6] NA NA NA NA NA 45
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s  Named int [1:6] NA NA NA NA NA 45
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s integer: NAs = TRUE, lag = 2, differences = 1, setNames = 1, useNames = 1
370s  Named int [1:8] -9 NA NA NA NA 9 3 -6
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s  Named int [1:8] -9 NA NA NA NA 9 3 -6
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s integer: NAs = TRUE, lag = 2, differences = 2, setNames = 1, useNames = 1
370s  Named int [1:6] NA NA NA NA NA -15
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s  Named int [1:6] NA NA NA NA NA -15
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s integer: NAs = TRUE, lag = 2, differences = 3, setNames = 1, useNames = 1
370s  Named int [1:4] NA NA NA NA
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s  Named int [1:4] NA NA NA NA
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s integer: NAs = TRUE, lag = 2, differences = 4, setNames = 1, useNames = 1
370s  Named int [1:2] NA NA
370s  - attr(*, "names")= chr [1:2] "I" "J"
370s  Named int [1:2] NA NA
370s  - attr(*, "names")= chr [1:2] "I" "J"
370s integer: NAs = TRUE, lag = 3, differences = 1, setNames = 1, useNames = 1
370s  Named int [1:7] NA NA -5 NA NA 3 3
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s  Named int [1:7] NA NA -5 NA NA 3 3
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s integer: NAs = TRUE, lag = 3, differences = 2, setNames = 1, useNames = 1
370s  Named int [1:4] NA NA 8 NA
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s  Named int [1:4] NA NA 8 NA
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s integer: NAs = TRUE, lag = 3, differences = 3, setNames = 1, useNames = 1
370s  Named int NA
370s  - attr(*, "names")= chr "J"
370s  Named int NA
370s  - attr(*, "names")= chr "J"
370s integer: NAs = TRUE, lag = 3, differences = 4, setNames = 1, useNames = 1
370s  Named int(0) 
370s  - attr(*, "names")= chr(0) 
370s  Named int(0) 
370s  - attr(*, "names")= chr(0) 
370s integer: NAs = TRUE, lag = 1, differences = 1, setNames = 1, useNames = 0
370s  int [1:9] NA NA NA NA NA 0 9 NA NA
370s  int [1:9] NA NA NA NA NA 0 9 NA NA
370s integer: NAs = TRUE, lag = 1, differences = 2, setNames = 1, useNames = 0
370s  int [1:8] NA NA NA NA NA 9 NA NA
370s  int [1:8] NA NA NA NA NA 9 NA NA
370s integer: NAs = TRUE, lag = 1, differences = 3, setNames = 1, useNames = 0
370s  int [1:7] NA NA NA NA NA NA NA
370s  int [1:7] NA NA NA NA NA NA NA
370s integer: NAs = TRUE, lag = 1, differences = 4, setNames = 1, useNames = 0
370s  int [1:6] NA NA NA NA NA NA
370s  int [1:6] NA NA NA NA NA NA
370s integer: NAs = TRUE, lag = 2, differences = 1, setNames = 1, useNames = 0
370s  int [1:8] NA NA NA NA NA 9 NA -6
370s  int [1:8] NA NA NA NA NA 9 NA -6
370s integer: NAs = TRUE, lag = 2, differences = 2, setNames = 1, useNames = 0
370s  int [1:6] NA NA NA NA NA -15
370s  int [1:6] NA NA NA NA NA -15
370s integer: NAs = TRUE, lag = 2, differences = 3, setNames = 1, useNames = 0
370s  int [1:4] NA NA NA NA
370s  int [1:4] NA NA NA NA
370s integer: NAs = TRUE, lag = 2, differences = 4, setNames = 1, useNames = 0
370s  int [1:2] NA NA
370s  int [1:2] NA NA
370s integer: NAs = TRUE, lag = 3, differences = 1, setNames = 1, useNames = 0
370s  int [1:7] NA NA NA NA NA NA 3
370s  int [1:7] NA NA NA NA NA NA 3
370s integer: NAs = TRUE, lag = 3, differences = 2, setNames = 1, useNames = 0
370s  int [1:4] NA NA NA NA
370s  int [1:4] NA NA NA NA
370s integer: NAs = TRUE, lag = 3, differences = 3, setNames = 1, useNames = 0
370s  int NA
370s  int NA
370s integer: NAs = TRUE, lag = 3, differences = 4, setNames = 1, useNames = 0
370s  int(0) 
370s  int(0) 
370s integer: NAs = TRUE, lag = 1, differences = 1, setNames = 0, useNames = 1
370s  Named int [1:9] NA NA NA NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
370s  Named int [1:9] NA NA NA NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
370s integer: NAs = TRUE, lag = 1, differences = 2, setNames = 0, useNames = 1
370s  Named int [1:8] NA NA NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s  Named int [1:8] NA NA NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s integer: NAs = TRUE, lag = 1, differences = 3, setNames = 0, useNames = 1
370s  Named int [1:7] NA NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s  Named int [1:7] NA NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s integer: NAs = TRUE, lag = 1, differences = 4, setNames = 0, useNames = 1
370s  Named int [1:6] NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s  Named int [1:6] NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s integer: NAs = TRUE, lag = 2, differences = 1, setNames = 0, useNames = 1
370s  Named int [1:8] NA NA NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s  Named int [1:8] NA NA NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s integer: NAs = TRUE, lag = 2, differences = 2, setNames = 0, useNames = 1
370s  Named int [1:6] NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s  Named int [1:6] NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s integer: NAs = TRUE, lag = 2, differences = 3, setNames = 0, useNames = 1
370s  Named int [1:4] NA NA NA NA
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s  Named int [1:4] NA NA NA NA
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s integer: NAs = TRUE, lag = 2, differences = 4, setNames = 0, useNames = 1
370s  Named int [1:2] NA NA
370s  - attr(*, "names")= chr [1:2] "I" "J"
370s  Named int [1:2] NA NA
370s  - attr(*, "names")= chr [1:2] "I" "J"
370s integer: NAs = TRUE, lag = 3, differences = 1, setNames = 0, useNames = 1
370s  Named int [1:7] NA NA NA NA NA NA 3
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s  Named int [1:7] NA NA NA NA NA NA 3
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s integer: NAs = TRUE, lag = 3, differences = 2, setNames = 0, useNames = 1
370s  Named int [1:4] NA NA NA NA
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s  Named int [1:4] NA NA NA NA
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s integer: NAs = TRUE, lag = 3, differences = 3, setNames = 0, useNames = 1
370s  Named int NA
370s  - attr(*, "names")= chr "J"
370s  Named int NA
370s  - attr(*, "names")= chr "J"
370s integer: NAs = TRUE, lag = 3, differences = 4, setNames = 0, useNames = 1
370s  Named int(0) 
370s  - attr(*, "names")= chr(0) 
370s  Named int(0) 
370s  - attr(*, "names")= chr(0) 
370s integer: NAs = TRUE, lag = 1, differences = 1, setNames = 0, useNames = 0
370s  int [1:9] NA NA NA NA NA NA NA NA NA
370s  int [1:9] NA NA NA NA NA NA NA NA NA
370s integer: NAs = TRUE, lag = 1, differences = 2, setNames = 0, useNames = 0
370s  int [1:8] NA NA NA NA NA NA NA NA
370s  int [1:8] NA NA NA NA NA NA NA NA
370s integer: NAs = TRUE, lag = 1, differences = 3, setNames = 0, useNames = 0
370s  int [1:7] NA NA NA NA NA NA NA
370s  int [1:7] NA NA NA NA NA NA NA
370s integer: NAs = TRUE, lag = 1, differences = 4, setNames = 0, useNames = 0
370s  int [1:6] NA NA NA NA NA NA
370s  int [1:6] NA NA NA NA NA NA
370s integer: NAs = TRUE, lag = 2, differences = 1, setNames = 0, useNames = 0
370s  int [1:8] NA NA NA NA NA NA NA NA
370s  int [1:8] NA NA NA NA NA NA NA NA
370s integer: NAs = TRUE, lag = 2, differences = 2, setNames = 0, useNames = 0
370s  int [1:6] NA NA NA NA NA NA
370s  int [1:6] NA NA NA NA NA NA
370s integer: NAs = TRUE, lag = 2, differences = 3, setNames = 0, useNames = 0
370s  int [1:4] NA NA NA NA
370s  int [1:4] NA NA NA NA
370s integer: NAs = TRUE, lag = 2, differences = 4, setNames = 0, useNames = 0
370s  int [1:2] NA NA
370s  int [1:2] NA NA
370s integer: NAs = TRUE, lag = 3, differences = 1, setNames = 0, useNames = 0
370s  int [1:7] NA NA NA NA NA NA 3
370s  int [1:7] NA NA NA NA NA NA 3
370s integer: NAs = TRUE, lag = 3, differences = 2, setNames = 0, useNames = 0
370s  int [1:4] NA NA NA NA
370s  int [1:4] NA NA NA NA
370s integer: NAs = TRUE, lag = 3, differences = 3, setNames = 0, useNames = 0
370s  int NA
370s  int NA
370s integer: NAs = TRUE, lag = 3, differences = 4, setNames = 0, useNames = 0
370s  int(0) 
370s  int(0) 
370s  num [1:10] 2.586 -0.344 0.33 9.155 -3.254 ...
370s double: NAs = FALSE, lag = 1, differences = 1, setNames = 1, useNames = 1
370s  Named num [1:9] -2.929 0.673 8.826 -12.409 -1.221 ...
370s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
370s  Named num [1:9] -2.929 0.673 8.826 -12.409 -1.221 ...
370s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
370s double: NAs = FALSE, lag = 1, differences = 2, setNames = 1, useNames = 1
370s  Named num [1:8] 3.6 8.15 -21.23 11.19 -2.1 ...
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s  Named num [1:8] 3.6 8.15 -21.23 11.19 -2.1 ...
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s double: NAs = FALSE, lag = 1, differences = 3, setNames = 1, useNames = 1
370s  Named num [1:7] 4.55 -29.39 32.42 -13.29 14.97 ...
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s  Named num [1:7] 4.55 -29.39 32.42 -13.29 14.97 ...
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s double: NAs = FALSE, lag = 1, differences = 4, setNames = 1, useNames = 1
370s  Named num [1:6] -33.9 61.8 -45.7 28.3 -37 ...
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s  Named num [1:6] -33.9 61.8 -45.7 28.3 -37 ...
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s double: NAs = FALSE, lag = 2, differences = 1, setNames = 1, useNames = 1
370s  Named num [1:8] -2.26 9.5 -3.58 -13.63 -4.54 ...
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s  Named num [1:8] -2.26 9.5 -3.58 -13.63 -4.54 ...
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s double: NAs = FALSE, lag = 2, differences = 2, setNames = 1, useNames = 1
370s  Named num [1:6] -1.33 -23.13 -0.96 19.86 14.44 ...
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s  Named num [1:6] -1.33 -23.13 -0.96 19.86 14.44 ...
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s double: NAs = FALSE, lag = 2, differences = 3, setNames = 1, useNames = 1
370s  Named num [1:4] 0.368 42.988 15.396 -29.313
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s  Named num [1:4] 0.368 42.988 15.396 -29.313
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s double: NAs = FALSE, lag = 2, differences = 4, setNames = 1, useNames = 1
370s  Named num [1:2] 15 -72.3
370s  - attr(*, "names")= chr [1:2] "I" "J"
370s  Named num [1:2] 15 -72.3
370s  - attr(*, "names")= chr [1:2] "I" "J"
370s double: NAs = FALSE, lag = 3, differences = 1, setNames = 1, useNames = 1
370s  Named num [1:7] 6.57 -2.91 -4.81 -16.95 5.01 ...
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s  Named num [1:7] 6.57 -2.91 -4.81 -16.95 5.01 ...
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s double: NAs = FALSE, lag = 3, differences = 2, setNames = 1, useNames = 1
370s  Named num [1:4] -23.52 7.92 11.38 23.27
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s  Named num [1:4] -23.52 7.92 11.38 23.27
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s double: NAs = FALSE, lag = 3, differences = 3, setNames = 1, useNames = 1
370s  Named num 46.8
370s  - attr(*, "names")= chr "J"
370s  Named num 46.8
370s  - attr(*, "names")= chr "J"
370s double: NAs = FALSE, lag = 3, differences = 4, setNames = 1, useNames = 1
370s  Named num(0) 
370s  - attr(*, "names")= chr(0) 
370s  Named num(0) 
370s  - attr(*, "names")= chr(0) 
370s double: NAs = FALSE, lag = 1, differences = 1, setNames = 1, useNames = 0
370s  num [1:9] -2.929 0.673 8.826 -12.409 -1.221 ...
370s  num [1:9] -2.929 0.673 8.826 -12.409 -1.221 ...
370s double: NAs = FALSE, lag = 1, differences = 2, setNames = 1, useNames = 0
370s  num [1:8] 3.6 8.15 -21.23 11.19 -2.1 ...
370s  num [1:8] 3.6 8.15 -21.23 11.19 -2.1 ...
370s double: NAs = FALSE, lag = 1, differences = 3, setNames = 1, useNames = 0
370s  num [1:7] 4.55 -29.39 32.42 -13.29 14.97 ...
370s  num [1:7] 4.55 -29.39 32.42 -13.29 14.97 ...
370s double: NAs = FALSE, lag = 1, differences = 4, setNames = 1, useNames = 0
370s  num [1:6] -33.9 61.8 -45.7 28.3 -37 ...
370s  num [1:6] -33.9 61.8 -45.7 28.3 -37 ...
370s double: NAs = FALSE, lag = 2, differences = 1, setNames = 1, useNames = 0
370s  num [1:8] -2.26 9.5 -3.58 -13.63 -4.54 ...
370s  num [1:8] -2.26 9.5 -3.58 -13.63 -4.54 ...
370s double: NAs = FALSE, lag = 2, differences = 2, setNames = 1, useNames = 0
370s  num [1:6] -1.33 -23.13 -0.96 19.86 14.44 ...
370s  num [1:6] -1.33 -23.13 -0.96 19.86 14.44 ...
370s double: NAs = FALSE, lag = 2, differences = 3, setNames = 1, useNames = 0
370s  num [1:4] 0.368 42.988 15.396 -29.313
370s  num [1:4] 0.368 42.988 15.396 -29.313
370s double: NAs = FALSE, lag = 2, differences = 4, setNames = 1, useNames = 0
370s  num [1:2] 15 -72.3
370s  num [1:2] 15 -72.3
370s double: NAs = FALSE, lag = 3, differences = 1, setNames = 1, useNames = 0
370s  num [1:7] 6.57 -2.91 -4.81 -16.95 5.01 ...
370s  num [1:7] 6.57 -2.91 -4.81 -16.95 5.01 ...
370s double: NAs = FALSE, lag = 3, differences = 2, setNames = 1, useNames = 0
370s  num [1:4] -23.52 7.92 11.38 23.27
370s  num [1:4] -23.52 7.92 11.38 23.27
370s double: NAs = FALSE, lag = 3, differences = 3, setNames = 1, useNames = 0
370s  num 46.8
370s  num 46.8
370s double: NAs = FALSE, lag = 3, differences = 4, setNames = 1, useNames = 0
370s  num(0) 
370s  num(0) 
370s double: NAs = FALSE, lag = 1, differences = 1, setNames = 0, useNames = 1
370s  Named num [1:9] -2.929 0.673 8.826 -12.409 -1.221 ...
370s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
370s  Named num [1:9] -2.929 0.673 8.826 -12.409 -1.221 ...
370s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
370s double: NAs = FALSE, lag = 1, differences = 2, setNames = 0, useNames = 1
370s  Named num [1:8] 3.6 8.15 -21.23 11.19 -2.1 ...
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s  Named num [1:8] 3.6 8.15 -21.23 11.19 -2.1 ...
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s double: NAs = FALSE, lag = 1, differences = 3, setNames = 0, useNames = 1
370s  Named num [1:7] 4.55 -29.39 32.42 -13.29 14.97 ...
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s  Named num [1:7] 4.55 -29.39 32.42 -13.29 14.97 ...
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s double: NAs = FALSE, lag = 1, differences = 4, setNames = 0, useNames = 1
370s  Named num [1:6] -33.9 61.8 -45.7 28.3 -37 ...
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s  Named num [1:6] -33.9 61.8 -45.7 28.3 -37 ...
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s double: NAs = FALSE, lag = 2, differences = 1, setNames = 0, useNames = 1
370s  Named num [1:8] -2.26 9.5 -3.58 -13.63 -4.54 ...
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s  Named num [1:8] -2.26 9.5 -3.58 -13.63 -4.54 ...
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s double: NAs = FALSE, lag = 2, differences = 2, setNames = 0, useNames = 1
370s  Named num [1:6] -1.33 -23.13 -0.96 19.86 14.44 ...
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s  Named num [1:6] -1.33 -23.13 -0.96 19.86 14.44 ...
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s double: NAs = FALSE, lag = 2, differences = 3, setNames = 0, useNames = 1
370s  Named num [1:4] 0.368 42.988 15.396 -29.313
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s  Named num [1:4] 0.368 42.988 15.396 -29.313
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s double: NAs = FALSE, lag = 2, differences = 4, setNames = 0, useNames = 1
370s  Named num [1:2] 15 -72.3
370s  - attr(*, "names")= chr [1:2] "I" "J"
370s  Named num [1:2] 15 -72.3
370s  - attr(*, "names")= chr [1:2] "I" "J"
370s double: NAs = FALSE, lag = 3, differences = 1, setNames = 0, useNames = 1
370s  Named num [1:7] 6.57 -2.91 -4.81 -16.95 5.01 ...
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s  Named num [1:7] 6.57 -2.91 -4.81 -16.95 5.01 ...
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s double: NAs = FALSE, lag = 3, differences = 2, setNames = 0, useNames = 1
370s  Named num [1:4] -23.52 7.92 11.38 23.27
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s  Named num [1:4] -23.52 7.92 11.38 23.27
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s double: NAs = FALSE, lag = 3, differences = 3, setNames = 0, useNames = 1
370s  Named num 46.8
370s  - attr(*, "names")= chr "J"
370s  Named num 46.8
370s  - attr(*, "names")= chr "J"
370s double: NAs = FALSE, lag = 3, differences = 4, setNames = 0, useNames = 1
370s  Named num(0) 
370s  - attr(*, "names")= chr(0) 
370s  Named num(0) 
370s  - attr(*, "names")= chr(0) 
370s double: NAs = FALSE, lag = 1, differences = 1, setNames = 0, useNames = 0
370s  num [1:9] -2.929 0.673 8.826 -12.409 -1.221 ...
370s  num [1:9] -2.929 0.673 8.826 -12.409 -1.221 ...
370s double: NAs = FALSE, lag = 1, differences = 2, setNames = 0, useNames = 0
370s  num [1:8] 3.6 8.15 -21.23 11.19 -2.1 ...
370s  num [1:8] 3.6 8.15 -21.23 11.19 -2.1 ...
370s double: NAs = FALSE, lag = 1, differences = 3, setNames = 0, useNames = 0
370s  num [1:7] 4.55 -29.39 32.42 -13.29 14.97 ...
370s  num [1:7] 4.55 -29.39 32.42 -13.29 14.97 ...
370s double: NAs = FALSE, lag = 1, differences = 4, setNames = 0, useNames = 0
370s  num [1:6] -33.9 61.8 -45.7 28.3 -37 ...
370s  num [1:6] -33.9 61.8 -45.7 28.3 -37 ...
370s double: NAs = FALSE, lag = 2, differences = 1, setNames = 0, useNames = 0
370s  num [1:8] -2.26 9.5 -3.58 -13.63 -4.54 ...
370s  num [1:8] -2.26 9.5 -3.58 -13.63 -4.54 ...
370s double: NAs = FALSE, lag = 2, differences = 2, setNames = 0, useNames = 0
370s  num [1:6] -1.33 -23.13 -0.96 19.86 14.44 ...
370s  num [1:6] -1.33 -23.13 -0.96 19.86 14.44 ...
370s double: NAs = FALSE, lag = 2, differences = 3, setNames = 0, useNames = 0
370s  num [1:4] 0.368 42.988 15.396 -29.313
370s  num [1:4] 0.368 42.988 15.396 -29.313
370s double: NAs = FALSE, lag = 2, differences = 4, setNames = 0, useNames = 0
370s  num [1:2] 15 -72.3
370s  num [1:2] 15 -72.3
370s double: NAs = FALSE, lag = 3, differences = 1, setNames = 0, useNames = 0
370s  num [1:7] 6.57 -2.91 -4.81 -16.95 5.01 ...
370s  num [1:7] 6.57 -2.91 -4.81 -16.95 5.01 ...
370s double: NAs = FALSE, lag = 3, differences = 2, setNames = 0, useNames = 0
370s  num [1:4] -23.52 7.92 11.38 23.27
370s  num [1:4] -23.52 7.92 11.38 23.27
370s double: NAs = FALSE, lag = 3, differences = 3, setNames = 0, useNames = 0
370s  num 46.8
370s  num 46.8
370s double: NAs = FALSE, lag = 3, differences = 4, setNames = 0, useNames = 0
370s  num(0) 
370s  num(0) 
370s double: NAs = TRUE, lag = 1, differences = 1, setNames = 1, useNames = 1
370s  Named num [1:9] -2.929 0.673 8.826 NA NA ...
370s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
370s  Named num [1:9] -2.929 0.673 8.826 NA NA ...
370s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
370s double: NAs = TRUE, lag = 1, differences = 2, setNames = 1, useNames = 1
370s  Named num [1:8] 3.6 8.15 NA NA NA ...
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s  Named num [1:8] 3.6 8.15 NA NA NA ...
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s double: NAs = TRUE, lag = 1, differences = 3, setNames = 1, useNames = 1
370s  Named num [1:7] 4.55 NA NA NA NA ...
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s  Named num [1:7] 4.55 NA NA NA NA ...
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s double: NAs = TRUE, lag = 1, differences = 4, setNames = 1, useNames = 1
370s  Named num [1:6] NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s  Named num [1:6] NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s double: NAs = TRUE, lag = 2, differences = 1, setNames = 1, useNames = 1
370s  Named num [1:8] -2.26 9.5 NA NA NA ...
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s  Named num [1:8] -2.26 9.5 NA NA NA ...
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s double: NAs = TRUE, lag = 2, differences = 2, setNames = 1, useNames = 1
370s  Named num [1:6] NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s  Named num [1:6] NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s double: NAs = TRUE, lag = 2, differences = 3, setNames = 1, useNames = 1
370s  Named num [1:4] NA NA NA NA
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s  Named num [1:4] NA NA NA NA
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s double: NAs = TRUE, lag = 2, differences = 4, setNames = 1, useNames = 1
370s  Named num [1:2] NA NA
370s  - attr(*, "names")= chr [1:2] "I" "J"
370s  Named num [1:2] NA NA
370s  - attr(*, "names")= chr [1:2] "I" "J"
370s double: NAs = TRUE, lag = 3, differences = 1, setNames = 1, useNames = 1
370s  Named num [1:7] 6.57 NA NA -16.95 NA ...
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s  Named num [1:7] 6.57 NA NA -16.95 NA ...
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s double: NAs = TRUE, lag = 3, differences = 2, setNames = 1, useNames = 1
370s  Named num [1:4] -23.5 NA NA 23.3
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s  Named num [1:4] -23.5 NA NA 23.3
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s double: NAs = TRUE, lag = 3, differences = 3, setNames = 1, useNames = 1
370s  Named num 46.8
370s  - attr(*, "names")= chr "J"
370s  Named num 46.8
370s  - attr(*, "names")= chr "J"
370s double: NAs = TRUE, lag = 3, differences = 4, setNames = 1, useNames = 1
370s  Named num(0) 
370s  - attr(*, "names")= chr(0) 
370s  Named num(0) 
370s  - attr(*, "names")= chr(0) 
370s double: NAs = TRUE, lag = 1, differences = 1, setNames = 1, useNames = 0
370s  num [1:9] NA 0.673 8.826 NA NA ...
370s  num [1:9] NA 0.673 8.826 NA NA ...
370s double: NAs = TRUE, lag = 1, differences = 2, setNames = 1, useNames = 0
370s  num [1:8] NA 8.15 NA NA NA ...
370s  num [1:8] NA 8.15 NA NA NA ...
370s double: NAs = TRUE, lag = 1, differences = 3, setNames = 1, useNames = 0
370s  num [1:7] NA NA NA NA NA NA NA
370s  num [1:7] NA NA NA NA NA NA NA
370s double: NAs = TRUE, lag = 1, differences = 4, setNames = 1, useNames = 0
370s  num [1:6] NA NA NA NA NA NA
370s  num [1:6] NA NA NA NA NA NA
370s double: NAs = TRUE, lag = 2, differences = 1, setNames = 1, useNames = 0
370s  num [1:8] NA 9.5 NA NA NA ...
370s  num [1:8] NA 9.5 NA NA NA ...
370s double: NAs = TRUE, lag = 2, differences = 2, setNames = 1, useNames = 0
370s  num [1:6] NA NA NA NA NA NA
370s  num [1:6] NA NA NA NA NA NA
370s double: NAs = TRUE, lag = 2, differences = 3, setNames = 1, useNames = 0
370s  num [1:4] NA NA NA NA
370s  num [1:4] NA NA NA NA
370s double: NAs = TRUE, lag = 2, differences = 4, setNames = 1, useNames = 0
370s  num [1:2] NA NA
370s  num [1:2] NA NA
370s double: NAs = TRUE, lag = 3, differences = 1, setNames = 1, useNames = 0
370s  num [1:7] NA NA NA NA NA NA NA
370s  num [1:7] NA NA NA NA NA NA NA
370s double: NAs = TRUE, lag = 3, differences = 2, setNames = 1, useNames = 0
370s  num [1:4] NA NA NA NA
370s  num [1:4] NA NA NA NA
370s double: NAs = TRUE, lag = 3, differences = 3, setNames = 1, useNames = 0
370s  num NA
370s  num NA
370s double: NAs = TRUE, lag = 3, differences = 4, setNames = 1, useNames = 0
370s  num(0) 
370s  num(0) 
370s double: NAs = TRUE, lag = 1, differences = 1, setNames = 0, useNames = 1
370s  Named num [1:9] NA 0.673 8.826 NA NA ...
370s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
370s  Named num [1:9] NA 0.673 8.826 NA NA ...
370s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
370s double: NAs = TRUE, lag = 1, differences = 2, setNames = 0, useNames = 1
370s  Named num [1:8] NA 8.15 NA NA NA ...
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s  Named num [1:8] NA 8.15 NA NA NA ...
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s double: NAs = TRUE, lag = 1, differences = 3, setNames = 0, useNames = 1
370s  Named num [1:7] NA NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s  Named num [1:7] NA NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s double: NAs = TRUE, lag = 1, differences = 4, setNames = 0, useNames = 1
370s  Named num [1:6] NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s  Named num [1:6] NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s double: NAs = TRUE, lag = 2, differences = 1, setNames = 0, useNames = 1
370s  Named num [1:8] NA 9.5 NA NA NA ...
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s  Named num [1:8] NA 9.5 NA NA NA ...
370s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
370s double: NAs = TRUE, lag = 2, differences = 2, setNames = 0, useNames = 1
370s  Named num [1:6] NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s  Named num [1:6] NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
370s double: NAs = TRUE, lag = 2, differences = 3, setNames = 0, useNames = 1
370s  Named num [1:4] NA NA NA NA
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s  Named num [1:4] NA NA NA NA
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s double: NAs = TRUE, lag = 2, differences = 4, setNames = 0, useNames = 1
370s  Named num [1:2] NA NA
370s  - attr(*, "names")= chr [1:2] "I" "J"
370s  Named num [1:2] NA NA
370s  - attr(*, "names")= chr [1:2] "I" "J"
370s double: NAs = TRUE, lag = 3, differences = 1, setNames = 0, useNames = 1
370s  Named num [1:7] NA NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s  Named num [1:7] NA NA NA NA NA NA NA
370s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
370s double: NAs = TRUE, lag = 3, differences = 2, setNames = 0, useNames = 1
370s  Named num [1:4] NA NA NA NA
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s  Named num [1:4] NA NA NA NA
370s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
370s double: NAs = TRUE, lag = 3, differences = 3, setNames = 0, useNames = 1
370s  Named num NA
370s  - attr(*, "names")= chr "J"
370s  Named num NA
370s  - attr(*, "names")= chr "J"
370s double: NAs = TRUE, lag = 3, differences = 4, setNames = 0, useNames = 1
370s  Named num(0) 
370s  - attr(*, "names")= chr(0) 
370s  Named num(0) 
370s  - attr(*, "names")= chr(0) 
370s double: NAs = TRUE, lag = 1, differences = 1, setNames = 0, useNames = 0
370s  num [1:9] NA 0.673 8.826 NA NA ...
370s  num [1:9] NA 0.673 8.826 NA NA ...
370s double: NAs = TRUE, lag = 1, differences = 2, setNames = 0, useNames = 0
370s  num [1:8] NA 8.15 NA NA NA ...
370s  num [1:8] NA 8.15 NA NA NA ...
370s double: NAs = TRUE, lag = 1, differences = 3, setNames = 0, useNames = 0
370s  num [1:7] NA NA NA NA NA NA NA
370s  num [1:7] NA NA NA NA NA NA NA
370s double: NAs = TRUE, lag = 1, differences = 4, setNames = 0, useNames = 0
370s  num [1:6] NA NA NA NA NA NA
370s  num [1:6] NA NA NA NA NA NA
370s double: NAs = TRUE, lag = 2, differences = 1, setNames = 0, useNames = 0
370s  num [1:8] NA 9.5 NA NA NA ...
370s  num [1:8] NA 9.5 NA NA NA ...
370s double: NAs = TRUE, lag = 2, differences = 2, setNames = 0, useNames = 0
370s  num [1:6] NA NA NA NA NA NA
370s  num [1:6] NA NA NA NA NA NA
370s double: NAs = TRUE, lag = 2, differences = 3, setNames = 0, useNames = 0
370s  num [1:4] NA NA NA NA
370s  num [1:4] NA NA NA NA
370s double: NAs = TRUE, lag = 2, differences = 4, setNames = 0, useNames = 0
370s  num [1:2] NA NA
370s  num [1:2] NA NA
370s double: NAs = TRUE, lag = 3, differences = 1, setNames = 0, useNames = 0
370s  num [1:7] NA NA NA NA NA NA NA
370s  num [1:7] NA NA NA NA NA NA NA
370s double: NAs = TRUE, lag = 3, differences = 2, setNames = 0, useNames = 0
370s  num [1:4] NA NA NA NA
370s  num [1:4] NA NA NA NA
370s double: NAs = TRUE, lag = 3, differences = 3, setNames = 0, useNames = 0
370s  num NA
370s  num NA
370s double: NAs = TRUE, lag = 3, differences = 4, setNames = 0, useNames = 0
370s  num(0) 
370s  num(0) 
370s > 
370s 
370s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
370s Copyright (C) 2024 The R Foundation for Statistical Computing
370s Platform: arm-unknown-linux-gnueabihf (32-bit)
370s 
370s R is free software and comes with ABSOLUTELY NO WARRANTY.
370s You are welcome to redistribute it under certain conditions.
370s Type 'license()' or 'licence()' for distribution details.
370s 
370s R is a collaborative project with many contributors.
370s Type 'contributors()' for more information and
370s 'citation()' on how to cite R or R packages in publications.
370s 
370s Type 'demo()' for some demos, 'help()' for on-line help, or
370s 'help.start()' for an HTML browser interface to help.
370s Type 'q()' to quit R.
370s 
371s > library("matrixStats")
371s > 
371s > diff2_R <- function(..., useNames=NA){
371s +   res <- diff(...)
371s +   if (is.na(useNames) || !useNames) names(res) <- NULL
371s +   res
371s + }
371s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
371s > # Subsetted tests
371s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
371s > source("utils/validateIndicesFramework.R")
371s > x <- runif(6, min = -6, max = 6)
371s > for (setNames in c(TRUE, FALSE)) {
371s +   if (setNames) names(x) <- LETTERS[1:6]
371s +   else names(x) <- NULL
371s +   for (l in 1:2) {
371s +     for (d in 1:2) {
371s +       for (idxs in index_cases) {
371s +         for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
371s +           validateIndicesTestVector(x, idxs,
371s +                                     ftest = diff2, fsure = diff2_R,
371s +                                     lag = l, differences = d, useNames = useNames)
371s +         }
371s +       }
371s +     }
371s +   }
371s + }
371s > 
371s 
371s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
371s Copyright (C) 2024 The R Foundation for Statistical Computing
371s Platform: arm-unknown-linux-gnueabihf (32-bit)
371s 
371s R is free software and comes with ABSOLUTELY NO WARRANTY.
371s You are welcome to redistribute it under certain conditions.
371s Type 'license()' or 'licence()' for distribution details.
371s 
371s R is a collaborative project with many contributors.
371s Type 'contributors()' for more information and
371s 'citation()' on how to cite R or R packages in publications.
371s 
371s Type 'demo()' for some demos, 'help()' for on-line help, or
371s 'help.start()' for an HTML browser interface to help.
371s Type 'q()' to quit R.
371s 
371s > library("matrixStats")
371s > 
371s > indexByRow_R1 <- function(dim, idxs = NULL, ...) {
371s +   n <- prod(dim)
371s +   x <- matrix(seq_len(n), nrow = dim[2L], ncol = dim[1L], byrow = TRUE)
371s +   if (!is.null(idxs))
371s +     x <- x[idxs]
371s +   as.vector(x)
371s + }
371s > 
371s > 
371s > indexByRow_R2 <- function(dim, idxs = NULL, ...) {
371s +   n <- prod(dim)
371s +   if (is.null(idxs)) {
371s +     x <- matrix(seq_len(n), nrow = dim[2L], ncol = dim[1L], byrow = TRUE)
371s +     as.vector(x)
371s +   } else {
371s +     idxs <- idxs - 1L
371s +     cols <- idxs %/% dim[2L]
371s +     rows <- idxs  %% dim[2L]
371s +     cols + dim[1L] * rows + 1L
371s +   }
371s + }
371s > 
371s > 
371s > dim <- c(5L, 4L)
371s > x <- matrix(NA_integer_, nrow = dim[1L], ncol = dim[2L])
371s > y <- t(x)
371s > idxs_by_cols <- seq_along(x)
371s > 
371s > # Assign by columns
371s > x[idxs_by_cols] <- idxs_by_cols
371s > print(x)
371s      [,1] [,2] [,3] [,4]
371s [1,]    1    6   11   16
371s [2,]    2    7   12   17
371s [3,]    3    8   13   18
371s [4,]    4    9   14   19
371s [5,]    5   10   15   20
371s > 
371s > # Truth
371s > y0 <- t(x)
371s > idxs_by_rows <- as.vector(y0)
371s > 
371s > # Assert
371s > idxs <- indexByRow(dim)
371s > stopifnot(all.equal(idxs, idxs_by_rows))
371s > y <- x
371s > y[idxs_by_rows] <- idxs
371s > print(y)
371s      [,1] [,2] [,3] [,4]
371s [1,]    1    6   11   16
371s [2,]    2    7   12   17
371s [3,]    3    8   13   18
371s [4,]    4    9   14   19
371s [5,]    5   10   15   20
371s > stopifnot(all(as.vector(y) == as.vector(x)))
371s > 
371s > idxs_R1 <- indexByRow_R1(dim)
371s > stopifnot(all.equal(idxs_R1, idxs_by_rows))
371s > 
371s > idxs_R2 <- indexByRow_R2(dim)
371s > stopifnot(all.equal(idxs_R2, idxs_by_rows))
371s > 
371s > # Assert
371s > idxs_by_cols <- seq(from = 1, to = length(x), by = 3L)
371s > idxs_by_rows <- as.vector(t(x)[idxs_by_cols])
371s > 
371s > idxs <- indexByRow(dim, idxs = idxs_by_cols)
371s > stopifnot(all(idxs == idxs_by_rows))
371s > 
371s > idxs_R1 <- indexByRow_R1(dim, idxs = idxs_by_cols)
371s > stopifnot(all(idxs_R1 == idxs_by_rows))
371s > 
371s > idxs_R2 <- indexByRow_R2(dim, idxs = idxs_by_cols)
371s > stopifnot(all(idxs_R2 == idxs_by_rows))
371s > 
371s > 
371s > ## DEFUNCT: Backward compatibility
371s > res <- tryCatch({
371s +   idxs1 <- indexByRow(x)
371s + }, error = identity)
371s > stopifnot(inherits(res, "error"))
371s > 
371s > 
371s > ## Exceptions:
371s > ## Too large matrices are not supported, which happens
371s > ## when prod(dim) > .Machine$integer.max
371s > dim_too_large <- c(.Machine$integer.max, 2L)
371s > res <- tryCatch({
371s +   idxs <- indexByRow(dim_too_large, idxs = 1L)
371s + }, error = identity)
371s > stopifnot(inherits(res, "error"))
371s > 
371s > ## Non-positive indices are not supported
371s > res <- tryCatch({
371s +   idxs <- indexByRow(c(1,1), idxs = 0L)
371s + }, error = identity)
371s > stopifnot(inherits(res, "error"))
371s > 
371s > res <- tryCatch({
371s +   idxs <- indexByRow(c(1,1), idxs = -1L)
371s + }, error = identity)
371s > stopifnot(inherits(res, "error"))
371s > 
372s 
372s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
372s Copyright (C) 2024 The R Foundation for Statistical Computing
372s Platform: arm-unknown-linux-gnueabihf (32-bit)
372s 
372s R is free software and comes with ABSOLUTELY NO WARRANTY.
372s You are welcome to redistribute it under certain conditions.
372s Type 'license()' or 'licence()' for distribution details.
372s 
372s R is a collaborative project with many contributors.
372s Type 'contributors()' for more information and
372s 'citation()' on how to cite R or R packages in publications.
372s 
372s Type 'demo()' for some demos, 'help()' for on-line help, or
372s 'help.start()' for an HTML browser interface to help.
372s Type 'q()' to quit R.
372s 
372s > library("matrixStats")
372s > library("stats")
372s > 
372s > logSumExp_R <- function(lx, na.rm = FALSE) {
372s +   log(sum(exp(lx), na.rm = na.rm))
372s + }
372s > 
372s > ## R-help thread \emph{'[R] Beyond double-precision?'} on May 9, 2009.
372s > 
372s > for (mode in c("integer", "double")) {
372s +   cat("mode: ", mode, "\n", sep = "")
372s + 
372s +   set.seed(1)
372s +   x <- runif(20, min = 1.0, max = 3.0)
372s +   storage.mode(x) <- mode
372s +   str(x)
372s + 
372s +   ## The logarithm of the harmonic mean
372s +   y0 <- log(1 / mean(1 / x))
372s +   print(y0)  ## -1.600885
372s + 
372s +   lx <- log(x)
372s +   y1 <- log(length(x)) - logSumExp(-lx)
372s +   print(y1)  ## [1] -1.600885
372s + 
372s +   # Sanity check
372s +   stopifnot(all.equal(y1, y0))
372s + 
372s +   y2 <- log(length(x)) - logSumExp_R(-lx)
372s +   # Sanity check
372s +   stopifnot(all.equal(y2, y0))
372s + } # for (mode ...)
372s mode: integer
372s  int [1:20] 1 1 2 2 1 2 2 2 2 1 ...
372s [1] 0.3215836
372s [1] 0.3215836
372s mode: double
372s  num [1:20] 1.53 1.74 2.15 2.82 1.4 ...
372s [1] 0.6673156
372s [1] 0.6673156
372s > 
372s > 
372s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
372s > # Missing values
372s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
372s > ## NA values
372s > lx <- c(1, 2, 3)
372s > lx[2] <- NA_real_
372s > y0 <- logSumExp_R(lx, na.rm = FALSE)
372s > y <- logSumExp(lx, na.rm = FALSE)
372s > print(y)
372s [1] NA
372s > stopifnot(identical(y, NA_real_))
372s > stopifnot(all.equal(y, y0))
372s > 
372s > y0 <- logSumExp_R(lx, na.rm = TRUE)
372s > y <- logSumExp(lx, na.rm = TRUE)
372s > print(y)
372s [1] 3.126928
372s > stopifnot(all.equal(y, y0))
372s > 
372s > ## NaN values
372s > lx <- c(1, 2, 3)
372s > lx[2] <- NaN
372s > y0 <- logSumExp_R(lx, na.rm = FALSE)
372s > y <- logSumExp(lx, na.rm = FALSE)
372s > print(y)
372s [1] NA
372s > stopifnot(identical(y, NA_real_))
372s > stopifnot(all.equal(y, y0))
372s > 
372s > y0 <- logSumExp_R(lx, na.rm = TRUE)
372s > y <- logSumExp(lx, na.rm = TRUE)
372s > print(y)
372s [1] 3.126928
372s > stopifnot(all.equal(y, y0))
372s > 
372s > 
372s > 
372s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
372s > # Corner cases
372s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
372s > ## Zero-length vectors
372s > lx <- numeric(0L)
372s > y0 <- logSumExp_R(lx)
372s > y <- logSumExp(lx)
372s > print(y)
372s [1] -Inf
372s > stopifnot(identical(y, -Inf))
372s > stopifnot(all.equal(y, y0))
372s > 
372s > ## Vectors of length one
372s > lx <- 1.0
372s > y0 <- logSumExp_R(lx)
372s > y <- logSumExp(lx)
372s > print(y)
372s [1] 1
372s > stopifnot(identical(y, lx))
372s > stopifnot(all.equal(y, y0))
372s > 
372s > lx <- NA_real_
372s > y0 <- logSumExp_R(lx, na.rm = TRUE)
372s > y <- logSumExp(lx, na.rm = TRUE)
372s > print(y)
372s [1] -Inf
372s > stopifnot(identical(y, -Inf))
372s > stopifnot(all.equal(y, y0))
372s > 
372s > ## All missing values
372s > lx <- c(NA_real_, NA_real_)
372s > y0 <- logSumExp_R(lx, na.rm = TRUE)
372s > y <- logSumExp(lx, na.rm = TRUE)
372s > print(y)
372s [1] -Inf
372s > stopifnot(identical(y, -Inf))
372s > stopifnot(all.equal(y, y0))
372s > 
372s > lx <- c(NA_real_, NA_real_)
372s > y0 <- logSumExp_R(lx, na.rm = FALSE)
372s > y <- logSumExp(lx, na.rm = FALSE)
372s > print(y)
372s [1] NA
372s > stopifnot(identical(y, NA_real_))
372s > stopifnot(all.equal(y, y0))
372s > 
372s > 
372s > ## +Inf values
372s > lx <- c(1, 2, +Inf)
372s > y0 <- logSumExp_R(lx)
372s > y <- logSumExp(lx)
372s > print(y)
372s [1] Inf
372s > stopifnot(identical(y, +Inf))
372s > stopifnot(all.equal(y, y0))
372s > 
372s > ## First element is a missing value, cf. PR #33
372s > lx <- c(NA_real_, 1)
372s > y0 <- logSumExp_R(lx)
372s > print(y0)
372s [1] NA
372s > y <- logSumExp(lx, na.rm = FALSE)
372s > print(y)
372s [1] NA
372s > stopifnot(identical(y, NA_real_))
372s > stopifnot(all.equal(y, y0))
372s > 
372s > y0 <- logSumExp_R(lx, na.rm = TRUE)
372s > print(y0)
372s [1] 1
372s > y <- logSumExp(lx, na.rm = TRUE)
372s > print(y)
372s [1] 1
372s > stopifnot(identical(y, 1))
372s > stopifnot(all.equal(y, y0))
372s > 
372s > ## Multiple -Inf values, cf. issue #84
372s > lx <- c(-Inf, -Inf)
372s > y0 <- logSumExp_R(lx)
372s > y <- logSumExp(lx)
372s > print(y)
372s [1] -Inf
372s > stopifnot(identical(y, -Inf))
372s > stopifnot(all.equal(y, y0))
372s > 
372s > lx <- c(-Inf, 5, -Inf)
372s > y0 <- logSumExp_R(lx)
372s > y <- logSumExp(lx)
372s > print(y)
372s [1] 5
372s > stopifnot(identical(y, 5))
372s > stopifnot(all.equal(y, y0))
372s > 
372s 
372s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
372s Copyright (C) 2024 The R Foundation for Statistical Computing
372s Platform: arm-unknown-linux-gnueabihf (32-bit)
372s 
372s R is free software and comes with ABSOLUTELY NO WARRANTY.
372s You are welcome to redistribute it under certain conditions.
372s Type 'license()' or 'licence()' for distribution details.
372s 
372s R is a collaborative project with many contributors.
372s Type 'contributors()' for more information and
372s 'citation()' on how to cite R or R packages in publications.
372s 
372s Type 'demo()' for some demos, 'help()' for on-line help, or
372s 'help.start()' for an HTML browser interface to help.
372s Type 'q()' to quit R.
372s 
372s > library("matrixStats")
372s > 
372s > logSumExp_R <- function(lx, na.rm = FALSE) {
372s +   log(sum(exp(lx), na.rm = na.rm))
372s + }
372s > 
372s > 
372s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
372s > # Subsetted tests
372s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
372s > source("utils/validateIndicesFramework.R")
372s > x <- runif(6, min = -6, max = 6)
372s > for (idxs in index_cases) {
372s +   validateIndicesTestVector(x, idxs,
372s +                             ftest = logSumExp, fsure = logSumExp_R,
372s +                             na.rm = FALSE)
372s +   validateIndicesTestVector(x, idxs,
372s +                             ftest = logSumExp, fsure = logSumExp_R,
372s +                             na.rm = TRUE)
372s + }
373s > 
373s 
373s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
373s Copyright (C) 2024 The R Foundation for Statistical Computing
373s Platform: arm-unknown-linux-gnueabihf (32-bit)
373s 
373s R is free software and comes with ABSOLUTELY NO WARRANTY.
373s You are welcome to redistribute it under certain conditions.
373s Type 'license()' or 'licence()' for distribution details.
373s 
373s R is a collaborative project with many contributors.
373s Type 'contributors()' for more information and
373s 'citation()' on how to cite R or R packages in publications.
373s 
373s Type 'demo()' for some demos, 'help()' for on-line help, or
373s 'help.start()' for an HTML browser interface to help.
373s Type 'q()' to quit R.
373s 
373s > library("matrixStats")
373s > 
373s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
373s > # Consistency checks
373s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
373s > set.seed(1)
373s > 
373s > mean2_R <- function(x, na.rm = FALSE, idxs = NULL) {
373s +   if (is.null(idxs)) {
373s +     mean(x, na.rm = na.rm)
373s +   } else {
373s +     mean(x[idxs], na.rm = na.rm)
373s +   }
373s + } # mean2_R()
373s > 
373s > 
373s > cat("Consistency checks:\n")
373s Consistency checks:
373s > for (kk in 1:20) {
373s +   cat("Random test #", kk, "\n", sep = "")
373s + 
373s +   # Simulate data in a matrix of any shape
373s +   n <- sample(100L, size = 1L)
373s +   x <- rnorm(n, sd = 100)
373s + 
373s +   # Add NAs?
373s +   if ((kk %% 4) %in% c(3, 0)) {
373s +     cat("Adding NAs\n")
373s +     nna <- sample(n, size = 1L)
373s +     na_values <- c(NA_real_, NaN)
373s +     t <- sample(na_values, size = nna, replace = TRUE)
373s +     x[sample(length(x), size = nna)] <- t
373s +   }
373s + 
373s +   # Integer or double?
373s +   if ((kk %% 4) %in% c(2, 0)) {
373s +     cat("Coercing to integers\n")
373s +     storage.mode(x) <- "integer"
373s +   }
373s + 
373s +   na.rm <- sample(c(TRUE, FALSE), size = 1L)
373s + 
373s +   # Sum over all
373s +   y0 <- mean2_R(x, na.rm = na.rm)
373s +   y1 <- mean2(x, na.rm = na.rm)
373s +   stopifnot(all.equal(y1, y0))
373s + 
373s +   # Sum over subset
373s +   nidxs <- sample(n, size = 1L)
373s +   idxs <- sample(n, size = nidxs)
373s +   y0 <- mean2_R(x, na.rm = na.rm, idxs = idxs)
373s +   y1 <- mean2(x, na.rm = na.rm, idxs = idxs)
373s +   stopifnot(all.equal(y1, y0))
373s + 
373s +   if (storage.mode(x) == "integer") {
373s +     storage.mode(x) <- "logical"
373s +     
373s +     y0 <- mean2_R(x, na.rm = na.rm)
373s +     y1 <- mean2(x, na.rm = na.rm)
373s +     stopifnot(all.equal(y1, y0))
373s +     
373s +     y0 <- mean2_R(x, na.rm = na.rm, idxs = idxs)
373s +     y1 <- mean2(x, na.rm = na.rm, idxs = idxs)
373s +     stopifnot(all.equal(y1, y0))
373s +   }
373s + } # for (kk ...)
373s Random test #1
373s Random test #2
373s Coercing to integers
373s Random test #3
373s Adding NAs
373s Random test #4
373s Adding NAs
373s Coercing to integers
373s Random test #5
373s Random test #6
373s Coercing to integers
373s Random test #7
373s Adding NAs
373s Random test #8
373s Adding NAs
373s Coercing to integers
373s Random test #9
373s Random test #10
373s Coercing to integers
373s Random test #11
373s Adding NAs
373s Random test #12
373s Adding NAs
373s Coercing to integers
373s Random test #13
373s Random test #14
373s Coercing to integers
373s Random test #15
373s Adding NAs
373s Random test #16
373s Adding NAs
373s Coercing to integers
373s Random test #17
373s Random test #18
373s Coercing to integers
373s Random test #19
373s Adding NAs
373s Random test #20
373s Adding NAs
373s Coercing to integers
373s > 
373s > 
373s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
373s > # Special cases
373s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
373s > for (na.rm in c(FALSE, TRUE)) {
373s +   # Averaging over zero elements (integers)
373s +   x <- integer(0)
373s +   s1 <- mean(x, na.rm = na.rm)
373s +   s2 <- mean2(x, na.rm = na.rm)
373s +   stopifnot(identical(s1, s2))
373s + 
373s +   x <- 1:5
373s +   idxs <- integer(0)
373s +   s1 <- mean(x[idxs], na.rm = na.rm)
373s +   s2 <- mean2(x, idxs = idxs, na.rm = na.rm)
373s +   stopifnot(identical(s1, s2))
373s + 
373s +   # Averaging over NA_integer_:s
373s +   x <- rep(NA_integer_, times = 5L)
373s +   s1 <- mean(x, na.rm = na.rm)
373s +   s2 <- mean2(x, na.rm = na.rm)
373s +   stopifnot(identical(s1, s2))
373s + 
373s +   x <- rep(NA_integer_, times = 5L)
373s +   idxs <- 1:3
373s +   s1 <- mean(x[idxs], na.rm = na.rm)
373s +   s2 <- mean2(x, idxs = idxs, na.rm = na.rm)
373s +   stopifnot(identical(s1, s2))
373s + 
373s + 
373s +   # Averaging over zero elements (doubles)
373s +   x <- double(0)
373s +   s1 <- mean(x)
373s +   s2 <- mean2(x)
373s +   stopifnot(identical(s1, s2))
373s + 
373s +   x <- as.double(1:10)
373s +   idxs <- integer(0)
373s +   s1 <- mean(x[idxs])
373s +   s2 <- mean2(x, idxs = idxs)
373s +   stopifnot(identical(s1, s2))
373s + 
373s +   # Averaging over NA_real_:s
373s +   x <- rep(NA_real_, times = 5L)
373s +   s1 <- mean(x, na.rm = na.rm)
373s +   s2 <- mean2(x, na.rm = na.rm)
373s +   stopifnot(identical(s1, s2))
373s + 
373s +   x <- rep(NA_real_, times = 5L)
373s +   idxs <- 1:3
373s +   s1 <- mean(x[idxs], na.rm = na.rm)
373s +   s2 <- mean2(x, idxs = idxs, na.rm = na.rm)
373s +   stopifnot(identical(s1, s2))
373s + 
373s +   # Averaging over -Inf:s
373s +   x <- rep(-Inf, times = 3L)
373s +   s1 <- mean(x, na.rm = na.rm)
373s +   s2 <- mean2(x, na.rm = na.rm)
373s +   stopifnot(identical(s1, s2))
373s + 
373s +   # Averaging over +Inf:s
373s +   x <- rep(+Inf, times = 3L)
373s +   s1 <- mean(x, na.rm = na.rm)
373s +   s2 <- mean2(x, na.rm = na.rm)
373s +   stopifnot(identical(s1, s2))
373s + 
373s +   # Averaging over mix of -Inf:s and +Inf:s
373s +   x <- rep(c(-Inf, +Inf), times = 3L)
373s +   s1 <- mean(x, na.rm = na.rm)
373s +   s2 <- mean2(x, na.rm = na.rm)
373s +   stopifnot(identical(s1, s2))
373s + 
373s +   # Averaging over mix of -Inf:s and +Inf:s and numerics
373s +   x <- rep(c(-Inf, +Inf, 3.14), times = 2L)
373s +   s1 <- mean(x, na.rm = na.rm)
373s +   s2 <- mean2(x, na.rm = na.rm)
373s +   stopifnot(identical(s1, s2))
373s + 
373s +   # Averaging over mix of NaN, NA, +Inf, and numerics
373s +   x <- c(NaN, NA, +Inf, 3.14)
373s +   s1 <- mean(x, na.rm = na.rm)
373s +   s2 <- mean2(x, na.rm = na.rm)
373s +   if (na.rm) {
373s +     stopifnot(identical(s2, s1))
373s +   } else {
373s +     stopifnot(is.na(s1), is.na(s2))
373s +     ## NOTE, due to compiler optimization, it is not guaranteed that NA is
373s +     ## returned here (as one would expect). NaN might very well be returned,
373s +     ## when both NA and NaN are involved.  This is an accepted feature in R,
373s +     ## which is documented in help("is.nan").  See also
373s +     ## https://stat.ethz.ch/pipermail/r-devel/2017-April/074009.html.
373s +     ## Thus, we cannot guarantee that s1 is identical to s0.
373s +   }
373s + 
373s +   # Averaging over mix of NaN, NA_real_, +Inf, and numerics
373s +   x <- c(NA_real_, NaN, +Inf, 3.14)
373s +   s1 <- mean(x, na.rm = na.rm)
373s +   s2 <- mean2(x, na.rm = na.rm)
373s +   if (na.rm) {
373s +     stopifnot(identical(s2, s1))
373s +   } else {
373s +     stopifnot(is.na(s1), is.na(s2))
373s +     ## NOTE, due to compiler optimization, it is not guaranteed that NA is
373s +     ## returned here (as one would expect). NaN might very well be returned,
373s +     ## when both NA and NaN are involved.  This is an accepted feature in R,
373s +     ## which is documented in help("is.nan").  See also
373s +     ## https://stat.ethz.ch/pipermail/r-devel/2017-April/074009.html.
373s +     ## Thus, we cannot guarantee that s1 is identical to s0.
373s +   }
373s + }
373s > 
373s > 
373s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
373s > # Argument 'idxs'
373s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
373s > x <- 1:5
373s > idxs_list <- list(
373s +   integer = 1:3,
373s +   double  = as.double(1:3),
373s +   logical = (x <= 3)
373s + )
373s > 
373s > for (idxs in idxs_list) {
373s +   cat("idxs:\n")
373s +   str(idxs)
373s +   s1 <- mean(x[idxs], na.rm = TRUE)
373s +   s2 <- mean2(x, idxs = idxs, na.rm = TRUE)
373s +   stopifnot(identical(s1, s2))
373s + }
373s idxs:
374s  int [1:3] 1 2 3
374s idxs:
374s  num [1:3] 1 2 3
374s idxs:
374s  logi [1:5] TRUE TRUE TRUE FALSE FALSE
374s > 
374s 
374s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
374s Copyright (C) 2024 The R Foundation for Statistical Computing
374s Platform: arm-unknown-linux-gnueabihf (32-bit)
374s 
374s R is free software and comes with ABSOLUTELY NO WARRANTY.
374s You are welcome to redistribute it under certain conditions.
374s Type 'license()' or 'licence()' for distribution details.
374s 
374s R is a collaborative project with many contributors.
374s Type 'contributors()' for more information and
374s 'citation()' on how to cite R or R packages in publications.
374s 
374s Type 'demo()' for some demos, 'help()' for on-line help, or
374s 'help.start()' for an HTML browser interface to help.
374s Type 'q()' to quit R.
374s 
374s > library("matrixStats")
374s > 
374s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
374s > # Subsetted tests
374s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
374s > source("utils/validateIndicesFramework.R")
374s > x <- runif(6, min = -6, max = 6)
374s > storage.mode(x) <- "integer"
374s > for (idxs in index_cases) {
374s +   validateIndicesTestVector(x, idxs,
374s +                             ftest = mean2, fsure = mean,
374s +                             na.rm = FALSE)
374s +   validateIndicesTestVector(x, idxs,
374s +                             ftest = mean2, fsure = mean,
374s +                             na.rm = TRUE)
374s + }
374s > 
374s 
374s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
374s Copyright (C) 2024 The R Foundation for Statistical Computing
374s Platform: arm-unknown-linux-gnueabihf (32-bit)
374s 
374s R is free software and comes with ABSOLUTELY NO WARRANTY.
374s You are welcome to redistribute it under certain conditions.
374s Type 'license()' or 'licence()' for distribution details.
374s 
374s R is a collaborative project with many contributors.
374s Type 'contributors()' for more information and
374s 'citation()' on how to cite R or R packages in publications.
374s 
374s Type 'demo()' for some demos, 'help()' for on-line help, or
374s 'help.start()' for an HTML browser interface to help.
374s Type 'q()' to quit R.
374s 
375s > library("matrixStats")
375s > 
375s > for (mode in c("integer", "double")) {
375s +   cat("mode: ", mode, "\n", sep = "")
375s + 
375s +   # Empty vector
375s +   x <- 0
375s +   storage.mode(x) <- mode
375s +   y <- prod(x, na.rm = TRUE)
375s +   print(y)
375s +   z <- product(x, na.rm = TRUE)
375s +   print(z)
375s +   stopifnot(all.equal(z, y))
375s + 
375s +   # Test negative values
375s +   x <- c(1, -4, 2)
375s +   storage.mode(x) <- mode
375s +   y <- prod(x, na.rm = TRUE)
375s +   print(y)
375s +   z <- product(x, na.rm = TRUE)
375s +   print(z)
375s +   stopifnot(all.equal(z, y))
375s + 
375s +   # Test missing values
375s +   x <- c(1, NA, NaN, 2)
375s +   storage.mode(x) <- mode
375s +   y <- prod(x, na.rm = TRUE)
375s +   print(y)
375s +   z <- product(x, na.rm = TRUE)
375s +   print(z)
375s +   stopifnot(all.equal(z, y))
375s + 
375s +   x <- c(1, NA, NaN, 2)
375s +   storage.mode(x) <- mode
375s +   y <- prod(x, na.rm = FALSE)
375s +   print(y)
375s +   z <- product(x, na.rm = FALSE)
375s +   print(z)
375s +   stopifnot(all(is.na(z), is.na(y)))
375s + 
375s +   x <- c(1, NaN, 2)
375s +   storage.mode(x) <- mode
375s +   y <- prod(x, na.rm = FALSE)
375s +   print(y)
375s +   stopifnot(is.na(y))
375s +   z <- product(x, na.rm = FALSE)
375s +   print(z)
375s +   stopifnot(is.na(z))
375s + 
375s + } # for (mode ...)
375s mode: integer
375s [1] 0
375s [1] 0
375s [1] -8
375s [1] -8
375s [1] 2
375s [1] 2
375s [1] NA
375s [1] NA
375s [1] NA
375s [1] NA
375s mode: double
375s [1] 0
375s [1] 0
375s [1] -8
375s [1] -8
375s [1] 2
375s [1] 2
375s [1] NA
375s [1] NA
375s [1] NaN
375s [1] NA
375s > 
375s > 
375s > # NAs following 0s
375s > x <- c(0L, NA_integer_)
375s > y <- prod(x, na.rm = FALSE)
375s > print(y)
375s [1] NA
375s > z <- product(x, na.rm = FALSE)
375s > print(z)
375s [1] NA
375s > stopifnot(identical(z, y))
375s > 
375s 
375s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
375s Copyright (C) 2024 The R Foundation for Statistical Computing
375s Platform: arm-unknown-linux-gnueabihf (32-bit)
375s 
375s R is free software and comes with ABSOLUTELY NO WARRANTY.
375s You are welcome to redistribute it under certain conditions.
375s Type 'license()' or 'licence()' for distribution details.
375s 
375s R is a collaborative project with many contributors.
375s Type 'contributors()' for more information and
375s 'citation()' on how to cite R or R packages in publications.
375s 
375s Type 'demo()' for some demos, 'help()' for on-line help, or
375s 'help.start()' for an HTML browser interface to help.
375s Type 'q()' to quit R.
375s 
375s > library("matrixStats")
375s > 
375s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
375s > # Subsetted tests
375s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
375s > source("utils/validateIndicesFramework.R")
375s > x <- runif(6, min = -6, max = 6)
375s > storage.mode(x) <- "integer"
375s > for (idxs in index_cases) {
375s +   validateIndicesTestVector(x, idxs,
375s +                             ftest = product, fsure = prod,
375s +                             na.rm = TRUE)
375s +   validateIndicesTestVector(x, idxs,
375s +                             ftest = product, fsure = prod,
375s +                             na.rm = FALSE)
375s + }
375s > 
375s 
375s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
375s Copyright (C) 2024 The R Foundation for Statistical Computing
375s Platform: arm-unknown-linux-gnueabihf (32-bit)
375s 
375s R is free software and comes with ABSOLUTELY NO WARRANTY.
375s You are welcome to redistribute it under certain conditions.
375s Type 'license()' or 'licence()' for distribution details.
375s 
375s R is a collaborative project with many contributors.
375s Type 'contributors()' for more information and
375s 'citation()' on how to cite R or R packages in publications.
375s 
375s Type 'demo()' for some demos, 'help()' for on-line help, or
375s 'help.start()' for an HTML browser interface to help.
375s Type 'q()' to quit R.
375s 
376s > library("matrixStats")
376s > library("utils")  ## utils::str
376s > 
376s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
376s > # Local functions
376s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
376s > psortKM_R <- function(x, k, m) {
376s +   x <- sort(x)
376s +   x[(k - m + 1):k]
376s + }
376s > 
376s > psortKM_R2 <- function(x, k, m) {
376s +   partial <- (k - m + 1):k
376s +   x <- sort.int(x, partial = partial)
376s +   x[partial]
376s + }
376s > 
376s > 
376s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
376s > # Consistency checks
376s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
376s > set.seed(1)
376s > 
376s > cat("Consistency checks:\n")
376s Consistency checks:
376s > x <- 1:30
376s > x[18:20] <- 20
376s > y <- sample(x)
376s > cat("x:\n")
376s x:
376s > str(x)
376s  num [1:30] 1 2 3 4 5 6 7 8 9 10 ...
376s > cat("sample(x):\n")
376s sample(x):
376s > str(y)
376s  num [1:30] 25 4 7 1 2 23 11 14 20 20 ...
376s > 
376s > for (k in c(1L, 2L, 20L, 21L, length(x))) {
376s +   for (m in 1:min(5L, k)) {
376s +     px0 <- psortKM_R(x, k = k, m = m)
376s +     px0b <- psortKM_R2(x, k = k, m = m)
376s +     stopifnot(identical(px0b, px0))
376s +     px1 <- matrixStats:::.psortKM(x, k = k, m = m)
376s +     cat(sprintf(".psortKM(x, k = %d, m = %d):\n", k, m))
376s +     print(px1)
376s +     stopifnot(identical(px1, px0))
376s + 
376s +     py0 <- psortKM_R(y, k = k, m = m)
376s +     py0b <- psortKM_R2(y, k = k, m = m)
376s +     stopifnot(identical(py0b, py0))
376s +     py1 <- matrixStats:::.psortKM(y, k = k, m = m)
376s +     cat(sprintf(".psortKM(y, k = %d, m = %d):\n", k, m))
376s +     print(py1)
376s +     stopifnot(identical(py1, py0))
376s +     stopifnot(identical(py1, px1))
376s +   } # for (m ...)
376s + } # for (k ...)
376s .psortKM(x, k = 1, m = 1):
376s [1] 1
376s .psortKM(y, k = 1, m = 1):
376s [1] 1
376s .psortKM(x, k = 2, m = 1):
376s [1] 2
376s .psortKM(y, k = 2, m = 1):
376s [1] 2
376s .psortKM(x, k = 2, m = 2):
376s [1] 1 2
376s .psortKM(y, k = 2, m = 2):
376s [1] 1 2
376s .psortKM(x, k = 20, m = 1):
376s [1] 20
376s .psortKM(y, k = 20, m = 1):
376s [1] 20
376s .psortKM(x, k = 20, m = 2):
376s [1] 20 20
376s .psortKM(y, k = 20, m = 2):
376s [1] 20 20
376s .psortKM(x, k = 20, m = 3):
376s [1] 20 20 20
376s .psortKM(y, k = 20, m = 3):
376s [1] 20 20 20
376s .psortKM(x, k = 20, m = 4):
376s [1] 17 20 20 20
376s .psortKM(y, k = 20, m = 4):
376s [1] 17 20 20 20
376s .psortKM(x, k = 20, m = 5):
376s [1] 16 17 20 20 20
376s .psortKM(y, k = 20, m = 5):
376s [1] 16 17 20 20 20
376s .psortKM(x, k = 21, m = 1):
376s [1] 21
376s .psortKM(y, k = 21, m = 1):
376s [1] 21
376s .psortKM(x, k = 21, m = 2):
376s [1] 20 21
376s .psortKM(y, k = 21, m = 2):
376s [1] 20 21
376s .psortKM(x, k = 21, m = 3):
376s [1] 20 20 21
376s .psortKM(y, k = 21, m = 3):
376s [1] 20 20 21
376s .psortKM(x, k = 21, m = 4):
376s [1] 20 20 20 21
376s .psortKM(y, k = 21, m = 4):
376s [1] 20 20 20 21
376s .psortKM(x, k = 21, m = 5):
376s [1] 17 20 20 20 21
376s .psortKM(y, k = 21, m = 5):
376s [1] 17 20 20 20 21
376s .psortKM(x, k = 30, m = 1):
376s [1] 30
376s .psortKM(y, k = 30, m = 1):
376s [1] 30
376s .psortKM(x, k = 30, m = 2):
376s [1] 29 30
376s .psortKM(y, k = 30, m = 2):
376s [1] 29 30
376s .psortKM(x, k = 30, m = 3):
376s [1] 28 29 30
376s .psortKM(y, k = 30, m = 3):
376s [1] 28 29 30
376s .psortKM(x, k = 30, m = 4):
376s [1] 27 28 29 30
376s .psortKM(y, k = 30, m = 4):
376s [1] 27 28 29 30
376s .psortKM(x, k = 30, m = 5):
376s [1] 26 27 28 29 30
376s .psortKM(y, k = 30, m = 5):
376s [1] 26 27 28 29 30
376s > 
376s 
376s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
376s Copyright (C) 2024 The R Foundation for Statistical Computing
376s Platform: arm-unknown-linux-gnueabihf (32-bit)
376s 
376s R is free software and comes with ABSOLUTELY NO WARRANTY.
376s You are welcome to redistribute it under certain conditions.
376s Type 'license()' or 'licence()' for distribution details.
376s 
376s R is a collaborative project with many contributors.
376s Type 'contributors()' for more information and
376s 'citation()' on how to cite R or R packages in publications.
376s 
376s Type 'demo()' for some demos, 'help()' for on-line help, or
376s 'help.start()' for an HTML browser interface to help.
376s Type 'q()' to quit R.
376s 
376s > library("matrixStats")
376s > 
376s > rowAlls_R <- function(x, value = TRUE, na.rm = FALSE, ..., useNames = NA) {
376s +   if (is.na(value)) {
376s +     res <- apply(is.na(x), MARGIN = 1L, FUN = all, na.rm = na.rm)
376s +   } else {
376s +     y <- x == value
376s +     
376s +     # Preserve dimnames attribute
376s +     dim <- dim(x) # for 0xN and Mx0 cases; needed in R (< 3.4.0)
376s +     if (!isTRUE(all.equal(dim(y), dim))) {
376s +       dim(y) <- dim
376s +       dimnames(y) <- dimnames(x)
376s +     }
376s +     
376s +     res <- apply(y, MARGIN = 1L, FUN = all, na.rm = na.rm)
376s +   }
376s +   if (is.na(useNames) || !useNames) names(res) <- NULL
376s +   res
376s + }
376s > 
376s > rowAnys_R <- function(x, value = TRUE, na.rm = FALSE, ..., useNames = NA) {
376s +   if (is.na(value)) {
376s +     res <- apply(is.na(x), MARGIN = 1L, FUN = any, na.rm = na.rm)
376s +   } else {
376s +     y <- x == value
376s +     
376s +     # Preserve dimnames attribute
376s +     dim <- dim(x) # for 0xN and Mx0 cases; needed in R (< 3.4.0)
376s +     if (!isTRUE(all.equal(dim(y), dim))) {
376s +       dim(y) <- dim
376s +       dimnames(y) <- dimnames(x)
376s +     }
376s +     
376s +     res <- apply(y, MARGIN = 1L, FUN = any, na.rm = na.rm)
376s +   }
376s +   if (is.na(useNames) || !useNames) names(res) <- NULL
376s +   res
376s + }
376s > 
376s > rowAnyMissings_R <- function(x, ..., useNames = NA) {
376s +   res <- apply(x, MARGIN = 1L, FUN = anyMissing)
376s +   if (is.na(useNames) || !useNames) names(res) <- NULL
376s +   res
376s + }
376s > 
376s > 
376s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
376s > # Data type: logical
376s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
376s > x <- matrix(FALSE, nrow = 10L, ncol = 4L)
376s > x[7:8, 2:3] <- TRUE
376s > x[1:3, ] <- TRUE
376s > x[, 1] <- TRUE
376s > x[4, ] <- FALSE
376s > x[, 4] <- FALSE
376s > x[2, ] <- FALSE
376s > x[3, ] <- TRUE
376s > 
376s > # To check names attribute
376s > dimnames <- list(letters[1:10], LETTERS[1:4])
376s > 
376s > for (kk in 1:3) {
376s +   if (kk == 2) {
376s +     x[2, 2] <- NA
376s +   } else if (kk == 3) {
376s +     x[, 2] <- NA
376s +     x[2, ] <- NA
376s +   }
376s + 
376s +   # Test with and without dimnames on x
376s +   for (setDimnames in c(TRUE, FALSE)) {
376s +     dimnames(x) <- if (setDimnames) dimnames else NULL
376s + 
376s +     for (na.rm in c(FALSE, TRUE)) {
376s +       # Check names attribute
376s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
376s +         m0 <- rowAlls_R(x, na.rm = na.rm, useNames = useNames)
376s +         m1 <- rowAlls(x, na.rm = na.rm, useNames = useNames)
376s +         m2 <- colAlls(t(x), na.rm = na.rm, useNames = useNames)
376s +         str(list("all()", m0 = m0, m1 = m1, m2 = m2))
376s +         stopifnot(identical(m1, m0))
376s +         stopifnot(identical(m2, m0))        
376s + 
376s +         m0 <- rowAnys_R(x, na.rm = na.rm, useNames = useNames)
376s +         m1 <- rowAnys(x, na.rm = na.rm, useNames = useNames)
376s +         m2 <- colAnys(t(x), na.rm = na.rm, useNames = useNames)
376s +         str(list("any()", m0 = m0, m1 = m1, m2 = m2))
376s +         stopifnot(identical(m1, m0))
376s +         stopifnot(identical(m2, m0))
376s +         
376s +         m0 <- rowAnyMissings_R(x, useNames = useNames)
376s +         m1 <- rowAnyMissings(x, useNames = useNames)
376s +         m2 <- colAnyMissings(t(x), useNames = useNames)
376s +         str(list("anyMissing()", m0 = m0, m1 = m1, m2 = m2))
376s +         stopifnot(identical(m1, m0))
376s +         stopifnot(identical(m2, m0))
376s +       }
376s +     }
376s +   }
376s + } # for (kk ...)
377s List of 4
377s  $   : chr "all()"
377s  $ m0: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m1: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m2: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m1: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m2: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: Named logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m1: Named logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m2: Named logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m1: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m2: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m1: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m2: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: Named logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m1: Named logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m2: Named logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m1: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m2: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: Named logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m1: Named logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m2: Named logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: Named logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m1: Named logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m2: Named logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m1: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m2: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m1: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m2: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: Named logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m1: Named logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m2: Named logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: Named logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m1: Named logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m2: Named logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: Named logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m1: Named logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m2: Named logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: Named logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m1: Named logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m2: Named logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: Named logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m1: Named logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m2: Named logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m1: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m2: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: Named logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m1: Named logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s  $ m2: Named logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s List of 4
377s  $   : chr "all()"
377s  $ m0: logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
377s  $ m1: logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
377s  $ m2: logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
377s List of 4
377s  $   : chr "any()"
377s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
377s List of 4
377s  $   : chr "anyMissing()"
377s  $ m0: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s  $ m1: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s  $ m2: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
377s > 
377s > 
377s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
377s > # Data type: integer
377s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
377s > x <- matrix(rep(1:6, length.out = 4 * 5), nrow = 4L, ncol = 5L)
377s > x[2, ] <- 7L
377s > x[3, 1] <- 7L
377s > x[2:3, 3:4] <- NA_integer_
377s > 
377s > # To check names attribute
377s > dimnames <- list(letters[1:4], LETTERS[1:5])
377s > 
377s > # Row/column counts
377s > value <- 7L
377s > 
377s > # Test with and without dimnames on x
377s > for (setDimnames in c(TRUE, FALSE)) {
377s +   dimnames(x) <- if (setDimnames) dimnames else NULL
377s +   for (na.rm in c(FALSE, TRUE)) {
377s +     # Check names attribute
377s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
377s +       r0 <- rowAlls_R(x, value = value, na.rm = na.rm, useNames = useNames)
377s +       r1 <- rowAlls(x, value = value, na.rm = na.rm, useNames = useNames)
377s +       r2 <- colAlls(t(x), value = value, na.rm = na.rm, useNames = useNames)
377s +       stopifnot(identical(r1, r0))
377s +       stopifnot(identical(r2, r1))
377s +       if (!is.na(useNames) && !useNames && !setDimnames) {
377s +         for (rr in seq_len(nrow(x))) {
377s +           c <- allValue(x[rr, ], value = value, na.rm = na.rm)
377s +           stopifnot(identical(c, r1[rr]))
377s +           c <- allValue(x[rr, ], value = value, na.rm = na.rm)
377s +           stopifnot(identical(c, r1[rr]))
377s +         }
377s +       }
377s + 
377s +       r0 <- rowAnys_R(x, value = value, na.rm = na.rm, useNames = useNames)
377s +       r1 <- rowAnys(x, value = value, na.rm = na.rm, useNames = useNames)
377s +       r2 <- colAnys(t(x), value = value, na.rm = na.rm, useNames = useNames)
377s +       stopifnot(identical(r1, r0))
377s +       stopifnot(identical(r2, r1))        
377s +       if (!is.na(useNames) && !useNames && !setDimnames) {
377s +         for (rr in seq_len(nrow(x))) {
377s +           c <- anyValue(x[rr, ], value = value, na.rm = na.rm)
377s +           stopifnot(identical(c, r1[rr]))
377s +           c <- anyValue(x[rr, ], value = value, na.rm = na.rm)
377s +           stopifnot(identical(c, r1[rr]))
377s +         }
377s +       }
377s +     }
377s +   }
377s + }
377s > 
377s > 
377s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
377s > # rowAlls(x) et al. on numeric 'x' with logical 'value'
377s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
377s > x <- matrix(0, nrow = 4L, ncol = 5L)
377s > x[2:4, 2] <- (1:3) / 4
377s > x[2, 2:4] <- (1:3) / 4
377s > x[3:4, 3] <- (3:4) / 4
377s > x[3, 3:4] <- (3:4) / 4
377s > x[1:4, 5] <- (1:4) / 5
377s > x[4, 4] <- NA_real_
377s > 
377s > # To check names attribute
377s > dimnames <- list(letters[1:4], LETTERS[1:5])
377s > 
377s > for (value in c(TRUE, FALSE)) {
377s +   for (na.rm in c(FALSE, TRUE)) {
377s +     y0 <- suppressWarnings(apply(x, MARGIN = 1L, FUN = function(e) any(as.logical(e) == value, na.rm = na.rm)))
377s +     y <- rowAnys(x, na.rm = na.rm, value = value)
377s +     stopifnot(identical(y, y0))
377s +     # Check names attribute
377s +     dimnames(x) <- dimnames
377s +     y <- rowAnys(x, na.rm = na.rm, value = value, useNames = FALSE)
377s +     stopifnot(all.equal(y, y0))
377s +     y0 <- suppressWarnings(apply(x, MARGIN = 1L, FUN = function(e) any(as.logical(e) == value, na.rm = na.rm)))
377s +     y <- rowAnys(x, na.rm = na.rm, value = value, useNames = TRUE)
377s +     stopifnot(all.equal(y, y0))
377s +     dimnames(x) <- NULL
377s +   
377s +     y0 <- suppressWarnings(apply(x, MARGIN = 2L, FUN = function(e) any(as.logical(e) == value, na.rm = na.rm)))
377s +     y <- colAnys(x, na.rm = na.rm, value = value)
377s +     stopifnot(identical(y, y0))
377s +     # Check names attribute
377s +     dimnames(x) <- dimnames
377s +     y <- colAnys(x, na.rm = na.rm, value = value, useNames = FALSE)
377s +     stopifnot(all.equal(y, y0))
377s +     y0 <- suppressWarnings(apply(x, MARGIN = 2L, FUN = function(e) any(as.logical(e) == value, na.rm = na.rm)))
377s +     y <- colAnys(x, na.rm = na.rm, value = value, useNames = TRUE)
377s +     stopifnot(all.equal(y, y0))
377s +     dimnames(x) <- NULL
377s +   
377s +     y0 <- suppressWarnings(apply(x, MARGIN = 1L, FUN = function(e) all(as.logical(e) == value, na.rm = na.rm)))
377s +     y <- rowAlls(x, na.rm = na.rm, value = value)
377s +     stopifnot(identical(y, y0))
377s +     # Check names attribute
377s +     dimnames(x) <- dimnames
377s +     y <- rowAlls(x, na.rm = na.rm, value = value, useNames = FALSE)
377s +     stopifnot(all.equal(y, y0))  
377s +     y0 <- suppressWarnings(apply(x, MARGIN = 1L, FUN = function(e) all(as.logical(e) == value, na.rm = na.rm)))
377s +     y <- rowAlls(x, na.rm = na.rm, value = value, useNames = TRUE)
377s +     stopifnot(all.equal(y, y0))    
377s +     dimnames(x) <- NULL
377s +   
377s +     y0 <- suppressWarnings(apply(x, MARGIN = 2L, FUN = function(e) all(as.logical(e) == value, na.rm = na.rm)))
377s +     y <- colAlls(x, na.rm = na.rm, value = value)
377s +     stopifnot(identical(y, y0))
377s +     print(y0)
377s +     # Check names attribute
377s +     dimnames(x) <- dimnames
377s +     y <- colAlls(x, na.rm = na.rm, value = value, useNames = FALSE)
377s +     stopifnot(all.equal(y, y0))     
377s +     y0 <- suppressWarnings(apply(x, MARGIN = 2L, FUN = function(e) all(as.logical(e) == value, na.rm = na.rm)))
377s +     y <- colAlls(x, na.rm = na.rm, value = value, useNames = TRUE)
377s +     stopifnot(all.equal(y, y0))     
377s +     dimnames(x) <- NULL
377s +   } ## for (na.rm ...)
377s + } ## for(value ...)
378s [1] FALSE FALSE FALSE FALSE  TRUE
378s [1] FALSE FALSE FALSE FALSE  TRUE
378s [1]  TRUE FALSE FALSE FALSE FALSE
378s [1]  TRUE FALSE FALSE FALSE FALSE
378s > 
378s > 
378s > 
378s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
378s > # Data type: character (not sure if this should be supported)
378s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
378s > all_R <- function(x, value = TRUE, ...) {
378s +   if (is.na(value)) {
378s +     all(is.na(x), ...)
378s +   } else {
378s +     all(x == value, ...)
378s +   }
378s + }
378s > 
378s > any_R <- function(x, value = TRUE, ...) {
378s +   if (is.na(value)) {
378s +     any(is.na(x), ...)
378s +   } else {
378s +     any(x == value, ...)
378s +   }
378s + }
378s > 
378s > x <- matrix(rep(letters, length.out = 10 * 5), nrow = 10L, ncol = 5L)
378s > x[2, ] <- "g"
378s > x[2:4, 3:4] <- NA_character_
378s > 
378s > # To check names attribute
378s > dimnames <- list(letters[1:10], LETTERS[1:5])
378s > 
378s > # Test with and without dimnames on x
378s > for (setDimnames in c(TRUE, FALSE)) {
378s +   dimnames(x) <- if (setDimnames) dimnames else NULL
378s + 
378s +   # Row/column counts
378s +   for (value in c("g", NA_character_)) {
378s +     for (na.rm in c(FALSE, TRUE)) {
378s +       # Check names attribute
378s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
378s +         r0 <- rowAlls_R(x, value = value, na.rm = na.rm, useNames = useNames)
378s +         r1 <- rowAlls(x, value = value, na.rm = na.rm, useNames = useNames)
378s +         r2 <- colAlls(t(x), value = value, na.rm = na.rm, useNames = useNames)
378s +         stopifnot(identical(r1, r0))
378s +         stopifnot(identical(r2, r1))
378s +         if (!is.na(useNames) && !useNames && !setDimnames) {
378s +           for (rr in seq_len(nrow(x))) {
378s +             c0 <- all_R(x[rr, ], value, na.rm = na.rm)
378s +             c <- allValue(x[rr, ], value = value, na.rm = na.rm)
378s +             stopifnot(identical(c, r1[rr]))
378s +             stopifnot(identical(c, c0))
378s +           }
378s +         }
378s +         
378s +         r0 <- rowAnys_R(x, value = value, na.rm = na.rm, useNames = useNames)
378s +         r1 <- rowAnys(x, value = value, na.rm = na.rm, useNames = useNames)
378s +         r2 <- colAnys(t(x), value = value, na.rm = na.rm, useNames = useNames)
378s +         stopifnot(identical(r1, r0))
378s +         stopifnot(identical(r2, r1))        
378s +         if (!is.na(useNames) && !useNames && !setDimnames) {
378s +           for (rr in seq_len(nrow(x))) {
378s +             c0 <- any_R(x[rr, ], value, na.rm = na.rm)
378s +             c <- anyValue(x[rr, ], value = value, na.rm = na.rm)
378s +             stopifnot(identical(c, c0))
378s +             stopifnot(identical(c, r1[rr]))
378s +           }
378s +         }
378s +       }
378s +     }
378s +   }
378s + }
378s > 
378s > 
378s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
378s > # NA 0 test
378s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
378s > x <- matrix(0, nrow = 3L, ncol = 3L)
378s > x[1, ] <- c(NA_real_, NA_real_, 0)
378s > x[3, ] <- c(1, 0, 1)
378s > 
378s > dimnames <- list(letters[1:3], LETTERS[1:3])
378s > 
378s > # Test with and without dimnames on x
378s > for (setDimnames in c(TRUE, FALSE)) {
378s +   dimnames(x) <- if (setDimnames) dimnames else NULL
378s +   # Check names attribute
378s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
378s +     r0 <- rowAnys_R(x, value = 0, useNames = useNames)
378s +     r1 <- rowAnys(x, value = 0, useNames = useNames)
378s +     stopifnot(identical(r0, r1))
378s +   }
378s + }
378s > 
378s 
378s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
378s Copyright (C) 2024 The R Foundation for Statistical Computing
378s Platform: arm-unknown-linux-gnueabihf (32-bit)
378s 
378s R is free software and comes with ABSOLUTELY NO WARRANTY.
378s You are welcome to redistribute it under certain conditions.
378s Type 'license()' or 'licence()' for distribution details.
378s 
378s R is a collaborative project with many contributors.
378s Type 'contributors()' for more information and
378s 'citation()' on how to cite R or R packages in publications.
378s 
378s Type 'demo()' for some demos, 'help()' for on-line help, or
378s 'help.start()' for an HTML browser interface to help.
378s Type 'q()' to quit R.
378s 
378s > library("matrixStats")
378s > 
378s > rowAlls_R <- function(x, value = TRUE, na.rm = FALSE, ..., useNames = NA) {
378s +   if (is.na(value)) {
378s +     res <- apply(is.na(x), MARGIN = 1L, FUN = all, na.rm = na.rm)
378s +   } else {
378s +     y <- x == value
378s +     
378s +     # Preserve dimnames attribute
378s +     dim <- dim(x) # for 0xN and Mx0 cases; needed in R (< 3.4.0)
378s +     if (!isTRUE(all.equal(dim(y), dim))) {
378s +       dim(y) <- dim
378s +       dimnames(y) <- dimnames(x)
378s +     }
378s +     
378s +     res <- apply(y, MARGIN = 1L, FUN = all, na.rm = na.rm)
378s +   }
378s +   if (is.na(useNames) || !useNames) names(res) <- NULL
378s +   res
378s + }
378s > 
378s > rowAnys_R <- function(x, value = TRUE, na.rm = FALSE, ..., useNames = NA) {
378s +   if (is.na(value)) {
378s +     res <- apply(is.na(x), MARGIN = 1L, FUN = any, na.rm = na.rm)
378s +   } else {
378s +     y <- x == value
378s +     
378s +     # Preserve dimnames attribute
378s +     dim <- dim(x) # for 0xN and Mx0 cases; needed in R (< 3.4.0)
378s +     if (!isTRUE(all.equal(dim(y), dim))) {
378s +       dim(y) <- dim
378s +       dimnames(y) <- dimnames(x)
378s +     }
378s +     
378s +     res <- apply(y, MARGIN = 1L, FUN = any, na.rm = na.rm)
378s +   }
378s +   if (is.na(useNames) || !useNames) names(res) <- NULL
378s +   res
378s + }
378s > 
378s > rowAnyMissings_R <- function(x, ..., useNames = NA) {
378s +   res <- apply(x, MARGIN = 1L, FUN = anyMissing)
378s +   if (is.na(useNames) || !useNames) names(res) <- NULL
378s +   res
378s + }
378s > 
378s > 
378s > all_R <- function(x, value = TRUE, ...) {
378s +   if (is.na(value)) {
378s +     all(is.na(x), ...)
378s +   } else {
378s +     all(x == value, ...)
378s +   }
378s + }
378s > 
378s > any_R <- function(x, value = TRUE, ...) {
378s +   if (is.na(value)) {
378s +     any(is.na(x), ...)
378s +   } else {
378s +     any(x == value, ...)
378s +   }
378s + }
378s > 
378s > 
378s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
378s > # Subsetted tests
378s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
378s > source("utils/validateIndicesFramework.R")
378s > x <- matrix(runif(6 * 6, min = -3, max = 3), nrow = 6, ncol = 6)
378s > storage.mode(x) <- "integer"
378s > x[2:3, ] <- NA_integer_
378s > x[2, 1] <- 0L
378s > x[4:5, ] <- 0L
378s > x[4, 6] <- NA_integer_
378s > 
378s > # To check names attribute
378s > dimnames <- list(letters[1:6], LETTERS[1:6])
378s > 
378s > # Test with and without dimnames on x
378s > for (setDimnames in c(TRUE, FALSE)) {
378s +   if (setDimnames) dimnames(x) <- dimnames
378s +   else dimnames(x) <- NULL
378s +   
378s +   count <- 0L
378s +   for (rows in index_cases) {
378s +     for (cols in index_cases) {
378s +       count <- count + 1L
378s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
378s +       useNames <- c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)
378s +       useNames <- useNames[count %% length(useNames) + 1]
378s +       
378s +       validateIndicesTestMatrix(x, rows, cols,
378s +                                 ftest = rowAlls, fsure = rowAlls_R,
378s +                                 value = 0, na.rm = TRUE, useNames = useNames)
378s +       validateIndicesTestMatrix(x, rows, cols,
378s +                                 ftest = rowAlls, fsure = rowAlls_R,
378s +                                 value = 0, na.rm = FALSE, useNames = useNames)
378s +       validateIndicesTestMatrix(x, rows, cols,
378s +                                 ftest = rowAlls, fsure = rowAlls_R,
378s +                                 value = NA_integer_, useNames = useNames)
378s +       validateIndicesTestMatrix(x, rows, cols,
378s +                                 fcoltest = colAlls, fsure = rowAlls_R,
378s +                                 value = 0, na.rm = TRUE, useNames = useNames)
378s +       validateIndicesTestMatrix(x, rows, cols,
378s +                                 fcoltest = colAlls, fsure = rowAlls_R,
378s +                                 value = 0, na.rm = FALSE, useNames = useNames)
378s +       validateIndicesTestMatrix(x, rows, cols,
378s +                                 fcoltest = colAlls, fsure = rowAlls_R,
378s +                                 value = NA_integer_, useNames = useNames)
378s +   
378s +       validateIndicesTestMatrix(x, rows, cols,
378s +                                 ftest = rowAnys, fsure = rowAnys_R,
378s +                                 value = 0, na.rm = TRUE, useNames = useNames)
378s +       validateIndicesTestMatrix(x, rows, cols,
378s +                                 ftest = rowAnys, fsure = rowAnys_R,
378s +                                 value = 0, na.rm = FALSE, useNames = useNames)
378s +       validateIndicesTestMatrix(x, rows, cols,
378s +                                 ftest = rowAnys, fsure = rowAnys_R,
378s +                                 value = NA_integer_, useNames = useNames)
378s +       validateIndicesTestMatrix(x, rows, cols,
378s +                                 fcoltest = colAnys, fsure = rowAnys_R,
378s +                                 value = 0, na.rm = TRUE, useNames = useNames)
378s +       validateIndicesTestMatrix(x, rows, cols,
378s +                                 fcoltest = colAnys, fsure = rowAnys_R,
378s +                                 value = 0, na.rm = FALSE, useNames = useNames)
378s +       validateIndicesTestMatrix(x, rows, cols,
378s +                                 fcoltest = colAnys, fsure = rowAnys_R,
378s +                                 value = NA_integer_, useNames = useNames)
378s +   
378s +       validateIndicesTestMatrix(x, rows, cols,
378s +                                 ftest = rowAnyMissings,
378s +                                 fsure = rowAnyMissings_R, useNames = useNames)
378s +       validateIndicesTestMatrix(x, rows, cols,
378s +                                 fcoltest = colAnyMissings,
378s +                                 fsure = rowAnyMissings_R, useNames = useNames)
378s +     }
378s +   }
378s + }
384s > 
384s > for (rr in seq_len(nrow(x))) {
384s +   for (idxs in index_cases) {
384s +     validateIndicesTestVector(x[rr, ], idxs,
384s +                               ftest = allValue, fsure = all_R,
384s +                               value = 0, na.rm = TRUE)
384s +     validateIndicesTestVector(x[rr, ], idxs,
384s +                               ftest = allValue, fsure = all_R,
384s +                               value = 0, na.rm = FALSE)
384s +     validateIndicesTestVector(x[rr, ], idxs,
384s +                               ftest = allValue, fsure = all_R,
384s +                               value = NA_integer_)
384s + 
384s +     validateIndicesTestVector(x[rr, ], idxs,
384s +                               ftest = anyValue, fsure = any_R,
384s +                               value = 0, na.rm = TRUE)
384s +     validateIndicesTestVector(x[rr, ], idxs,
384s +                               ftest = anyValue, fsure = any_R,
384s +                               value = 0, na.rm = FALSE)
384s +     validateIndicesTestVector(x[rr, ], idxs,
384s +                               ftest = anyValue, fsure = any_R,
384s +                               value = NA_integer_)
384s +   }
384s + }
384s > 
384s > 
384s > storage.mode(x) <- "character"
384s > # Test with and without dimnames on x
384s > for (setDimnames in c(TRUE, FALSE)) {
384s +   if (setDimnames) dimnames(x) <- dimnames
384s +   else dimnames(x) <- NULL
384s +   for (rows in index_cases) {
384s +     for (cols in index_cases) {
384s +       # Check names attribute
384s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
384s +         validateIndicesTestMatrix(x, rows, cols,
384s +                                   ftest = rowAlls, fsure = rowAlls_R,
384s +                                   value = "0", na.rm = TRUE, useNames = useNames)
384s +         validateIndicesTestMatrix(x, rows, cols,
384s +                                   ftest = rowAlls, fsure = rowAlls_R,
384s +                                   value = "0", na.rm = FALSE, useNames = useNames)
384s +         validateIndicesTestMatrix(x, rows, cols,
384s +                                   ftest = rowAlls, fsure = rowAlls_R,
384s +                                   value = NA_character_, useNames = useNames)
384s +         validateIndicesTestMatrix(x, rows, cols,
384s +                                   fcoltest = colAlls, fsure = rowAlls_R,
384s +                                   value = "0", na.rm = TRUE, useNames = useNames)
384s +         validateIndicesTestMatrix(x, rows, cols,
384s +                                   fcoltest = colAlls, fsure = rowAlls_R,
384s +                                   value = "0", na.rm = FALSE, useNames = useNames)
384s +         validateIndicesTestMatrix(x, rows, cols,
384s +                                   fcoltest = colAlls, fsure = rowAlls_R,
384s +                                   value = NA_character_, useNames = useNames)
384s +     
384s +         validateIndicesTestMatrix(x, rows, cols,
384s +                                   ftest = rowAnys, fsure = rowAnys_R,
384s +                                   value = "0", na.rm = TRUE, useNames = useNames)
384s +         validateIndicesTestMatrix(x, rows, cols,
384s +                                   ftest = rowAnys, fsure = rowAnys_R,
384s +                                   value = "0", na.rm = FALSE, useNames = useNames)
384s +         validateIndicesTestMatrix(x, rows, cols,
384s +                                   ftest = rowAnys, fsure = rowAnys_R,
384s +                                   value = NA_character_, useNames = useNames)
384s +         validateIndicesTestMatrix(x, rows, cols,
384s +                                   fcoltest = colAnys, fsure = rowAnys_R,
384s +                                   value = "0", na.rm = TRUE, useNames = useNames)
384s +         validateIndicesTestMatrix(x, rows, cols,
384s +                                   fcoltest = colAnys, fsure = rowAnys_R,
384s +                                   value = "0", na.rm = FALSE, useNames = useNames)
384s +         validateIndicesTestMatrix(x, rows, cols,
384s +                                   fcoltest = colAnys, fsure = rowAnys_R,
384s +                                   value = NA_character_, useNames = useNames)
384s +     
384s +         validateIndicesTestMatrix(x, rows, cols,
384s +                                   ftest = rowAnyMissings,
384s +                                   fsure = rowAnyMissings_R, useNames = useNames)
384s +         validateIndicesTestMatrix(x, rows, cols,
384s +                                   fcoltest = colAnyMissings,
384s +                                   fsure = rowAnyMissings_R, useNames = useNames)        
384s +       }
384s +     }
384s +   }
384s + }
396s > 
396s > for (rr in seq_len(nrow(x))) {
396s +   for (idxs in index_cases) {
396s +     validateIndicesTestVector(x[rr, ], idxs,
396s +                               ftest = allValue, fsure = all_R,
396s +                               value = "0", na.rm = TRUE)
396s +     validateIndicesTestVector(x[rr, ], idxs,
396s +                               ftest = allValue, fsure = all_R,
396s +                               value = "0", na.rm = FALSE)
396s +     validateIndicesTestVector(x[rr, ], idxs,
396s +                               ftest = allValue, fsure = all_R,
396s +                               value = NA_integer_)
396s + 
396s +     validateIndicesTestVector(x[rr, ], idxs,
396s +                               ftest = anyValue, fsure = any_R,
396s +                               value = "0", na.rm = TRUE)
396s +     validateIndicesTestVector(x[rr, ], idxs,
396s +                               ftest = anyValue, fsure = any_R,
396s +                               value = "0", na.rm = FALSE)
396s +     validateIndicesTestVector(x[rr, ], idxs,
396s +                               ftest = anyValue, fsure = any_R,
396s +                               value = NA_integer_)
396s +   }
396s + }
396s > 
397s 
397s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
397s Copyright (C) 2024 The R Foundation for Statistical Computing
397s Platform: arm-unknown-linux-gnueabihf (32-bit)
397s 
397s R is free software and comes with ABSOLUTELY NO WARRANTY.
397s You are welcome to redistribute it under certain conditions.
397s Type 'license()' or 'licence()' for distribution details.
397s 
397s R is a collaborative project with many contributors.
397s Type 'contributors()' for more information and
397s 'citation()' on how to cite R or R packages in publications.
397s 
397s Type 'demo()' for some demos, 'help()' for on-line help, or
397s 'help.start()' for an HTML browser interface to help.
397s Type 'q()' to quit R.
397s 
397s > library("matrixStats")
397s > 
397s > X <- matrix(rnorm(20 * 6), nrow = 20, ncol = 6)
397s > rownames(X) <- LETTERS[1:nrow(X)]
397s > colnames(X) <- letters[1:ncol(X)]
397s > print(X)
397s             a           b            c           d            e           f
397s A  0.24755802  0.78725362  1.817437783  0.49043022 -1.970867986 -0.21447018
397s B  1.52991248 -0.31612605 -0.627909763 -0.64239510  0.078793508 -0.53001451
397s C  1.62494184  0.12505493  0.129710156  0.18129344 -0.589465458  1.24434125
397s D -0.62789450  1.97626930  1.042860727 -0.49450495  0.775122959  0.65897072
397s E -1.27661046 -0.54748568 -1.797639761  0.17343191  0.448319283 -0.68754177
397s F  0.94190608  1.45786668  2.296576906 -0.99208386 -0.323983810 -0.42461257
397s G -0.91031169  1.20027048  0.551340887 -0.82985355  0.816238033 -1.98745718
397s H  0.37449912  0.70823779  0.380754862 -0.72839684 -0.606466439  0.71520895
397s I  0.61616812  1.14246413  2.146720647  1.31154529  0.834303719  2.20299753
397s J  0.94182677 -0.61911255  1.195840261 -0.34348517  0.945112355  0.08350315
397s K  0.43560166 -1.01884421 -0.005459353 -1.91851754  0.614635592  0.18138340
397s L -1.74428932  0.39600835 -0.039401289  0.39448634  0.124168722 -1.56032129
397s M -0.04716203  2.23366367 -2.714259211  0.71315088  1.373660261  0.29968997
397s N -0.83864279  0.69164539 -1.095680917  1.81064225 -0.009257926 -0.10876738
397s O  0.50732849 -0.57983042 -1.512027943  1.09591180 -0.700318671 -0.22125037
397s P -1.62780584  1.37871689 -0.656988886  2.03332022 -0.282365704  0.88041191
397s Q  0.46276336 -0.09729563 -0.728130532 -1.25366612  0.516118721  1.46533430
397s R  0.89587930 -0.82172558  1.625835393  0.09099432  0.401872995  0.75590357
397s S  0.94043428  0.18660576 -0.968303756  0.95437880  0.411551338 -0.26131770
397s T  0.88422145 -1.05012116  0.861511799  0.19102103  1.351167883  1.64093516
397s > 
397s > 
397s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
397s > # Apply rowMeans() for 3 sets of 2 columns
397s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
397s > nbr_of_sets <- 3L
397s > S <- matrix(1:ncol(X), ncol = nbr_of_sets)
397s > colnames(S) <- sprintf("s%d", 1:nbr_of_sets)
397s > print(S)
397s      s1 s2 s3
397s [1,]  1  3  5
397s [2,]  2  4  6
397s > 
397s > Z <- rowAvgsPerColSet(X, S = S)
397s > print(Z)
397s            s1           s2          s3
397s A  0.51740582  1.153934004 -1.09266908
397s B  0.60689322 -0.635152433 -0.22561050
397s C  0.87499839  0.155501799  0.32743790
397s D  0.67418740  0.274177891  0.71704684
397s E -0.91204807 -0.812103924 -0.11961124
397s F  1.19988638  0.652246521 -0.37429819
397s G  0.14497939 -0.139256330 -0.58560957
397s H  0.54136846 -0.173820988  0.05437125
397s I  0.87931612  1.729132970  1.51865063
397s J  0.16135711  0.426177547  0.51430775
397s K -0.29162127 -0.961988445  0.39800949
397s L -0.67414049  0.177542526 -0.71807628
397s M  1.09325082 -1.000554165  0.83667511
397s N -0.07349870  0.357480668 -0.05901266
397s O -0.03625096 -0.208058070 -0.46078452
397s P -0.12454448  0.688165665  0.29902310
397s Q  0.18273387 -0.990898323  0.99072651
397s R  0.03707686  0.858414857  0.57888828
397s S  0.56352002 -0.006962479  0.07511682
397s T -0.08294986  0.526266412  1.49605152
397s > 
397s > # Validation
397s > Z0 <- cbind(s1 = rowMeans(X[, 1:2]), s2 = rowMeans(X[, 3:4]),
397s +             s3 = rowMeans(X[, 5:6]))
397s > stopifnot(identical(drop(Z), Z0))
397s > 
397s > 
397s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
397s > # Apply colMeans() for 5 sets of 4 rows
397s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
397s > nbr_of_sets <- 5L
397s > S <- matrix(1:nrow(X), ncol = nbr_of_sets)
397s > colnames(S) <- sprintf("s%d", 1:nbr_of_sets)
397s > print(S)
397s      s1 s2 s3 s4 s5
397s [1,]  1  5  9 13 17
397s [2,]  2  6 10 14 18
397s [3,]  3  7 11 15 19
397s [4,]  4  8 12 16 20
397s > 
397s > Z <- colAvgsPerRowSet(X, S = S)
397s > print(Z)
397s             a           b          c            d           e          f
397s s1  0.6936295  0.64311295  0.5905247 -0.116294095 -0.42660424  0.2897068
397s s2 -0.2176292  0.70472232  0.3577582 -0.594225584  0.08352677 -0.5961006
397s s3  0.0623268 -0.02487107  0.8244251 -0.138992768  0.62955510  0.2268907
397s s4 -0.5015705  0.93104888 -1.4947392  1.413256288  0.09542949  0.2125210
397s s5  0.7958246 -0.44563415  0.1977282 -0.004317993  0.67017773  0.9002138
397s > 
397s > # Validation
397s > Z0 <- rbind(s1 = colMeans(X[1:4, ]), s2 = colMeans(X[5:8, ]),
397s +             s3 = colMeans(X[9:12, ]), s4 = colMeans(X[13:16, ]),
397s +             s5 = colMeans(X[17:20, ]))
397s > stopifnot(identical(drop(Z), Z0))
397s > 
397s > 
397s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
397s > # When there is only one "complete" set
397s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
397s > nbr_of_sets <- 1L
397s > S <- matrix(1:ncol(X), ncol = nbr_of_sets)
397s > colnames(S) <- sprintf("s%d", 1:nbr_of_sets)
397s > print(S)
397s      s1
397s [1,]  1
397s [2,]  2
397s [3,]  3
397s [4,]  4
397s [5,]  5
397s [6,]  6
397s > 
397s > Z <- rowAvgsPerColSet(X, S = S, FUN = rowMeans)
397s > print(Z)
397s            s1
397s A  0.19289025
397s B -0.08462324
397s C  0.45264603
397s D  0.55513738
397s E -0.61458774
397s F  0.49261157
397s G -0.19329550
397s H  0.14063957
397s I  1.37569991
397s J  0.36728080
397s K -0.28520007
397s L -0.40489141
397s M  0.30979059
397s N  0.07498977
397s O -0.23503118
397s P  0.28754810
397s Q  0.06085402
397s R  0.49146000
397s S  0.21055812
397s T  0.64645603
397s > 
397s > Z0 <- rowMeans(X)
397s > stopifnot(identical(drop(Z), Z0))
397s > 
397s > 
397s > nbr_of_sets <- 1L
397s > S <- matrix(1:nrow(X), ncol = nbr_of_sets)
397s > colnames(S) <- sprintf("s%d", 1:nbr_of_sets)
397s > print(S)
397s       s1
397s  [1,]  1
397s  [2,]  2
397s  [3,]  3
397s  [4,]  4
397s  [5,]  5
397s  [6,]  6
397s  [7,]  7
397s  [8,]  8
397s  [9,]  9
397s [10,] 10
397s [11,] 11
397s [12,] 12
397s [13,] 13
397s [14,] 14
397s [15,] 15
397s [16,] 16
397s [17,] 17
397s [18,] 18
397s [19,] 19
397s [20,] 20
397s > 
397s > Z <- colAvgsPerRowSet(X, S = S, FUN = colMeans)
397s > print(Z)
397s            a         b         c         d        e         f
397s s1 0.1665162 0.3616758 0.0951394 0.1118852 0.210417 0.2066463
397s > 
397s > Z0 <- colMeans(X)
397s > stopifnot(identical(drop(Z), Z0))
397s > 
397s > 
397s > 
397s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
397s > # Use weights
397s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
397s > nbr_of_sets <- 3L
397s > S <- matrix(1:ncol(X), ncol = nbr_of_sets)
397s > colnames(S) <- sprintf("s%d", 1:nbr_of_sets)
397s > print(S)
397s      s1 s2 s3
397s [1,]  1  3  5
397s [2,]  2  4  6
397s > 
397s > W <- matrix(runif(length(X)), nrow = nrow(X), ncol = ncol(X))
397s > Z1 <- rowAvgsPerColSet(X, W = W, S = S, FUN = rowWeightedMeans)
397s > print(Z1)
397s            s1           s2          s3
397s A  0.51740582  1.153934004 -1.09266908
397s B  0.60689322 -0.635152433 -0.22561050
397s C  0.87499839  0.155501799  0.32743790
397s D  0.67418740  0.274177891  0.71704684
397s E -0.91204807 -0.812103924 -0.11961124
397s F  1.19988638  0.652246521 -0.37429819
397s G  0.14497939 -0.139256330 -0.58560957
397s H  0.54136846 -0.173820988  0.05437125
397s I  0.87931612  1.729132970  1.51865063
397s J  0.16135711  0.426177547  0.51430775
397s K -0.29162127 -0.961988445  0.39800949
397s L -0.67414049  0.177542526 -0.71807628
397s M  1.09325082 -1.000554165  0.83667511
397s N -0.07349870  0.357480668 -0.05901266
397s O -0.03625096 -0.208058070 -0.46078452
397s P -0.12454448  0.688165665  0.29902310
397s Q  0.18273387 -0.990898323  0.99072651
397s R  0.03707686  0.858414857  0.57888828
397s S  0.56352002 -0.006962479  0.07511682
397s T -0.08294986  0.526266412  1.49605152
397s > Z2 <- colAvgsPerRowSet(X, W = W, S = S, FUN = colWeightedMeans)
397s > print(Z2)
397s             a         b         c           d           e          f
397s s1  0.8887353 0.2355638 0.5947640 -0.07598244 -0.94603724 -0.3722423
397s s2  0.4985237 1.0506621 0.5862854 -0.15660575  0.09282875  0.9516560
397s s3 -0.1673522 0.4551905 0.2494686 -0.40932598  0.06216774 -0.5560772
397s > 
397s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
397s > # Result should always be a matrix, including when nrow(X) <= 1
397s > # (https://github.com/HenrikBengtsson/matrixStats/issues/108)
397s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
397s > X <- matrix(1:3, nrow = 1L, ncol = 3L)
397s > S <- matrix(1, nrow = 1L, ncol = 1L)
397s > Z1 <- rowAvgsPerColSet(X, S = S)
397s > stopifnot(is.matrix(Z1))
397s > Z2 <- rowAvgsPerColSet(X, S = S, rows = 0)
397s > stopifnot(is.matrix(Z2))
397s > 
397s > 
397s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
397s > # Works with many, one or zero columns / rows
397s > # (https://github.com/HenrikBengtsson/matrixStats/issues/172)
397s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
397s > S <- cbind(1:2, 3:4, 5:6)
397s > X <- matrix(rnorm(2 * 6), nrow = 6, ncol = 2)
397s > Z2 <- colAvgsPerRowSet(X, S = S, FUN = colSums2)
397s > Z2_ref <- rbind(colSums2(X[S[,1], ,drop=FALSE]),
397s +                 colSums2(X[S[,2], ,drop=FALSE]),
397s +                 colSums2(X[S[,3], ,drop=FALSE]))
397s > stopifnot(identical(Z2, Z2_ref))
397s > X <- matrix(rnorm(6), nrow = 6, ncol = 1)
397s > Z1 <- colAvgsPerRowSet(X, S = S, FUN = colSums2)
397s > Z1_ref <- rbind(colSums2(X[S[,1], ,drop=FALSE]),
397s +                 colSums2(X[S[,2], ,drop=FALSE]),
397s +                 colSums2(X[S[,3], ,drop=FALSE]))
397s > stopifnot(identical(Z1, Z1_ref))
397s > X <- matrix(numeric(0), nrow = 6, ncol = 0)
397s > Z0 <- colAvgsPerRowSet(X, S = S, FUN = colSums2)
397s > Z0_ref <- matrix(numeric(0), nrow = ncol(S), ncol = 0)
397s > stopifnot(identical(Z0, unname(Z0_ref)))
397s > 
397s > 
397s > S <- rbind(1:4, 5:8)
397s > X <- matrix(rnorm(n = 2 * 8), nrow = 2, ncol = 8)
397s > Z2 <- rowAvgsPerColSet(X, S = S, FUN = rowMeans2)
397s > Z2_ref <- cbind(rowMeans2(X[,S[,1],drop=FALSE]),
397s +                 rowMeans2(X[,S[,2],drop=FALSE]),
397s +                 rowMeans2(X[,S[,3],drop=FALSE]),
397s +                 rowMeans2(X[,S[,4],drop=FALSE]))
397s > stopifnot(identical(Z2, Z2_ref))
397s > X <- matrix(rnorm(n = 8), nrow = 1, ncol = 8)
397s > Z1 <- rowAvgsPerColSet(X, S = S, FUN = rowMeans2)
397s > Z1_ref <- cbind(rowMeans2(X[,S[,1],drop=FALSE]),
397s +                 rowMeans2(X[,S[,2],drop=FALSE]),
397s +                 rowMeans2(X[,S[,3],drop=FALSE]),
397s +                 rowMeans2(X[,S[,4],drop=FALSE]))
397s > stopifnot(identical(Z1, Z1_ref))
397s > X <- matrix(numeric(0), nrow = 0, ncol = 8)
397s > Z0 <- rowAvgsPerColSet(X, S = S, FUN = rowMeans2)
397s > Z0_ref <- matrix(numeric(0), nrow = 0, ncol = ncol(S))
397s > stopifnot(identical(Z0, Z0_ref))
397s > 
397s 
397s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
397s Copyright (C) 2024 The R Foundation for Statistical Computing
397s Platform: arm-unknown-linux-gnueabihf (32-bit)
397s 
397s R is free software and comes with ABSOLUTELY NO WARRANTY.
397s You are welcome to redistribute it under certain conditions.
397s Type 'license()' or 'licence()' for distribution details.
397s 
397s R is a collaborative project with many contributors.
397s Type 'contributors()' for more information and
397s 'citation()' on how to cite R or R packages in publications.
397s 
397s Type 'demo()' for some demos, 'help()' for on-line help, or
397s 'help.start()' for an HTML browser interface to help.
397s Type 'q()' to quit R.
397s 
397s > library("matrixStats")
397s > 
397s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
397s > # Subsetted tests
397s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
397s > source("utils/validateIndicesFramework.R")
397s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
397s > #W <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
397s > for (rows in index_cases) {
397s +   for (cols in index_cases) {
397s +     if (is.null(rows)) {
397s +       rows <- seq_len(nrow(x))
397s +       rows_finite <- rows
397s +     } else {
397s +       rows_finite <- rows[is.finite(rows)]
397s +     }
397s + 
397s +     if (is.null(cols)) {
397s +       cols <- seq_len(ncol(x))
397s +       cols_finite <- cols
397s +     } else {
397s +       cols_finite <- cols[is.finite(cols)]
397s +     }
397s + 
397s +     suppressWarnings({
397s +       actual <- tryCatch({
397s +         rowAvgsPerColSet(x, rows = rows, S = matrix(cols, ncol = 1),
397s +                          FUN = rowMeans)
397s +       }, error = function(c) "error")
397s +       expect <- tryCatch({
397s +         rowMeans(x[rows, cols_finite, drop = FALSE], na.rm = TRUE)
397s +       }, error = function(c) "error")
397s +     })
397s +     stopifnot(all.equal(as.vector(actual), expect))
397s + 
397s +     suppressWarnings({
397s +       actual <- tryCatch({
397s +         colAvgsPerRowSet(x, cols = cols, S = matrix(rows, ncol = 1),
397s +                          FUN = colMeans)
397s +       }, error = function(c) "error")
397s +       expect <- tryCatch({
397s +         colMeans(x[rows_finite, cols, drop = FALSE], na.rm = TRUE)
397s +       }, error = function(c) "error")
397s +     })
397s +     stopifnot(all.equal(as.vector(actual), expect))
397s +   }
397s + }
398s > 
398s 
398s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
398s Copyright (C) 2024 The R Foundation for Statistical Computing
398s Platform: arm-unknown-linux-gnueabihf (32-bit)
398s 
398s R is free software and comes with ABSOLUTELY NO WARRANTY.
398s You are welcome to redistribute it under certain conditions.
398s Type 'license()' or 'licence()' for distribution details.
398s 
398s R is a collaborative project with many contributors.
398s Type 'contributors()' for more information and
398s 'citation()' on how to cite R or R packages in publications.
398s 
398s Type 'demo()' for some demos, 'help()' for on-line help, or
398s 'help.start()' for an HTML browser interface to help.
398s Type 'q()' to quit R.
398s 
399s > library("matrixStats")
399s > 
399s > x <- matrix(1:27, ncol = 3)
399s > 
399s > # To check names attribute
399s > dimnames <- list(letters[1:9], LETTERS[1:3])
399s > 
399s > rowCollapse_R <- function(x, idxs, ..., useNames = NA) {
399s +   res <- x[, idxs]
399s +   # Preserve names attribute?
399s +   if (is.na(useNames) || !useNames) names(res) <- NULL
399s +   res
399s + }
399s > 
399s > idxs <- 1L
399s > # Test with and without dimnames on x
399s > for (setDimnames in c(TRUE, FALSE)) {
399s +   if (setDimnames) dimnames(x) <- dimnames
399s +   else dimnames(x) <- NULL
399s +   # Check names attribute
399s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
399s +     y_truth <- rowCollapse_R(x, idxs, useNames = useNames)
399s +     y <- rowCollapse(x, idxs, useNames = useNames)
399s +     stopifnot(identical(y, y_truth))
399s +     y2 <- colCollapse(t(x), idxs, useNames = useNames)
399s +     stopifnot(identical(y2, y))
399s +   }
399s + }
399s > 
399s > idxs <- 2L
399s > # Test with and without dimnames on x
399s > for (setDimnames in c(TRUE, FALSE)) {
399s +   if (setDimnames) dimnames(x) <- dimnames
399s +   else dimnames(x) <- NULL
399s +   # Check names attribute
399s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
399s +     y_truth <- rowCollapse_R(x, idxs, useNames = useNames)
399s +     y <- rowCollapse(x, idxs, useNames = useNames)
399s +     stopifnot(identical(y, y_truth))
399s +     y2 <- colCollapse(t(x), idxs, useNames = useNames)
399s +     stopifnot(identical(y2, y))
399s +   }
399s + }
399s > 
399s > 
399s > rowCollapse_R <- function(x, idxs, ..., useNames = NA) {
399s +   res <- c(x[1:5, 1], x[6:9, 3])
399s +   # Preserve names attribute?
399s +   if (is.na(useNames) || !useNames) names(res) <- NULL
399s +   res
399s + }
399s > 
399s > idxs <- c(1, 1, 1, 1, 1, 3, 3, 3, 3)
399s > # Test with and without dimnames on x
399s > for (setDimnames in c(TRUE, FALSE)) {
399s +   if (setDimnames) dimnames(x) <- dimnames
399s +   else dimnames(x) <- NULL
399s +   # Check names attribute
399s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
399s +     y_truth <- rowCollapse_R(x, idxs, useNames = useNames)
399s +     y <- rowCollapse(x, idxs, useNames = useNames)
399s +     stopifnot(identical(y, y_truth))
399s +     y2 <- colCollapse(t(x), idxs, useNames = useNames)
399s +     stopifnot(identical(y2, y))
399s +   }
399s + }
399s > 
399s > 
399s > rowCollapse_R <- function(x, idxs, ..., useNames = NA) {
399s +   res <- c(x[1, 1], x[2, 2], x[3, 3], x[4, 1], x[5, 2],
399s +            x[6, 3], x[7, 1], x[8, 2], x[9, 3])
399s +   # Preserve names attribute?
399s +   if (isTRUE(useNames)) {
399s +     names <- rownames(x)
399s +     if (!is.null(names)) names(res) <- names
399s +   }
399s +   res
399s + }
399s > 
399s > idxs <- 1:3
399s > # Test with and without dimnames on x
399s > for (setDimnames in c(TRUE, FALSE)) {
399s +   if (setDimnames) dimnames(x) <- dimnames
399s +   else dimnames(x) <- NULL
399s +   # Check names attribute
399s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
399s +     y_truth <- rowCollapse_R(x, idxs, useNames = useNames)
399s +     y <- rowCollapse(x, idxs, useNames = useNames)
399s +     stopifnot(identical(y, y_truth))
399s +     y2 <- colCollapse(t(x), idxs, useNames = useNames)
399s +     stopifnot(identical(y2, y))
399s +   }
399s + }
399s > 
399s 
399s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
399s Copyright (C) 2024 The R Foundation for Statistical Computing
399s Platform: arm-unknown-linux-gnueabihf (32-bit)
399s 
399s R is free software and comes with ABSOLUTELY NO WARRANTY.
399s You are welcome to redistribute it under certain conditions.
399s Type 'license()' or 'licence()' for distribution details.
399s 
399s R is a collaborative project with many contributors.
399s Type 'contributors()' for more information and
399s 'citation()' on how to cite R or R packages in publications.
399s 
399s Type 'demo()' for some demos, 'help()' for on-line help, or
399s 'help.start()' for an HTML browser interface to help.
399s Type 'q()' to quit R.
399s 
399s > library("matrixStats")
399s > 
399s > rowCollapse_R <- function(x, idxs, ..., useNames = NA) {
399s +   ans <- c()
399s +   storage.mode(ans) <- storage.mode(x)
399s +   for (ii in seq_len(length(idxs))) {
399s +     ans[ii] <- x[ii, idxs[ii]]
399s +   }
399s +   
399s +   # Preserve names attribute
399s +   if (isTRUE(useNames)) {
399s +     names <- rownames(x)
399s +     if (!is.null(names)) names(ans) <- names
399s +   }
399s + 
399s +   ans
399s + }
399s > 
399s > 
399s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
399s > # Subsetted tests
399s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
399s > source("utils/validateIndicesFramework.R")
399s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
399s > storage.mode(x) <- "integer"
399s > 
399s > # To check names attribute
399s > dimnames <- list(letters[1:6], LETTERS[1:6])
399s > 
399s > for (rows in index_cases) {
399s +   if (is.null(rows)) rows <- seq_len(nrow(x))
399s + 
399s +   for (idxs in list(2L, seq_len(6L))) {
399s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
399s +       suppressWarnings({
399s +         actual <- tryCatch(rowCollapse(x, idxs, rows = rows, useNames = useNames),
399s +                            error = function(c) "error")
399s +         expect <- tryCatch({
399s +           idxs_0 <- rep(idxs, length.out = nrow(x))[rows]
399s +           rowCollapse_R(x[rows, , drop = FALSE], idxs_0, useNames = useNames)
399s +         }, error = function(c) "error")
399s +       })
399s +       stopifnot(all.equal(actual, expect))
399s +     
399s +       suppressWarnings({
399s +         actual <- tryCatch(colCollapse(t(x), idxs, cols = rows, useNames = useNames),
399s +                            error = function(c) "error")
399s +       })
399s +       stopifnot(all.equal(actual, expect))
399s +       
399s +       # Check names attribute
399s +       dimnames(x) <- dimnames
399s +       suppressWarnings({
399s +         actual <- tryCatch(rowCollapse(x, idxs, rows = rows, useNames = useNames),
399s +                            error = function(c) "error")
399s +         expect <- tryCatch({
399s +           idxs_0 <- rep(idxs, length.out = nrow(x))[rows]
399s +           rowCollapse_R(x[rows, , drop = FALSE], idxs_0, useNames = useNames)
399s +         }, error = function(c) "error")
399s +       })
399s +       stopifnot(all.equal(actual, expect))
399s +       
399s +       suppressWarnings({
399s +         actual <- tryCatch(colCollapse(t(x), idxs, cols = rows, useNames = useNames),
399s +                            error = function(c) "error")
399s +       })
399s +       stopifnot(all.equal(actual, expect))
399s +       
399s +       dimnames(x) <- NULL
399s +     }
399s +   }
399s + }
400s > 
400s 
400s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
400s Copyright (C) 2024 The R Foundation for Statistical Computing
400s Platform: arm-unknown-linux-gnueabihf (32-bit)
400s 
400s R is free software and comes with ABSOLUTELY NO WARRANTY.
400s You are welcome to redistribute it under certain conditions.
400s Type 'license()' or 'licence()' for distribution details.
400s 
400s R is a collaborative project with many contributors.
400s Type 'contributors()' for more information and
400s 'citation()' on how to cite R or R packages in publications.
400s 
400s Type 'demo()' for some demos, 'help()' for on-line help, or
400s 'help.start()' for an HTML browser interface to help.
400s Type 'q()' to quit R.
400s 
400s > library("matrixStats")
400s > 
400s > rowCounts_R <- function(x, value = TRUE, na.rm = FALSE, ...) {
400s +   if (is.na(value)) {
400s +     counts <- apply(x, MARGIN = 1L, FUN = function(x)
400s +       sum(is.na(x))
400s +     )
400s +   } else {
400s +     counts <- apply(x, MARGIN = 1L, FUN = function(x)
400s +       sum(x == value, na.rm = na.rm)
400s +     )
400s +   }
400s +   # Preserve names attribute
400s +   names <- names(counts)  
400s +   counts <- as.integer(counts)
400s +   if (isTRUE(useNames) && !is.null(names)) names(counts) <- names
400s +   counts
400s + }
400s > 
400s > 
400s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
400s > # Data type: integer and numeric
400s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
400s > for (mode in c("integer", "double")) {
400s +   x <- matrix(runif(10 * 5, min = -3, max = 3), nrow = 10L, ncol = 5L)
400s +   x[sample.int(length(x), size = 7L)] <- 0
400s +   storage.mode(x) <- mode
400s +   
400s +   dimnames = list(letters[1:10], LETTERS[1:5])
400s +   
400s +   # Test with and without dimnames on x
400s +   for (setDimnames in c(TRUE, FALSE)) {
400s +     if (setDimnames) dimnames(x) <- dimnames
400s +     else dimnames(x) <- NULL    
400s +     for (na.rm in c(FALSE, TRUE)) {
400s +       # Check names attribute
400s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
400s +         # Count zeros
400s +         r0 <- rowCounts_R(x, value = 0, na.rm = na.rm, useNames = useNames)
400s +         r1 <- rowCounts(x, value = 0, na.rm = na.rm, useNames = useNames)
400s +         r2 <- colCounts(t(x), value = 0, na.rm = na.rm, useNames = useNames)
400s +         stopifnot(identical(r1, r0))
400s +         stopifnot(identical(r2, r0))
400s +         
400s +         # Count NAs
400s +         r0 <- rowCounts_R(x, value = NA, na.rm = na.rm, useNames = useNames)
400s +         r1 <- rowCounts(x, value = NA, na.rm = na.rm, useNames = useNames)
400s +         r2 <- colCounts(t(x), value = NA, na.rm = na.rm, useNames = useNames)
400s +         stopifnot(identical(r1, r0))
400s +         stopifnot(identical(r2, r0))
400s +         
400s +         if (mode == "integer") {
400s +           ux <- unique(as.vector(x))
400s +           r0 <- r1 <- r2 <- integer(nrow(x))
400s +           for (value in ux) {
400s +             r0 <- r0 + rowCounts_R(x, value = value, na.rm = na.rm, useNames = useNames)
400s +             r1 <- r1 + rowCounts(x, value = value, na.rm = na.rm, useNames = useNames)
400s +             r2 <- r2 + colCounts(t(x), value = value, na.rm = na.rm, useNames = useNames)
400s +             stopifnot(identical(r1, r0))
400s +             stopifnot(identical(r2, r0))
400s +           }
400s +           stopifnot(all(r0 == ncol(x)))
400s +         } # if (mode == "integer")
400s +       } # for (useNames ...)
400s +     } # for (na.rm ...)
400s +   } # for (setDimnames ...)
400s + } # for (mode ...)
400s > 
400s > 
400s > # All NAs
400s > na_list <- list(NA_integer_, NA_real_, NaN)
400s > for (na_value in na_list) {
400s +   x <- matrix(na_value, nrow = 10L, ncol = 5L)
400s +   # Test with and without dimnames on x
400s +   for (setDimnames in c(TRUE, FALSE)) {
400s +     if (setDimnames) dimnames(x) <- dimnames
400s +     else dimnames(x) <- NULL    
400s +     for (na.rm in c(FALSE, TRUE)) {
400s +       # Check names attribute
400s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
400s +         r0 <- rowCounts_R(x, na.rm = na.rm, useNames = useNames)
400s +         r1 <- rowCounts(x, na.rm = na.rm, useNames = useNames)
400s +         r2 <- colCounts(t(x), na.rm = na.rm, useNames = useNames)
400s +         stopifnot(identical(r1, r0))
400s +         stopifnot(identical(r2, r0))
400s +         
400s +         # Count NAs
400s +         r0 <- rowCounts_R(x, value = NA, na.rm = na.rm, useNames = useNames)
400s +         r1 <- rowCounts(x, value = NA, na.rm = na.rm, useNames = useNames)
400s +         r2 <- colCounts(t(x), value = NA, na.rm = na.rm, useNames = useNames)
400s +         stopifnot(all(r0 == ncol(x)))
400s +         stopifnot(identical(r1, r0))
400s +         stopifnot(identical(r2, r0))
400s +       }
400s +     }
400s +   }
400s + } # for (na_value ...)
400s > 
400s > 
400s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
400s > # Data type: logical
400s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
400s > x <- matrix(FALSE, nrow = 10L, ncol = 4L)
400s > x[7:8, 2:3] <- TRUE
400s > x[1:3, ] <- TRUE
400s > x[, 1] <- TRUE
400s > x[4, ] <- FALSE
400s > x[, 4] <- FALSE
400s > x[2, ] <- FALSE
400s > x[3, ] <- TRUE
400s > 
400s > # To check names attribute
400s > dimnames <- list(letters[1:10], LETTERS[1:4])
400s > 
400s > # Test with and without dimnames on x
400s > for (setDimnames in c(TRUE, FALSE)) {
400s +   if (setDimnames) dimnames(x) <- dimnames
400s +   else dimnames(x) <- NULL
400s +   # Row/column counts
400s +   for (na.rm in c(FALSE, TRUE)) {
400s +     # Check names attribute
400s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
400s +       r0 <- rowCounts_R(x, na.rm = na.rm, useNames = useNames)
400s +       r1 <- rowCounts(x, na.rm = na.rm, useNames = useNames)
400s +       r2 <- colCounts(t(x), na.rm = na.rm, useNames = useNames)
400s +       stopifnot(identical(r1, r0))
400s +       stopifnot(identical(r2, r0))
400s +       
400s +       r_true <- rowCounts(x, value = TRUE, na.rm = na.rm, useNames = useNames)
400s +       r_false <- rowCounts(x, value = FALSE, na.rm = na.rm, useNames = useNames)
400s +       stopifnot(r_true + r_false == ncol(x))
400s +       
400s +       c_true <- colCounts(x, value = TRUE, na.rm = na.rm, useNames = useNames)
400s +       c_false <- colCounts(x, value = FALSE, na.rm = na.rm, useNames = useNames)
400s +       stopifnot(c_true + c_false == nrow(x))
400s +       
400s +       # Count NAs
400s +       r0 <- rowCounts_R(x, value = NA, na.rm = na.rm, useNames = useNames)
400s +       r1 <- rowCounts(x, value = NA, na.rm = na.rm, useNames = useNames)
400s +       r2 <- colCounts(t(x), value = NA, na.rm = na.rm, useNames = useNames)
400s +       stopifnot(identical(r1, r0))
400s +       stopifnot(identical(r2, r0))
400s +     }
400s +   }
400s + }
400s > 
400s > 
400s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
400s > # Data type: character (not sure if this should be supported)
400s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
400s > x <- matrix(rep(letters, length.out = 10 * 5), nrow = 10L, ncol = 5L)
400s > x[2:3, 3:4] <- NA_character_
400s > 
400s > # Row/column counts
400s > for (na.rm in c(FALSE, TRUE)) {
400s +   for (value in c("g", NA_character_)) {
400s +     r0 <- rowCounts_R(x, value = value, na.rm = na.rm)
400s +     r1 <- rowCounts(x, value = value, na.rm = na.rm)
400s +     r2 <- colCounts(t(x), value = value, na.rm = na.rm)
400s +     stopifnot(identical(r1, r0))
400s +     stopifnot(identical(r2, r0))
400s + 
400s +     c <- count(x[1, ], value = value, na.rm = na.rm)
400s +     stopifnot(identical(c, r1[1]))
400s + 
400s +     c <- count(x[2, ], value = value, na.rm = na.rm)
400s +     stopifnot(identical(c, r1[2]))
400s +   }
400s + }
401s > 
401s > # NA row
401s > x <- matrix(0, nrow = 2L, ncol = 2L)
401s > x[1, ] <- NA_integer_
401s > 
401s > dimnames <- list(letters[1:2], LETTERS[1:2])
401s > 
401s > # Test with and without dimnames on x
401s > for (setDimnames in c(TRUE, FALSE)) {
401s +   if (setDimnames) dimnames(x) <- dimnames
401s +   else dimnames(x) <- NULL    
401s +   # Check names attribute
401s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
401s +     r0 <- rowCounts(x, value = 0, useNames = useNames)
401s +     r1 <- rowCounts_R(x, value = 0, useNames = useNames)
401s +     stopifnot(identical(r0, r1))
401s +   }
401s + }
401s > 
401s 
401s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
401s Copyright (C) 2024 The R Foundation for Statistical Computing
401s Platform: arm-unknown-linux-gnueabihf (32-bit)
401s 
401s R is free software and comes with ABSOLUTELY NO WARRANTY.
401s You are welcome to redistribute it under certain conditions.
401s Type 'license()' or 'licence()' for distribution details.
401s 
401s R is a collaborative project with many contributors.
401s Type 'contributors()' for more information and
401s 'citation()' on how to cite R or R packages in publications.
401s 
401s Type 'demo()' for some demos, 'help()' for on-line help, or
401s 'help.start()' for an HTML browser interface to help.
401s Type 'q()' to quit R.
401s 
401s > library("matrixStats")
401s > 
401s > rowCounts_R <- function(x, value = TRUE, na.rm = FALSE, ..., useNames = NA) {
401s +   if (is.na(value)) {
401s +     counts <- apply(x, MARGIN = 1L, FUN = function(x)
401s +       sum(is.na(x))
401s +     )
401s +   } else {
401s +     counts <- apply(x, MARGIN = 1L, FUN = function(x)
401s +       sum(x == value, na.rm = na.rm)
401s +     )
401s +   }
401s +   # Preserve names attribute
401s +   names <- names(counts)  
401s +   counts <- as.integer(counts)
401s +   if (isTRUE(useNames) && !is.null(names)) names(counts) <- names
401s +   counts
401s + } # rowCounts_R()
401s > 
401s > 
401s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
401s > # Subsetted tests
401s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
401s > source("utils/validateIndicesFramework.R")
401s > x <- matrix(runif(6 * 6, min = -3, max = 3), nrow = 6, ncol = 6)
401s > x[2:3, 3:4] <- NA_real_
401s > storage.mode(x) <- "integer"
401s > 
401s > # To check names attribute
401s > dimnames <- list(letters[1:6], LETTERS[1:6])
401s > 
401s > # Test with and without dimnames on x
401s > for (setDimnames in c(TRUE, FALSE)) {
401s +   if (setDimnames) dimnames(x) <- dimnames
401s +   else dimnames(x) <- NULL
401s +   for (rows in index_cases) {
401s +     for (cols in index_cases) {
401s +       # Check names attribute
401s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
401s +         validateIndicesTestMatrix(x, rows, cols,
401s +                                   ftest = rowCounts, fsure = rowCounts_R,
401s +                                   value = 0, na.rm = TRUE, useNames = useNames)
401s +         validateIndicesTestMatrix(x, rows, cols,
401s +                                   fcoltest = colCounts, fsure = rowCounts_R,
401s +                                   value = 0, na.rm = TRUE, useNames = useNames)
401s +         for (value in c(0, NA_integer_)) {
401s +           validateIndicesTestMatrix(x, rows, cols,
401s +                                     ftest = rowCounts, fsure = rowCounts_R,
401s +                                     value = value, useNames = useNames)
401s +           validateIndicesTestMatrix(x, rows, cols,
401s +                                     fcoltest = colCounts, fsure = rowCounts_R,
401s +                                     value = value, useNames = useNames)
401s +         }
401s +       }
401s +     }
401s +   }
401s + }
406s > 
406s > x <- matrix(rep(letters, length.out = 6 * 6), nrow = 6, ncol = 6)
406s > x[2:3, 3:4] <- NA_character_
406s > # Test with and without dimnames on x
406s > for (setDimnames in c(TRUE, FALSE)) {
406s +   if (setDimnames) dimnames(x) <- dimnames
406s +   else dimnames(x) <- NULL
406s +   
406s +   count <- 0L
406s +   for (rows in index_cases) {
406s +     for (cols in index_cases) {
406s +       count <- count + 1L
406s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
406s +       useNames <- c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)
406s +       useNames <- useNames[count %% length(useNames) + 1]
406s +       
406s +       validateIndicesTestMatrix(x, rows, cols,
406s +                                 ftest = rowCounts, fsure = rowCounts_R,
406s +                                 value = "g", na.rm = TRUE, useNames = useNames)
406s +       validateIndicesTestMatrix(x, rows, cols,
406s +                                 fcoltest = colCounts, fsure = rowCounts_R,
406s +                                 value = "g", na.rm = TRUE, useNames = useNames)
406s +       for (value in c("g", NA_character_)) {
406s +         validateIndicesTestMatrix(x, rows, cols,
406s +                                   ftest = rowCounts, fsure = rowCounts_R,
406s +                                   value = value, useNames = useNames)
406s +         validateIndicesTestMatrix(x, rows, cols,
406s +                                   fcoltest = colCounts, fsure = rowCounts_R,
406s +                                   value = value, useNames = useNames)
406s +       }
406s +     }
406s +   }
406s + }
409s > 
409s 
409s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
409s Copyright (C) 2024 The R Foundation for Statistical Computing
409s Platform: arm-unknown-linux-gnueabihf (32-bit)
409s 
409s R is free software and comes with ABSOLUTELY NO WARRANTY.
409s You are welcome to redistribute it under certain conditions.
409s Type 'license()' or 'licence()' for distribution details.
409s 
409s R is a collaborative project with many contributors.
409s Type 'contributors()' for more information and
409s 'citation()' on how to cite R or R packages in publications.
409s 
409s Type 'demo()' for some demos, 'help()' for on-line help, or
409s 'help.start()' for an HTML browser interface to help.
409s Type 'q()' to quit R.
409s 
409s > library("matrixStats")
409s > 
409s > rowCummins_R <- function(x, ..., useNames = NA) {
409s +   suppressWarnings({
409s +     y <- t(apply(x, MARGIN = 1L, FUN = cummin))
409s +   })
409s +  
409s +   # Preserve dimnames attribute?
409s +   dim(y) <- dim(x)
409s +   dimnames(y) <- if (isTRUE(useNames)) dimnames(x) else NULL
409s +   y
409s + }
409s > 
409s > rowCummaxs_R <- function(x, ..., useNames = NA) {
409s +   mode <- storage.mode(x)
409s +   # Change mode because a bug is detected on cummax for integer in R-3.2.0
409s +   storage.mode(x) <- "numeric"
409s +   suppressWarnings({
409s +     y <- t(apply(x, MARGIN = 1L, FUN = cummax))
409s +   })
409s +   
409s +   # Preserve dimnames attribute?
409s +   dim(y) <- dim(x)
409s +   dimnames(y) <- if (isTRUE(useNames)) dimnames(x) else NULL
409s +   
409s +   y
409s + }
409s > 
409s > 
409s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
409s > # With and without some NAs
409s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
409s > for (mode in c("logical", "integer", "double")) {
409s +   for (add_na in c(FALSE, TRUE)) {
409s +     cat("add_na = ", add_na, "\n", sep = "")
409s + 
409s +     x <- matrix(1:50, nrow = 10L, ncol = 5L)
409s +     diag(x) <- 0
409s +     if (add_na) {
409s +       x[3:7, c(2, 4)] <- NA_real_
409s +     }
409s +     cat("mode: ", mode, "\n", sep = "")
409s +     storage.mode(x) <- mode
409s +     str(x)
409s +     
409s +     # To check dimnames attribute
409s +     dimnames <- list(letters[1:10], LETTERS[1:5])
409s +     
409s +     # Test with and without dimnames on x
409s +     for (setDimnames in c(TRUE, FALSE)) {
409s +       if (setDimnames) dimnames(x) <- dimnames
409s +       else dimnames(x) <- NULL    
409s +       # Check names attribute
409s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
409s +         # Row/column ranges
409s +         r0 <- rowCummins_R(x, useNames = useNames)
409s +         r1 <- rowCummins(x, useNames = useNames)
409s +         r2 <- t(colCummins(t(x), useNames = useNames))
409s +         stopifnot(all.equal(r1, r2))
409s +         stopifnot(all.equal(r1, r0))
409s +         stopifnot(all.equal(r2, r0))
409s + 
409s +         r0 <- rowCummaxs_R(x, useNames = useNames)
409s +         r1 <- rowCummaxs(x, useNames = useNames)
409s +         r2 <- t(colCummaxs(t(x), useNames = useNames))
409s +         stopifnot(all.equal(r1, r2))
409s +         stopifnot(all.equal(r1, r0))
409s +         stopifnot(all.equal(r2, r0))
409s +       } # for (useNames ...)
409s +     } # for (setDimnames ...)
409s +   } # for (add_na ...)
409s + } # for (mode ...)
409s add_na = FALSE
409s mode: logical
410s  logi [1:10, 1:5] FALSE TRUE TRUE TRUE TRUE TRUE ...
410s add_na = TRUE
410s mode: logical
410s  logi [1:10, 1:5] FALSE TRUE TRUE TRUE TRUE TRUE ...
410s add_na = FALSE
410s mode: integer
410s  int [1:10, 1:5] 0 2 3 4 5 6 7 8 9 10 ...
410s add_na = TRUE
410s mode: integer
410s  int [1:10, 1:5] 0 2 3 4 5 6 7 8 9 10 ...
410s add_na = FALSE
410s mode: double
410s  num [1:10, 1:5] 0 2 3 4 5 6 7 8 9 10 ...
410s add_na = TRUE
410s mode: double
410s  num [1:10, 1:5] 0 2 3 4 5 6 7 8 9 10 ...
410s > 
410s > 
410s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
410s > # All NAs
410s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
410s > for (mode in c("logical", "integer", "double")) {
410s +   x <- matrix(NA_real_, nrow = 10L, ncol = 5L)
410s +   cat("mode: ", mode, "\n", sep = "")
410s +   storage.mode(x) <- mode
410s +   str(x)
410s +   
410s +   # Test with and without dimnames on x
410s +   for (setDimnames in c(TRUE, FALSE)) {
410s +     if (setDimnames) dimnames(x) <- dimnames
410s +     else dimnames(x) <- NULL    
410s +     # Check names attribute
410s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
410s +       r0 <- rowCummins_R(x, useNames = useNames)
410s +       r1 <- rowCummins(x, useNames = useNames)
410s +       r2 <- t(colCummins(t(x), useNames = useNames))
410s +       stopifnot(all.equal(r1, r2))
410s +       stopifnot(all.equal(r1, r0))
410s +       stopifnot(all.equal(r2, r0))
410s +       
410s +       r0 <- rowCummaxs_R(x, useNames = useNames)
410s +       r1 <- rowCummaxs(x, useNames = useNames)
410s +       r2 <- t(colCummaxs(t(x), useNames = useNames))
410s +       stopifnot(all.equal(r1, r2))
410s +       stopifnot(all.equal(r1, r0))
410s +       stopifnot(all.equal(r2, r0))
410s +     } # for (useNames ...)
410s +   } # for (setDimnames ...)
410s + } # for (mode ...)
410s mode: logical
410s  logi [1:10, 1:5] NA NA NA NA NA NA ...
410s mode: integer
410s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
410s mode: double
410s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
410s > 
410s > 
410s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
410s > # A 1x1 matrix
410s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
410s > for (mode in c("logical", "integer", "double")) {
410s +   x <- matrix(0, nrow = 1L, ncol = 1L)
410s +   cat("mode: ", mode, "\n", sep = "")
410s +   storage.mode(x) <- mode
410s +   str(x)
410s + 
410s +   # To check dimnames attribute
410s +   dimnames <- list("a", "A")
410s +   
410s +   # Test with and without dimnames on x
410s +   for (setDimnames in c(TRUE, FALSE)) {
410s +     if (setDimnames) dimnames(x) <- dimnames
410s +     else dimnames(x) <- NULL    
410s +     # Check names attribute
410s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
410s +       r0 <- rowCummins_R(x, useNames = useNames)
410s +       r1 <- rowCummins(x, useNames = useNames)
410s +       r2 <- t(colCummins(t(x), useNames = useNames))
410s +       stopifnot(all.equal(r1, r2))
410s +       stopifnot(all.equal(r1, r0))
410s +       stopifnot(all.equal(r2, r0))
410s +       
410s +       r0 <- rowCummaxs_R(x, useNames = useNames)
410s +       r1 <- rowCummaxs(x, useNames = useNames)
410s +       r2 <- t(colCummaxs(t(x), useNames = useNames))
410s +       stopifnot(all.equal(r1, r2))
410s +       stopifnot(all.equal(r1, r0))
410s +       stopifnot(all.equal(r2, r0))
410s +     } # for (useNames ...)
410s +   } # for (setDimnames ...)
410s + } # for (mode ...)
410s mode: logical
410s  logi [1, 1] FALSE
410s mode: integer
410s  int [1, 1] 0
410s mode: double
410s  num [1, 1] 0
410s > 
410s > 
410s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
410s > # Corner cases
410s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
410s > for (mode in c("logical", "integer", "double")) {
410s +   cat("mode: ", mode, "\n", sep = "")
410s +   value <- 0
410s +   storage.mode(value) <- mode
410s +   value0 <- if (mode == "logical") 0L else value
410s + 
410s +   # A 0x0 matrix
410s +   x <- matrix(value, nrow = 0L, ncol = 0L)
410s +   str(x)
410s +   r0 <- matrix(value0, nrow = nrow(x), ncol = ncol(x))
410s +   r1 <- rowCummins(x)
410s +   r2 <- t(colCummins(t(x)))
410s +   stopifnot(all.equal(r1, r2))
410s +   stopifnot(all.equal(r1, r0))
410s +   stopifnot(all.equal(r2, r0))
410s + 
410s +   # A 0xK matrix
410s +   x <- matrix(value, nrow = 0L, ncol = 5L)
410s +   str(x)
410s +   colnames <- LETTERS[1:5]
410s +   # Test with and without dimnames on x
410s +   for (setDimnames in c(TRUE, FALSE)) {
410s +     if (setDimnames) colnames(x) <- colnames
410s +     else dimnames(x) <- NULL
410s +     # Check names attribute
410s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
410s +       r0 <- rowCummins_R(x, useNames = useNames)
410s +       r1 <- rowCummins(x, useNames = useNames)
410s +       r2 <- t(colCummins(t(x), useNames = useNames))
410s +       stopifnot(all.equal(r1, r2))
410s +       stopifnot(all.equal(r1, r0))
410s +       stopifnot(all.equal(r2, r0))
410s +       r0 <- rowCummaxs_R(x, useNames = useNames)
410s +       r1 <- rowCummaxs(x, useNames = useNames)
410s +       r2 <- t(colCummaxs(t(x), useNames = useNames))
410s +       stopifnot(all.equal(r1, r2))
410s +       stopifnot(all.equal(r1, r0))
410s +       stopifnot(all.equal(r2, r0))
410s +     } # for (useNames ...)
410s +   } # for (setDimnames ...)
410s + 
410s +   # A Nx0 matrix
410s +   x <- matrix(value, nrow = 5L, ncol = 0L)
410s +   str(x)
410s +   rownames <- LETTERS[1:5]
410s +   # Test with and without dimnames on x
410s +   for (setDimnames in c(TRUE, FALSE)) {
410s +     if (setDimnames) rownames(x) <- rownames
410s +     else dimnames(x) <- NULL
410s +     # Check names attribute
410s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
410s +       r0 <- rowCummins_R(x, useNames = useNames)
410s +       r1 <- rowCummins(x, useNames = useNames)
410s +       r2 <- t(colCummins(t(x), useNames = useNames))
410s +       stopifnot(all.equal(r1, r2))
410s +       stopifnot(all.equal(r1, r0))
410s +       stopifnot(all.equal(r2, r0))
410s +       
410s +       r0 <- rowCummaxs_R(x, useNames = useNames)
410s +       r1 <- rowCummaxs(x, useNames = useNames)
410s +       r2 <- t(colCummaxs(t(x), useNames = useNames))
410s +       stopifnot(all.equal(r1, r2))
410s +       stopifnot(all.equal(r1, r0))
410s +       stopifnot(all.equal(r2, r0))
410s +     } # for (useNames ...)
410s +   } # for (setDimnames ...)
410s + } # for (mode ...)
410s mode: logical
410s  logi[0 , 0 ] 
410s  logi[0 , 1:5] 
410s  logi[1:5, 0 ] 
410s mode: integer
410s  int[0 , 0 ] 
410s  int[0 , 1:5] 
410s  int[1:5, 0 ] 
410s mode: double
410s  num[0 , 0 ] 
410s  num[0 , 1:5] 
410s  num[1:5, 0 ] 
410s > 
410s 
410s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
410s Copyright (C) 2024 The R Foundation for Statistical Computing
410s Platform: arm-unknown-linux-gnueabihf (32-bit)
410s 
410s R is free software and comes with ABSOLUTELY NO WARRANTY.
410s You are welcome to redistribute it under certain conditions.
410s Type 'license()' or 'licence()' for distribution details.
410s 
410s R is a collaborative project with many contributors.
410s Type 'contributors()' for more information and
410s 'citation()' on how to cite R or R packages in publications.
410s 
410s Type 'demo()' for some demos, 'help()' for on-line help, or
410s 'help.start()' for an HTML browser interface to help.
410s Type 'q()' to quit R.
410s 
410s > library("matrixStats")
410s > 
410s > rowCummins_R <- function(x, ..., useNames = NA) {
410s +   suppressWarnings({
410s +     y <- t(apply(x, MARGIN = 1L, FUN = cummin))
410s +   })
410s +   
410s +   # Preserve dimnames attribute?
410s +   dim(y) <- dim(x)
410s +   dimnames(y) <- if (isTRUE(useNames)) dimnames(x) else NULL
410s +   
410s +   y
410s + }
410s > 
410s > rowCummaxs_R <- function(x, ..., useNames = NA) {
410s +   mode <- storage.mode(x)
410s +   # Change mode because a bug is detected on cummax for integer in R-3.2.0
410s +   storage.mode(x) <- "numeric"
410s +   suppressWarnings({
410s +     y <- t(apply(x, MARGIN = 1L, FUN = cummax))
410s +   })
410s +   
410s +   # Preserve dimnames attribute?
410s +   dim(y) <- dim(x)
410s +   dimnames(y) <- if (isTRUE(useNames)) dimnames(x) else NULL
410s +   
410s +   storage.mode(y) <- mode
410s +   y
410s + }
410s > 
410s > 
410s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
410s > # Subsetted tests
410s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
410s > source("utils/validateIndicesFramework.R")
410s > x <- matrix(runif(6 * 6, min = -3, max = 3), nrow = 6, ncol = 6)
410s > storage.mode(x) <- "integer"
410s > 
410s > # To check dimnames attribute
410s > dimnames <- list(letters[1:6], LETTERS[1:6])
410s > 
410s > # Test with and without dimnames on x
410s > for (setDimnames in c(TRUE, FALSE)) {
410s +   if (setDimnames) dimnames(x) <- dimnames
410s +   else dimnames(x) <- NULL
410s +   for (rows in index_cases) {
410s +     for (cols in index_cases) {
410s +       # Check names attribute
410s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
410s +         validateIndicesTestMatrix(x, rows, cols,
410s +                                   ftest = rowCummins, fsure = rowCummins_R, useNames = useNames,verbose=TRUE)
410s +         validateIndicesTestMatrix(x, rows, cols,
410s +                                   ftest = function(x, rows, cols, ..., useNames) {
410s +           t(colCummins(t(x), rows = cols, cols = rows, useNames = useNames))
410s +         }, fsure = rowCummins_R, useNames = useNames)
410s + 
410s +         validateIndicesTestMatrix(x, rows, cols,
410s +                                   ftest = rowCummaxs, fsure = rowCummaxs_R, useNames = useNames)
410s +         validateIndicesTestMatrix(x, rows, cols,
410s +                                   ftest = function(x, rows, cols, ..., useNames) {
410s +           t(colCummaxs(t(x), rows = cols, cols = rows, useNames = useNames))
410s +         }, fsure = rowCummaxs_R, useNames = useNames)
410s +       }
410s +     }
410s +   }
410s + }
417s > 
417s 
417s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
417s Copyright (C) 2024 The R Foundation for Statistical Computing
417s Platform: arm-unknown-linux-gnueabihf (32-bit)
417s 
417s R is free software and comes with ABSOLUTELY NO WARRANTY.
417s You are welcome to redistribute it under certain conditions.
417s Type 'license()' or 'licence()' for distribution details.
417s 
417s R is a collaborative project with many contributors.
417s Type 'contributors()' for more information and
417s 'citation()' on how to cite R or R packages in publications.
417s 
417s Type 'demo()' for some demos, 'help()' for on-line help, or
417s 'help.start()' for an HTML browser interface to help.
417s Type 'q()' to quit R.
417s 
418s > library("matrixStats")
418s > 
418s > rowCumprods_R <- function(x, ..., useNames = NA) {
418s +   suppressWarnings({
418s +     y <- t(apply(x, MARGIN = 1L, FUN = cumprod))
418s +   })
418s +   
418s +   # Preserve dimnames attribute?
418s +   dim(y) <- dim(x)
418s +   dimnames(y) <- if (isTRUE(useNames)) dimnames(x) else NULL
418s +   
418s +   y
418s + }
418s > 
418s > 
418s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
418s > # With and without some NAs
418s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
418s > for (mode in c("logical", "integer", "double")) {
418s +   for (add_na in c(FALSE, TRUE)) {
418s +     cat("add_na = ", add_na, "\n", sep = "")
418s + 
418s +     x <- matrix(1:50, nrow = 10L, ncol = 5L)
418s +     if (add_na) {
418s +       x[3:7, c(2, 4)] <- NA_real_
418s +     }
418s +     cat("mode: ", mode, "\n", sep = "")
418s +     storage.mode(x) <- mode
418s +     str(x)
418s +     
418s +     # To check dimnames attribute
418s +     dimnames <- list(letters[1:10], LETTERS[1:5])
418s +     
418s +     # Test with and without dimnames on x
418s +     for (setDimnames in c(TRUE, FALSE)) {
418s +       if (setDimnames) dimnames(x) <- dimnames
418s +       else dimnames(x) <- NULL    
418s +       # Check names attribute
418s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
418s +         # Row/column ranges
418s +         r0 <- rowCumprods_R(x, useNames = useNames)
418s +         r1 <- rowCumprods(x, useNames = useNames)
418s +         r2 <- t(colCumprods(t(x), useNames = useNames))
418s +         stopifnot(all.equal(r1, r2))
418s +         stopifnot(all.equal(r1, r0))
418s +         stopifnot(all.equal(r2, r0))
418s +       } # for (useNames ...)
418s +     } # for (setDimnames ...)
418s +   } # for (add_na ...)
418s + } # for (mode ...)
418s add_na = FALSE
418s mode: logical
418s  logi [1:10, 1:5] TRUE TRUE TRUE TRUE TRUE TRUE ...
418s add_na = TRUE
418s mode: logical
418s  logi [1:10, 1:5] TRUE TRUE TRUE TRUE TRUE TRUE ...
418s add_na = FALSE
418s mode: integer
418s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
418s add_na = TRUE
418s mode: integer
418s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
418s add_na = FALSE
418s mode: double
418s  num [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
418s add_na = TRUE
418s mode: double
418s  num [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
418s > 
418s > 
418s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
418s > # All NAs
418s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
418s > for (mode in c("logical", "integer", "double")) {
418s +   x <- matrix(NA_real_, nrow = 10L, ncol = 5L)
418s +   cat("mode: ", mode, "\n", sep = "")
418s +   storage.mode(x) <- mode
418s +   str(x)
418s +   
418s +   # Test with and without dimnames on x
418s +   for (setDimnames in c(TRUE, FALSE)) {
418s +     if (setDimnames) dimnames(x) <- dimnames
418s +     else dimnames(x) <- NULL    
418s +     # Check names attribute
418s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
418s +       # Row/column ranges
418s +       r0 <- rowCumprods_R(x, useNames = useNames)
418s +       r1 <- rowCumprods(x, useNames = useNames)
418s +       r2 <- t(colCumprods(t(x), useNames = useNames))
418s +       stopifnot(all.equal(r1, r2))
418s +       stopifnot(all.equal(r1, r0))
418s +       stopifnot(all.equal(r2, r0))
418s +     } # for (useNames ...)
418s +   } # for (setDimnames ...)
418s + } # for (mode ...)
418s mode: logical
418s  logi [1:10, 1:5] NA NA NA NA NA NA ...
418s mode: integer
418s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
418s mode: double
418s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
418s > 
418s > 
418s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
418s > # A 1x1 matrix
418s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
418s > for (mode in c("logical", "integer", "double")) {
418s +   x <- matrix(0, nrow = 1L, ncol = 1L)
418s +   cat("mode: ", mode, "\n", sep = "")
418s +   storage.mode(x) <- mode
418s +   str(x)
418s +   
418s +   dimnames <- list("a", "A")
418s +   # Test with and without dimnames on x
418s +   for (setDimnames in c(TRUE, FALSE)) {
418s +     if (setDimnames) dimnames(x) <- dimnames
418s +     else dimnames(x) <- NULL    
418s +     # Check names attribute
418s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
418s +       # Row/column ranges
418s +       r0 <- rowCumprods_R(x, useNames = useNames)
418s +       r1 <- rowCumprods(x, useNames = useNames)
418s +       r2 <- t(colCumprods(t(x), useNames = useNames))
418s +       stopifnot(all.equal(r1, r2))
418s +       stopifnot(all.equal(r1, r0))
418s +       stopifnot(all.equal(r2, r0))
418s +     } # for (useNames ...)
418s +   } # for (setDimnames ...)
418s + }
418s mode: logical
418s  logi [1, 1] FALSE
418s mode: integer
418s  int [1, 1] 0
418s mode: double
418s  num [1, 1] 0
418s > 
418s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
418s > # BUG FIX TEST: Assert zeros don't trump NAs in integer matrices
418s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
418s > for (mode in c("logical", "integer", "double")) {
418s +   x <- matrix(NA_real_, nrow = 3L, ncol = 2L)
418s +   x[1, 2] <- 0
418s +   x[2, 2] <- 1
418s +   x[3, 1] <- 0
418s +   storage.mode(x) <- mode
418s +   cat("mode: ", mode, "\n", sep = "")
418s +   str(x)
418s +   
418s +   dimnames <- list(letters[1:3], LETTERS[1:2])
418s +   # Test with and without dimnames on x
418s +   for (setDimnames in c(TRUE, FALSE)) {
418s +     if (setDimnames) dimnames(x) <- dimnames
418s +     else dimnames(x) <- NULL    
418s +     # Check names attribute
418s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
418s +       # Row/column ranges
418s +       r0 <- rowCumprods_R(x, useNames = useNames)
418s +       r1 <- rowCumprods(x, useNames = useNames)
418s +       r2 <- t(colCumprods(t(x), useNames = useNames))
418s +       stopifnot(all.equal(r1, r2))
418s +       stopifnot(all.equal(r1, r0))
418s +       stopifnot(all.equal(r2, r0))
418s +     } # for (useNames ...)
418s +   } # for (setDimnames ...)
418s + }
418s mode: logical
418s  logi [1:3, 1:2] NA NA FALSE FALSE TRUE NA
418s mode: integer
418s  int [1:3, 1:2] NA NA 0 0 1 NA
418s mode: double
418s  num [1:3, 1:2] NA NA 0 0 1 NA
418s > 
418s > 
418s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
418s > # Corner cases
418s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
418s > for (mode in c("logical", "integer", "double")) {
418s +   cat("mode: ", mode, "\n", sep = "")
418s +   value <- 0
418s +   storage.mode(value) <- mode
418s +   if (mode == "logical") value2 <- 0L
418s + 
418s +   # A 0x0 matrix
418s +   x <- matrix(value, nrow = 0L, ncol = 0L)
418s +   str(x)
418s +   r0 <- matrix(value2, nrow = nrow(x), ncol = ncol(x))
418s +   r1 <- rowCumprods(x)
418s +   r2 <- t(colCumprods(t(x)))
418s +   stopifnot(all.equal(r1, r2))
418s +   stopifnot(all.equal(r1, r0))
418s +   stopifnot(all.equal(r2, r0))
418s + 
418s +   # A 0xK matrix
418s +   x <- matrix(value, nrow = 0L, ncol = 5L)
418s +   str(x)
418s +   colnames <- LETTERS[1:5]
418s +   # Test with and without dimnames on x
418s +   for (setDimnames in c(TRUE, FALSE)) {
418s +     if (setDimnames) colnames(x) <- colnames
418s +     else dimnames(x) <- NULL
418s +     # Check names attribute
418s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
418s +       r0 <- rowCumprods_R(x, useNames = useNames)
418s +       r1 <- rowCumprods(x, useNames = useNames)
418s +       r2 <- t(rowCumprods(t(x), useNames = useNames))
418s +       stopifnot(all.equal(r1, r2))
418s +       stopifnot(all.equal(r1, r0))
418s +       stopifnot(all.equal(r2, r0))
418s +     } # for (useNames ...)
418s +   } # for (setDimnames ...)
418s + 
418s +   # A Nx0 matrix
418s +   x <- matrix(value, nrow = 5L, ncol = 0L)
418s +   str(x)
418s +   rownames <- LETTERS[1:5]
418s +   # Test with and without dimnames on x
418s +   for (setDimnames in c(TRUE, FALSE)) {
418s +     if (setDimnames) rownames(x) <- rownames
418s +     else dimnames(x) <- NULL
418s +     # Check names attribute
418s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
418s +       r0 <- rowCumprods_R(x, useNames = useNames)
418s +       r1 <- rowCumprods(x, useNames = useNames)
418s +       r2 <- t(rowCumprods(t(x), useNames = useNames))
418s +       stopifnot(all.equal(r1, r2))
418s +       stopifnot(all.equal(r1, r0))
418s +       stopifnot(all.equal(r2, r0))
418s +     } # for (useNames ...)
418s +   } # for (setDimnames ...)
418s + } # for (mode ...)
418s mode: logical
418s  logi[0 , 0 ] 
418s  logi[0 , 1:5] 
418s  logi[1:5, 0 ] 
418s mode: integer
418s  int[0 , 0 ] 
418s  int[0 , 1:5] 
418s  int[1:5, 0 ] 
418s mode: double
418s  num[0 , 0 ] 
418s  num[0 , 1:5] 
418s  num[1:5, 0 ] 
418s > 
418s 
418s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
418s Copyright (C) 2024 The R Foundation for Statistical Computing
418s Platform: arm-unknown-linux-gnueabihf (32-bit)
418s 
418s R is free software and comes with ABSOLUTELY NO WARRANTY.
418s You are welcome to redistribute it under certain conditions.
418s Type 'license()' or 'licence()' for distribution details.
418s 
418s R is a collaborative project with many contributors.
418s Type 'contributors()' for more information and
418s 'citation()' on how to cite R or R packages in publications.
418s 
418s Type 'demo()' for some demos, 'help()' for on-line help, or
418s 'help.start()' for an HTML browser interface to help.
418s Type 'q()' to quit R.
418s 
419s > library("matrixStats")
419s > 
419s > rowCumprods_R <- function(x, ..., useNames = NA) {
419s +   suppressWarnings({
419s +     y <- t(apply(x, MARGIN = 1L, FUN = cumprod))
419s +   })
419s + 
419s +   # Preserve dimnames attribute?
419s +   dim(y) <- dim(x)
419s +   dimnames(y) <- if (isTRUE(useNames)) dimnames(x) else NULL
419s +   
419s +   y
419s + }
419s > 
419s > 
419s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
419s > # Subsetted tests
419s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
419s > source("utils/validateIndicesFramework.R")
419s > x <- matrix(runif(6 * 6, min = -3, max = 3), nrow = 6, ncol = 6)
419s > storage.mode(x) <- "integer"
419s > 
419s > # To check dimnames attribute
419s > dimnames <- list(letters[1:6], LETTERS[1:6])
419s > 
419s > # Test with and without dimnames on x
419s > for (setDimnames in c(TRUE, FALSE)) {
419s +   if (setDimnames) dimnames(x) <- dimnames
419s +   else dimnames(x) <- NULL
419s +   for (rows in index_cases) {
419s +     for (cols in index_cases) {
419s +       # Check names attribute
419s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
419s +         validateIndicesTestMatrix(x, rows, cols,
419s +                                   ftest = rowCumprods, fsure = rowCumprods_R, useNames = useNames)
419s +         validateIndicesTestMatrix(x, rows, cols,
419s +                                   ftest = function(x, rows, cols, ..., useNames) {
419s +           t(colCumprods(t(x), rows = cols, cols = rows, useNames = useNames))
419s +         }, fsure = rowCumprods_R, useNames = useNames)
419s +       }
419s +     }
419s +   }
419s + }
422s > 
422s 
422s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
422s Copyright (C) 2024 The R Foundation for Statistical Computing
422s Platform: arm-unknown-linux-gnueabihf (32-bit)
422s 
422s R is free software and comes with ABSOLUTELY NO WARRANTY.
422s You are welcome to redistribute it under certain conditions.
422s Type 'license()' or 'licence()' for distribution details.
422s 
422s R is a collaborative project with many contributors.
422s Type 'contributors()' for more information and
422s 'citation()' on how to cite R or R packages in publications.
422s 
422s Type 'demo()' for some demos, 'help()' for on-line help, or
422s 'help.start()' for an HTML browser interface to help.
422s Type 'q()' to quit R.
422s 
422s > library("matrixStats")
422s > 
422s > rowCumsums_R <- function(x, ..., useNames = NA) {
422s +   suppressWarnings({
422s +     y <- t(apply(x, MARGIN = 1L, FUN = cumsum))
422s +   })
422s +   
422s +   # Preserve dimnames attribute?
422s +   dim(y) <- dim(x)
422s +   dimnames(y) <- if (isTRUE(useNames)) dimnames(x) else NULL
422s +   
422s +   y
422s + }
422s > 
422s > 
422s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
422s > # With and without some NAs
422s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
422s > dimnames <- list(letters[1:10], LETTERS[1:5]) # to check dimnames attribute
422s > for (mode in c("logical", "integer", "double")) {
422s +   for (add_na in c(FALSE, TRUE)) {
422s +     cat("add_na = ", add_na, "\n", sep = "")
422s + 
422s +     x <- matrix(1:50, nrow = 10L, ncol = 5L)
422s +     if (add_na) {
422s +       x[3:7, c(2, 4)] <- NA_real_
422s +     }
422s +     cat("mode: ", mode, "\n", sep = "")
422s +     storage.mode(x) <- mode
422s +     str(x)
422s +     
422s +     # Test with and without dimnames on x
422s +     for (setDimnames in c(TRUE, FALSE)) {
422s +       if (setDimnames) dimnames(x) <- dimnames
422s +       else dimnames(x) <- NULL    
422s +       # Check names attribute
422s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
422s +         # Row/column ranges
422s +         r0 <- rowCumsums_R(x, useNames = useNames)
422s +         r1 <- rowCumsums(x, useNames = useNames)
422s +         r2 <- t(colCumsums(t(x), useNames = useNames))
422s +         stopifnot(all.equal(r1, r2))
422s +         stopifnot(all.equal(r1, r0))
422s +         stopifnot(all.equal(r2, r0))
422s +       } # for (useNames ...)
422s +     } # for (setDimnames ...)
422s +   } # for (add_na ...)
422s + }
422s add_na = FALSE
422s mode: logical
422s  logi [1:10, 1:5] TRUE TRUE TRUE TRUE TRUE TRUE ...
422s add_na = TRUE
422s mode: logical
422s  logi [1:10, 1:5] TRUE TRUE TRUE TRUE TRUE TRUE ...
422s add_na = FALSE
422s mode: integer
422s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
422s add_na = TRUE
422s mode: integer
422s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
422s add_na = FALSE
422s mode: double
422s  num [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
422s add_na = TRUE
422s mode: double
422s  num [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
422s > 
422s > 
422s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
422s > # All NAs
422s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
422s > for (mode in c("logical", "integer", "double")) {
422s +   x <- matrix(NA_real_, nrow = 10L, ncol = 5L)
422s +   cat("mode: ", mode, "\n", sep = "")
422s +   storage.mode(x) <- mode
422s +   str(x)
422s +   
422s +   # Test with and without dimnames on x
422s +   for (setDimnames in c(TRUE, FALSE)) {
422s +     if (setDimnames) dimnames(x) <- dimnames
422s +     else dimnames(x) <- NULL    
422s +     # Check names attribute
422s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
422s +       # Row/column ranges
422s +       r0 <- rowCumsums_R(x, useNames = useNames)
422s +       r1 <- rowCumsums(x, useNames = useNames)
422s +       r2 <- t(colCumsums(t(x), useNames = useNames))
422s +       stopifnot(all.equal(r1, r2))
422s +       stopifnot(all.equal(r1, r0))
422s +       stopifnot(all.equal(r2, r0))
422s +     } # for (useNames ...)
422s +   } # for (setDimnames ...)
422s + } # for (mode ...)
423s mode: logical
423s  logi [1:10, 1:5] NA NA NA NA NA NA ...
423s mode: integer
423s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
423s mode: double
423s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
423s > 
423s > 
423s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
423s > # A 1x1 matrix
423s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
423s > dimnames <- list("a", "A") # to check dimnames attribute
423s > for (mode in c("logical", "integer", "double")) {
423s +   x <- matrix(0, nrow = 1L, ncol = 1L)
423s +   cat("mode: ", mode, "\n", sep = "")
423s +   storage.mode(x) <- mode
423s +   str(x)
423s + 
423s +   r0 <- rowCumsums_R(x)
423s +   r1 <- rowCumsums(x)
423s +   r2 <- t(colCumsums(t(x)))
423s +   stopifnot(all.equal(r1, r2))
423s +   stopifnot(all.equal(r1, r0))
423s +   stopifnot(all.equal(r2, r0))
423s +   
423s +   # Check dimnames attribute
423s +   dimnames(x) <- dimnames
423s +   # r0 <- rowCumsums_R(x)
423s +   # > r0
423s +   #        a
423s +   #   [1,] 0
423s +   r1 <- rowCumsums(x, useNames = TRUE)
423s +   r2 <- t(colCumsums(t(x), useNames = TRUE))
423s +   stopifnot(identical(dimnames(r1), dimnames))
423s +   stopifnot(identical(dimnames(r2), dimnames))    
423s +   dimnames(x) <- NULL
423s + }
423s mode: logical
423s  logi [1, 1] FALSE
423s mode: integer
423s  int [1, 1] 0
423s mode: double
423s  num [1, 1] 0
423s > 
423s > 
423s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
423s > # Corner cases
423s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
423s > names <- LETTERS[1:5] # to check dimnames attribute
423s > for (mode in c("logical", "integer", "double")) {
423s +   cat("mode: ", mode, "\n", sep = "")
423s +   value <- 0
423s +   storage.mode(value) <- mode
423s +   value2 <- value
423s +   if (mode == "logical") value2 <- 0L
423s +   
423s +   # A 0x0 matrix
423s +   x <- matrix(value, nrow = 0L, ncol = 0L)
423s +   str(x)
423s +   r0 <- matrix(value2, nrow = nrow(x), ncol = ncol(x))
423s +   r1 <- rowCumsums(x)
423s +   r2 <- t(colCumsums(t(x)))
423s +   stopifnot(all.equal(r1, r2))
423s +   stopifnot(all.equal(r1, r0))
423s +   stopifnot(all.equal(r2, r0))
423s + 
423s +   # A 0xK matrix
423s +   x <- matrix(value, nrow = 0L, ncol = 5L)
423s +   str(x)
423s +   colnames <- LETTERS[1:5]
423s +   # Test with and without dimnames on x
423s +   for (setDimnames in c(TRUE, FALSE)) {
423s +     if (setDimnames) colnames(x) <- colnames
423s +     else dimnames(x) <- NULL
423s +     # Check names attribute
423s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
423s +       r0 <- rowCumsums_R(x, useNames = useNames)
423s +       r1 <- rowCumsums(x, useNames = useNames)
423s +       r2 <- t(rowCumsums(t(x), useNames = useNames))
423s +       stopifnot(all.equal(r1, r2))
423s +       stopifnot(all.equal(r1, r0))
423s +       stopifnot(all.equal(r2, r0))
423s +     } # for (useNames ...)
423s +   } # for (setDimnames ...)
423s + 
423s +   # A Nx0 matrix
423s +   x <- matrix(value, nrow = 5L, ncol = 0L)
423s +   str(x)
423s +   rownames <- LETTERS[1:5]
423s +   # Test with and without dimnames on x
423s +   for (setDimnames in c(TRUE, FALSE)) {
423s +     if (setDimnames) rownames(x) <- rownames
423s +     else dimnames(x) <- NULL
423s +     # Check names attribute
423s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
423s +       r0 <- rowCumsums_R(x, useNames = useNames)
423s +       r1 <- rowCumsums(x, useNames = useNames)
423s +       r2 <- t(rowCumsums(t(x), useNames = useNames))
423s +       stopifnot(all.equal(r1, r2))
423s +       stopifnot(all.equal(r1, r0))
423s +       stopifnot(all.equal(r2, r0))
423s +     } # for (useNames ...)
423s +   } # for (setDimnames ...)
423s + } # for (mode ...)
423s mode: logical
423s  logi[0 , 0 ] 
423s  logi[0 , 1:5] 
423s  logi[1:5, 0 ] 
423s mode: integer
423s  int[0 , 0 ] 
423s  int[0 , 1:5] 
423s  int[1:5, 0 ] 
423s mode: double
423s  num[0 , 0 ] 
423s  num[0 , 1:5] 
423s  num[1:5, 0 ] 
423s > 
423s 
423s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
423s Copyright (C) 2024 The R Foundation for Statistical Computing
423s Platform: arm-unknown-linux-gnueabihf (32-bit)
423s 
423s R is free software and comes with ABSOLUTELY NO WARRANTY.
423s You are welcome to redistribute it under certain conditions.
423s Type 'license()' or 'licence()' for distribution details.
423s 
423s R is a collaborative project with many contributors.
423s Type 'contributors()' for more information and
423s 'citation()' on how to cite R or R packages in publications.
423s 
423s Type 'demo()' for some demos, 'help()' for on-line help, or
423s 'help.start()' for an HTML browser interface to help.
423s Type 'q()' to quit R.
423s 
423s > library("matrixStats")
423s > 
423s > rowCumsums_R <- function(x, ..., useNames = NA) {
423s +   suppressWarnings({
423s +     y <- t(apply(x, MARGIN = 1L, FUN = cumsum))
423s +   })
423s +   
423s +   # Preserve dimnames attribute?
423s +   dim(y) <- dim(x)
423s +   dimnames(y) <- if (isTRUE(useNames)) dimnames(x) else NULL
423s + 
423s +   y
423s + }
423s > 
423s > 
423s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
423s > # Subsetted tests
423s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
423s > source("utils/validateIndicesFramework.R")
423s > x <- matrix(runif(6 * 6, min = -3, max = 3), nrow = 6, ncol = 6)
423s > storage.mode(x) <- "integer"
423s > 
423s > # To check dimnames attribute
423s > dimnames <- list(letters[1:6], LETTERS[1:6])
423s > 
423s > # Test with and without dimnames on x
423s > for (setDimnames in c(TRUE, FALSE)) {
423s +   if (setDimnames) dimnames(x) <- dimnames
423s +   else dimnames(x) <- NULL
423s +   for (rows in index_cases) {
423s +     for (cols in index_cases) {
423s +       # Check names attribute
423s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
423s +         validateIndicesTestMatrix(x, rows, cols,
423s +                                   ftest = rowCumsums, fsure = rowCumsums_R, useNames = useNames)
423s +         validateIndicesTestMatrix(x, rows, cols,
423s +                                   ftest = function(x, rows, cols, ..., useNames) {
423s +           t(colCumsums(t(x), rows = cols, cols = rows, useNames = useNames))
423s +         }, fsure = rowCumsums_R, useNames = useNames)
423s +       }
423s +     }
423s +   }
423s + }
426s > 
426s 
426s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
426s Copyright (C) 2024 The R Foundation for Statistical Computing
426s Platform: arm-unknown-linux-gnueabihf (32-bit)
426s 
426s R is free software and comes with ABSOLUTELY NO WARRANTY.
426s You are welcome to redistribute it under certain conditions.
426s Type 'license()' or 'licence()' for distribution details.
426s 
426s R is a collaborative project with many contributors.
426s Type 'contributors()' for more information and
426s 'citation()' on how to cite R or R packages in publications.
426s 
426s Type 'demo()' for some demos, 'help()' for on-line help, or
426s 'help.start()' for an HTML browser interface to help.
426s Type 'q()' to quit R.
426s 
427s > library("matrixStats")
427s > 
427s > rowDiffs_R <- function(x, lag = 1L, differences = 1L, ..., useNames = NA) {
427s +   ncol2 <- ncol(x) - lag * differences
427s +   if (ncol2 <= 0) {
427s +     y <- matrix(x[integer(0L)], nrow = nrow(x), ncol = 0L)
427s +     # Preserve names attribute
427s +     if (isTRUE(useNames) && !is.null(rownames(x))) rownames(y) <- rownames(x)
427s +     return(y)
427s +   }
427s +   suppressWarnings({
427s +     y <- apply(x, MARGIN = 1L, FUN = diff, lag = lag, differences = differences)
427s +   })
427s +   y <- t(y)
427s +   
427s +   # Preserve dimnames attribute
427s +   dim(y) <- c(nrow(x), ncol2)
427s +   if (isTRUE(useNames) && !is.null(dimnames(x))) {
427s +     colnames <- colnames(x)
427s +     if (!is.null(colnames)) {
427s +       len <- length(colnames)
427s +       colnames <- colnames[(len - ncol2 + 1):len]
427s +     }
427s +     dimnames(y) <- list(rownames(x), colnames)      
427s +   }
427s +   else dimnames(y) <- NULL
427s +   
427s +   y
427s + }
427s > 
427s > 
427s > set.seed(0x42)
427s > 
427s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
427s > # With and without some NAs
427s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
427s > for (mode in c("integer", "double")) {
427s +   cat("mode: ", mode, "\n", sep = "")
427s + 
427s +   for (add_na in c(FALSE, TRUE)) {
427s +     cat("add_na = ", add_na, "\n", sep = "")
427s + 
427s +     x <- matrix(sample(10 * 8) + 0.1, nrow = 10L, ncol = 8L)
427s +     if (add_na) {
427s +       x[3:7, c(2, 4)] <- NA_real_
427s +     }
427s +     storage.mode(x) <- mode
427s +     str(x)
427s +     
427s +     dimnames <- list(letters[1:10], LETTERS[1:8])
427s + 
427s +     # Test with and without dimnames on x
427s +     for (setDimnames in c(TRUE, FALSE)) {
427s +       if (setDimnames) dimnames(x) <- dimnames
427s +       else dimnames(x) <- NULL
427s +       # Check dimnames attribute
427s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
427s +         for (lag in 1:4) {
427s +           for (differences in 1:3) {
427s +             cat(sprintf("mode: %s, lag = %d, differences = %d\n",
427s +                         mode, lag, differences))
427s +             # Row/column ranges
427s +             r0 <- rowDiffs_R(x, lag = lag, differences = differences, useNames = useNames)
427s +             r1 <- rowDiffs(x, lag = lag, differences = differences, useNames = useNames)
427s +             r2 <- t(colDiffs(t(x), lag = lag, differences = differences, useNames = useNames))
427s +             stopifnot(all.equal(r1, r0))
427s +             stopifnot(all.equal(r2, r0))
427s +             stopifnot(all.equal(r1, r2))
427s +           }
427s +         }
427s +       } # for (useNames ...)
427s +     } # for (setDimnames ...)
427s +   } # for (add_na ...)
427s + } # for (mode ...)
427s mode: integer
427s add_na = FALSE
427s  int [1:10, 1:8] 68 26 29 47 48 10 1 38 16 40 ...
427s mode: integer, lag = 1, differences = 1
427s mode: integer, lag = 1, differences = 2
427s mode: integer, lag = 1, differences = 3
427s mode: integer, lag = 2, differences = 1
427s mode: integer, lag = 2, differences = 2
427s mode: integer, lag = 2, differences = 3
427s mode: integer, lag = 3, differences = 1
427s mode: integer, lag = 3, differences = 2
427s mode: integer, lag = 3, differences = 3
427s mode: integer, lag = 4, differences = 1
427s mode: integer, lag = 4, differences = 2
427s mode: integer, lag = 4, differences = 3
427s mode: integer, lag = 1, differences = 1
427s mode: integer, lag = 1, differences = 2
427s mode: integer, lag = 1, differences = 3
427s mode: integer, lag = 2, differences = 1
427s mode: integer, lag = 2, differences = 2
427s mode: integer, lag = 2, differences = 3
427s mode: integer, lag = 3, differences = 1
427s mode: integer, lag = 3, differences = 2
427s mode: integer, lag = 3, differences = 3
427s mode: integer, lag = 4, differences = 1
427s mode: integer, lag = 4, differences = 2
427s mode: integer, lag = 4, differences = 3
427s mode: integer, lag = 1, differences = 1
427s mode: integer, lag = 1, differences = 2
427s mode: integer, lag = 1, differences = 3
427s mode: integer, lag = 2, differences = 1
427s mode: integer, lag = 2, differences = 2
427s mode: integer, lag = 2, differences = 3
427s mode: integer, lag = 3, differences = 1
427s mode: integer, lag = 3, differences = 2
427s mode: integer, lag = 3, differences = 3
427s mode: integer, lag = 4, differences = 1
427s mode: integer, lag = 4, differences = 2
427s mode: integer, lag = 4, differences = 3
427s mode: integer, lag = 1, differences = 1
427s mode: integer, lag = 1, differences = 2
427s mode: integer, lag = 1, differences = 3
427s mode: integer, lag = 2, differences = 1
427s mode: integer, lag = 2, differences = 2
427s mode: integer, lag = 2, differences = 3
427s mode: integer, lag = 3, differences = 1
427s mode: integer, lag = 3, differences = 2
427s mode: integer, lag = 3, differences = 3
427s mode: integer, lag = 4, differences = 1
427s mode: integer, lag = 4, differences = 2
427s mode: integer, lag = 4, differences = 3
427s add_na = TRUE
427s  int [1:10, 1:8] 80 71 7 52 79 22 31 10 29 63 ...
427s mode: integer, lag = 1, differences = 1
427s mode: integer, lag = 1, differences = 2
427s mode: integer, lag = 1, differences = 3
427s mode: integer, lag = 2, differences = 1
427s mode: integer, lag = 2, differences = 2
427s mode: integer, lag = 2, differences = 3
427s mode: integer, lag = 3, differences = 1
427s mode: integer, lag = 3, differences = 2
427s mode: integer, lag = 3, differences = 3
427s mode: integer, lag = 4, differences = 1
427s mode: integer, lag = 4, differences = 2
427s mode: integer, lag = 4, differences = 3
427s mode: integer, lag = 1, differences = 1
427s mode: integer, lag = 1, differences = 2
427s mode: integer, lag = 1, differences = 3
427s mode: integer, lag = 2, differences = 1
427s mode: integer, lag = 2, differences = 2
427s mode: integer, lag = 2, differences = 3
427s mode: integer, lag = 3, differences = 1
427s mode: integer, lag = 3, differences = 2
427s mode: integer, lag = 3, differences = 3
427s mode: integer, lag = 4, differences = 1
427s mode: integer, lag = 4, differences = 2
427s mode: integer, lag = 4, differences = 3
427s mode: integer, lag = 1, differences = 1
427s mode: integer, lag = 1, differences = 2
427s mode: integer, lag = 1, differences = 3
427s mode: integer, lag = 2, differences = 1
427s mode: integer, lag = 2, differences = 2
427s mode: integer, lag = 2, differences = 3
427s mode: integer, lag = 3, differences = 1
427s mode: integer, lag = 3, differences = 2
427s mode: integer, lag = 3, differences = 3
427s mode: integer, lag = 4, differences = 1
427s mode: integer, lag = 4, differences = 2
427s mode: integer, lag = 4, differences = 3
427s mode: integer, lag = 1, differences = 1
427s mode: integer, lag = 1, differences = 2
427s mode: integer, lag = 1, differences = 3
427s mode: integer, lag = 2, differences = 1
427s mode: integer, lag = 2, differences = 2
427s mode: integer, lag = 2, differences = 3
427s mode: integer, lag = 3, differences = 1
427s mode: integer, lag = 3, differences = 2
427s mode: integer, lag = 3, differences = 3
427s mode: integer, lag = 4, differences = 1
427s mode: integer, lag = 4, differences = 2
427s mode: integer, lag = 4, differences = 3
427s mode: double
427s add_na = FALSE
427s  num [1:10, 1:8] 36.1 15.1 27.1 63.1 62.1 58.1 28.1 19.1 41.1 3.1 ...
427s mode: double, lag = 1, differences = 1
427s mode: double, lag = 1, differences = 2
427s mode: double, lag = 1, differences = 3
427s mode: double, lag = 2, differences = 1
427s mode: double, lag = 2, differences = 2
427s mode: double, lag = 2, differences = 3
427s mode: double, lag = 3, differences = 1
427s mode: double, lag = 3, differences = 2
427s mode: double, lag = 3, differences = 3
427s mode: double, lag = 4, differences = 1
427s mode: double, lag = 4, differences = 2
427s mode: double, lag = 4, differences = 3
427s mode: double, lag = 1, differences = 1
427s mode: double, lag = 1, differences = 2
427s mode: double, lag = 1, differences = 3
427s mode: double, lag = 2, differences = 1
427s mode: double, lag = 2, differences = 2
427s mode: double, lag = 2, differences = 3
427s mode: double, lag = 3, differences = 1
427s mode: double, lag = 3, differences = 2
427s mode: double, lag = 3, differences = 3
427s mode: double, lag = 4, differences = 1
427s mode: double, lag = 4, differences = 2
427s mode: double, lag = 4, differences = 3
427s mode: double, lag = 1, differences = 1
427s mode: double, lag = 1, differences = 2
427s mode: double, lag = 1, differences = 3
427s mode: double, lag = 2, differences = 1
427s mode: double, lag = 2, differences = 2
427s mode: double, lag = 2, differences = 3
427s mode: double, lag = 3, differences = 1
427s mode: double, lag = 3, differences = 2
427s mode: double, lag = 3, differences = 3
427s mode: double, lag = 4, differences = 1
427s mode: double, lag = 4, differences = 2
427s mode: double, lag = 4, differences = 3
427s mode: double, lag = 1, differences = 1
427s mode: double, lag = 1, differences = 2
427s mode: double, lag = 1, differences = 3
427s mode: double, lag = 2, differences = 1
427s mode: double, lag = 2, differences = 2
427s mode: double, lag = 2, differences = 3
427s mode: double, lag = 3, differences = 1
427s mode: double, lag = 3, differences = 2
427s mode: double, lag = 3, differences = 3
427s mode: double, lag = 4, differences = 1
427s mode: double, lag = 4, differences = 2
427s mode: double, lag = 4, differences = 3
427s add_na = TRUE
427s  num [1:10, 1:8] 67.1 80.1 45.1 8.1 39.1 66.1 27.1 71.1 47.1 46.1 ...
427s mode: double, lag = 1, differences = 1
427s mode: double, lag = 1, differences = 2
427s mode: double, lag = 1, differences = 3
427s mode: double, lag = 2, differences = 1
427s mode: double, lag = 2, differences = 2
427s mode: double, lag = 2, differences = 3
427s mode: double, lag = 3, differences = 1
427s mode: double, lag = 3, differences = 2
427s mode: double, lag = 3, differences = 3
427s mode: double, lag = 4, differences = 1
427s mode: double, lag = 4, differences = 2
427s mode: double, lag = 4, differences = 3
427s mode: double, lag = 1, differences = 1
427s mode: double, lag = 1, differences = 2
427s mode: double, lag = 1, differences = 3
427s mode: double, lag = 2, differences = 1
427s mode: double, lag = 2, differences = 2
427s mode: double, lag = 2, differences = 3
427s mode: double, lag = 3, differences = 1
427s mode: double, lag = 3, differences = 2
427s mode: double, lag = 3, differences = 3
427s mode: double, lag = 4, differences = 1
427s mode: double, lag = 4, differences = 2
427s mode: double, lag = 4, differences = 3
427s mode: double, lag = 1, differences = 1
427s mode: double, lag = 1, differences = 2
427s mode: double, lag = 1, differences = 3
427s mode: double, lag = 2, differences = 1
427s mode: double, lag = 2, differences = 2
427s mode: double, lag = 2, differences = 3
427s mode: double, lag = 3, differences = 1
427s mode: double, lag = 3, differences = 2
427s mode: double, lag = 3, differences = 3
427s mode: double, lag = 4, differences = 1
427s mode: double, lag = 4, differences = 2
427s mode: double, lag = 4, differences = 3
427s mode: double, lag = 1, differences = 1
427s mode: double, lag = 1, differences = 2
427s mode: double, lag = 1, differences = 3
427s mode: double, lag = 2, differences = 1
427s mode: double, lag = 2, differences = 2
427s mode: double, lag = 2, differences = 3
427s mode: double, lag = 3, differences = 1
427s mode: double, lag = 3, differences = 2
427s mode: double, lag = 3, differences = 3
427s mode: double, lag = 4, differences = 1
427s mode: double, lag = 4, differences = 2
427s mode: double, lag = 4, differences = 3
427s > 
427s > 
427s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
427s > # All NAs
427s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
427s > for (mode in c("integer", "double")) {
427s +   cat("mode: ", mode, "\n", sep = "")
427s +   x <- matrix(NA_real_, nrow = 10L, ncol = 5L)
427s +   storage.mode(x) <- mode
427s +   str(x)
427s +   
427s +   dimnames <- list(letters[1:10], LETTERS[1:5])
427s +   
427s +   # Test with and without dimnames on x
427s +   for (setDimnames in c(TRUE, FALSE)) {
427s +     if (setDimnames) dimnames(x) <- dimnames
427s +     else dimnames(x) <- NULL
427s +     # Check dimnames attribute
427s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
427s +       r0 <- rowDiffs_R(x, useNames = useNames)
427s +       r1 <- rowDiffs(x, useNames = useNames)
427s +       r2 <- t(colDiffs(t(x), useNames = useNames))
427s +       stopifnot(all.equal(r1, r0))
427s +       stopifnot(all.equal(r2, r0))
427s +       stopifnot(all.equal(r1, r2))
427s +     } # for (useNames ...)
427s +   } # for (setDimnames ...)
427s + } # for (mode ...)
427s mode: integer
427s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
427s mode: double
427s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
427s > 
427s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
427s > # A 1x1 matrix
427s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
427s > x <- matrix(0, nrow = 1L, ncol = 1L)
427s > dimnames <- list("a", "A")
427s > # Test with and without dimnames on x
427s > for (setDimnames in c(TRUE, FALSE)) {
427s +   if (setDimnames) dimnames(x) <- dimnames
427s +   else dimnames(x) <- NULL
427s +   # Check dimnames attribute
427s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
427s +     r0 <- rowDiffs_R(x, useNames = useNames)
427s +     r1 <- rowDiffs(x, useNames = useNames)
427s +     r2 <- t(colDiffs(t(x), useNames = useNames))
427s +     stopifnot(all.equal(r1, r0))
427s +     stopifnot(all.equal(r2, r0))
427s +     stopifnot(all.equal(r1, r2))
427s +   } # for (useNames ...)
427s + } # for (setDimnames ...)
427s > 
428s 
428s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
428s Copyright (C) 2024 The R Foundation for Statistical Computing
428s Platform: arm-unknown-linux-gnueabihf (32-bit)
428s 
428s R is free software and comes with ABSOLUTELY NO WARRANTY.
428s You are welcome to redistribute it under certain conditions.
428s Type 'license()' or 'licence()' for distribution details.
428s 
428s R is a collaborative project with many contributors.
428s Type 'contributors()' for more information and
428s 'citation()' on how to cite R or R packages in publications.
428s 
428s Type 'demo()' for some demos, 'help()' for on-line help, or
428s 'help.start()' for an HTML browser interface to help.
428s Type 'q()' to quit R.
428s 
428s > library("matrixStats")
428s > 
428s > rowDiffs_R <- function(x, lag = 1L, differences = 1L, ..., useNames = NA) {
428s +   ncol2 <- ncol(x) - lag * differences
428s +   if (ncol2 <= 0) {
428s +     y <- matrix(x[integer(0L)], nrow = nrow(x), ncol = 0L)
428s +     # Preserve names attribute
428s +     if (isTRUE(useNames) && !is.null(rownames(x))) rownames(y) <- rownames(x)
428s +     return(y)
428s +   }
428s +   suppressWarnings({
428s +     y <- apply(x, MARGIN = 1L, FUN = diff, lag = lag, differences = differences)
428s +   })
428s +   y <- t(y)
428s +   
428s +   # Preserve dimnames attribute
428s +   dim(y) <- c(nrow(x), ncol2)
428s +   if (isTRUE(useNames) && !is.null(dimnames(x))) {
428s +     colnames <- colnames(x)
428s +     if (!is.null(colnames)) {
428s +       len <- length(colnames)
428s +       colnames <- colnames[(len - ncol2 + 1):len]
428s +     }
428s +     dimnames(y) <- list(rownames(x), colnames)      
428s +   }
428s +   else dimnames(y) <- NULL
428s +   
428s +   y
428s + }
428s > 
428s > 
428s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
428s > # Subsetted tests
428s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
428s > source("utils/validateIndicesFramework.R")
428s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
428s > storage.mode(x) <- "integer"
428s > 
428s > # To check dimnames attribute
428s > dimnames <- list(letters[1:6], LETTERS[1:6])
428s > 
428s > # Test with and without dimnames on x
428s > for (setDimnames in c(TRUE, FALSE)) {
428s +   if (setDimnames) dimnames(x) <- dimnames
428s +   else dimnames(x) <- NULL
428s + 
428s +   count <- 0L
428s +   for (rows in index_cases) {
428s +     for (cols in index_cases) {
428s +       count <- count + 1L
428s +       for (lag in 1:2) {
428s +         for (differences in 1:3) {
428s +           # Check dimnames attribute
428s +           useNames <- c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)
428s +           useNames <- useNames[count %% length(useNames) + 1]
428s +           validateIndicesTestMatrix(x, rows, cols,
428s +                                     ftest = rowDiffs, fsure = rowDiffs_R,
428s +                                     lag = lag, differences = differences, useNames = useNames)
428s +           validateIndicesTestMatrix(x, rows, cols,
428s +                                     ftest = function(x, rows, cols, ..., useNames) {
428s +             t(colDiffs(t(x), rows = cols, cols = rows, ..., useNames = useNames))
428s +                                     }, fsure = rowDiffs_R,
428s +                                     lag = lag, differences = differences, useNames = useNames)
428s +         }
428s +       }
428s +     }
428s +   }
428s + }
437s > 
437s 
437s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
437s Copyright (C) 2024 The R Foundation for Statistical Computing
437s Platform: arm-unknown-linux-gnueabihf (32-bit)
437s 
437s R is free software and comes with ABSOLUTELY NO WARRANTY.
437s You are welcome to redistribute it under certain conditions.
437s Type 'license()' or 'licence()' for distribution details.
437s 
437s R is a collaborative project with many contributors.
437s Type 'contributors()' for more information and
437s 'citation()' on how to cite R or R packages in publications.
437s 
437s Type 'demo()' for some demos, 'help()' for on-line help, or
437s 'help.start()' for an HTML browser interface to help.
437s Type 'q()' to quit R.
437s 
437s > library("matrixStats")
437s > 
437s > rowIQRs_R <- function(x, na.rm = FALSE, ..., useNames = NA) {
437s +   quantile_na <- function(x, ..., na.rm = FALSE) {
437s +     if (!na.rm && anyMissing(x))
437s +       return(c(NA_real_, NA_real_))
437s +     quantile(x, ..., na.rm = na.rm)
437s +   }
437s +   q <- apply(x, MARGIN = 1L, FUN = quantile_na,
437s +              probs = c(0.25, 0.75), na.rm = na.rm)
437s +   rownames(q) <- NULL # Not needed anymore
437s +   
437s +   # Preserve names attribute
437s +   dim(q) <- c(2L, nrow(x))
437s +   colnames(q) <- if (isTRUE(useNames)) rownames(x) else NULL
437s +   
437s +   q[2L, , drop = TRUE] - q[1L, , drop = TRUE]
437s + }
437s > 
437s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
437s > # Test with multiple quantiles
437s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
437s > for (mode in c("integer", "double")) {
437s +   cat("mode: ", mode, "\n", sep = "")
437s +   x <- matrix(1:100 + 0.1, nrow = 10, ncol = 10)
437s +   storage.mode(x) <- mode
437s +   str(x)
437s +   
437s +   # To check names attribute
437s +   dimnames <- list(letters[1:10], LETTERS[1:10])
437s + 
437s +   for (add_na in c(FALSE, TRUE)) {
437s +     if (add_na) {
437s +       x[3:5, 6:9] <- NA
437s +     }
437s +     # Test with and without dimnames on x
437s +     for (setDimnames in c(TRUE, FALSE)) {
437s +       if (setDimnames) dimnames(x) <- dimnames
437s +       else dimnames(x) <- NULL
437s +       for (na.rm in c(FALSE, TRUE)) {
437s +         # Check names attribute
437s +         for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
437s +           probs <- c(0, 0.5, 1)
437s +           q0 <- rowIQRs_R(x, na.rm = na.rm, useNames = useNames)
437s +           print(q0)
437s +           q1 <- rowIQRs(x, na.rm = na.rm, useNames = useNames)
437s +           print(q1)
437s +           stopifnot(all.equal(q1, q0))
437s +           q2 <- colIQRs(t(x), na.rm = na.rm, useNames = useNames)
437s +           stopifnot(all.equal(q2, q0))
437s +           
437s +           q <- iqr(x[3, ], na.rm = na.rm)
437s +           print(q)
437s +         } # for (useNames ...)
437s +       } # for (na.rm ...)
437s +     } # for (setDimnames ...)
437s +   } # for (add_na ...)
437s + } # for (mode ...)
437s mode: integer
437s  int [1:10, 1:10] 1 2 3 4 5 6 7 8 9 10 ...
437s  a  b  c  d  e  f  g  h  i  j 
437s 45 45 45 45 45 45 45 45 45 45 
437s  a  b  c  d  e  f  g  h  i  j 
437s 45 45 45 45 45 45 45 45 45 45 
437s [1] 45
437s  [1] 45 45 45 45 45 45 45 45 45 45
437s  [1] 45 45 45 45 45 45 45 45 45 45
437s [1] 45
437s  a  b  c  d  e  f  g  h  i  j 
437s 45 45 45 45 45 45 45 45 45 45 
437s  a  b  c  d  e  f  g  h  i  j 
437s 45 45 45 45 45 45 45 45 45 45 
437s [1] 45
437s  [1] 45 45 45 45 45 45 45 45 45 45
437s  [1] 45 45 45 45 45 45 45 45 45 45
437s [1] 45
437s  [1] 45 45 45 45 45 45 45 45 45 45
437s  [1] 45 45 45 45 45 45 45 45 45 45
437s [1] 45
437s  [1] 45 45 45 45 45 45 45 45 45 45
437s  [1] 45 45 45 45 45 45 45 45 45 45
437s [1] 45
437s  [1] 45 45 45 45 45 45 45 45 45 45
437s  [1] 45 45 45 45 45 45 45 45 45 45
437s [1] 45
437s  [1] 45 45 45 45 45 45 45 45 45 45
437s  [1] 45 45 45 45 45 45 45 45 45 45
437s [1] 45
437s  a  b  c  d  e  f  g  h  i  j 
437s 45 45 NA NA NA 45 45 45 45 45 
437s  a  b  c  d  e  f  g  h  i  j 
437s 45 45 NA NA NA 45 45 45 45 45 
437s [1] NA
437s  [1] 45 45 NA NA NA 45 45 45 45 45
437s  [1] 45 45 NA NA NA 45 45 45 45 45
437s [1] NA
437s  a  b  c  d  e  f  g  h  i  j 
437s 45 45 25 25 25 45 45 45 45 45 
437s  a  b  c  d  e  f  g  h  i  j 
437s 45 45 25 25 25 45 45 45 45 45 
437s [1] 25
437s  [1] 45 45 25 25 25 45 45 45 45 45
437s  [1] 45 45 25 25 25 45 45 45 45 45
437s [1] 25
437s  [1] 45 45 NA NA NA 45 45 45 45 45
437s  [1] 45 45 NA NA NA 45 45 45 45 45
437s [1] NA
437s  [1] 45 45 NA NA NA 45 45 45 45 45
437s  [1] 45 45 NA NA NA 45 45 45 45 45
437s [1] NA
437s  [1] 45 45 25 25 25 45 45 45 45 45
438s  [1] 45 45 25 25 25 45 45 45 45 45
438s [1] 25
438s  [1] 45 45 25 25 25 45 45 45 45 45
438s  [1] 45 45 25 25 25 45 45 45 45 45
438s [1] 25
438s mode: double
438s  num [1:10, 1:10] 1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1 10.1 ...
438s  a  b  c  d  e  f  g  h  i  j 
438s 45 45 45 45 45 45 45 45 45 45 
438s  a  b  c  d  e  f  g  h  i  j 
438s 45 45 45 45 45 45 45 45 45 45 
438s [1] 45
438s  [1] 45 45 45 45 45 45 45 45 45 45
438s  [1] 45 45 45 45 45 45 45 45 45 45
438s [1] 45
438s  a  b  c  d  e  f  g  h  i  j 
438s 45 45 45 45 45 45 45 45 45 45 
438s  a  b  c  d  e  f  g  h  i  j 
438s 45 45 45 45 45 45 45 45 45 45 
438s [1] 45
438s  [1] 45 45 45 45 45 45 45 45 45 45
438s  [1] 45 45 45 45 45 45 45 45 45 45
438s [1] 45
438s  [1] 45 45 45 45 45 45 45 45 45 45
438s  [1] 45 45 45 45 45 45 45 45 45 45
438s [1] 45
438s  [1] 45 45 45 45 45 45 45 45 45 45
438s  [1] 45 45 45 45 45 45 45 45 45 45
438s [1] 45
438s  [1] 45 45 45 45 45 45 45 45 45 45
438s  [1] 45 45 45 45 45 45 45 45 45 45
438s [1] 45
438s  [1] 45 45 45 45 45 45 45 45 45 45
438s  [1] 45 45 45 45 45 45 45 45 45 45
438s [1] 45
438s  a  b  c  d  e  f  g  h  i  j 
438s 45 45 NA NA NA 45 45 45 45 45 
438s  a  b  c  d  e  f  g  h  i  j 
438s 45 45 NA NA NA 45 45 45 45 45 
438s [1] NA
438s  [1] 45 45 NA NA NA 45 45 45 45 45
438s  [1] 45 45 NA NA NA 45 45 45 45 45
438s [1] NA
438s  a  b  c  d  e  f  g  h  i  j 
438s 45 45 25 25 25 45 45 45 45 45 
438s  a  b  c  d  e  f  g  h  i  j 
438s 45 45 25 25 25 45 45 45 45 45 
438s [1] 25
438s  [1] 45 45 25 25 25 45 45 45 45 45
438s  [1] 45 45 25 25 25 45 45 45 45 45
438s [1] 25
438s  [1] 45 45 NA NA NA 45 45 45 45 45
438s  [1] 45 45 NA NA NA 45 45 45 45 45
438s [1] NA
438s  [1] 45 45 NA NA NA 45 45 45 45 45
438s  [1] 45 45 NA NA NA 45 45 45 45 45
438s [1] NA
438s  [1] 45 45 25 25 25 45 45 45 45 45
438s  [1] 45 45 25 25 25 45 45 45 45 45
438s [1] 25
438s  [1] 45 45 25 25 25 45 45 45 45 45
438s  [1] 45 45 25 25 25 45 45 45 45 45
438s [1] 25
438s > 
438s > 
438s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
438s > # Test corner cases
438s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
438s > for (mode in c("integer", "double")) {
438s +   cat("mode: ", mode, "\n", sep = "")
438s +   # Empty vectors
438s +   x <- integer(0L)
438s +   storage.mode(x) <- mode
438s +   str(x)
438s +   q <- iqr(x)
438s +   print(q)
438s +   stopifnot(identical(q, NA_real_))
438s + 
438s +   # Scalar
438s +   x <- 1L
438s +   storage.mode(x) <- mode
438s +   str(x)
438s +   q <- iqr(x)
438s +   str(q)
438s +   stopifnot(identical(q, 0))
438s + }
438s mode: integer
438s  int(0) 
438s [1] NA
438s  int 1
438s  num 0
438s mode: double
438s  num(0) 
438s [1] NA
438s  num 1
438s  num 0
438s > 
438s > 
438s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
438s > # Single row matrices
438s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
438s > x <- matrix(1, nrow = 1L, ncol = 2L)
438s > dimnames <- list("a",  LETTERS[1:2])
438s > # Test with and without dimnames on x
438s > for (setDimnames in c(TRUE, FALSE)) {
438s +   if (setDimnames) dimnames(x) <- dimnames
438s +   else dimnames(x) <- NULL
438s +   # Check names attribute
438s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
438s +     q0 <- rowIQRs_R(x, useNames = useNames)
438s +     q1 <- rowIQRs(x, useNames = useNames)
438s +     q2 <- colIQRs(t(x), useNames = useNames)
438s +     stopifnot(all.equal(q0, q1))
438s +     stopifnot(all.equal(q0, q2))
438s +   }
438s + }
438s > 
438s > x <- matrix(1, nrow = 2L, ncol = 1L)
438s > q <- colIQRs(x)
438s > stopifnot(identical(q, 0))
438s > 
438s 
438s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
438s Copyright (C) 2024 The R Foundation for Statistical Computing
438s Platform: arm-unknown-linux-gnueabihf (32-bit)
438s 
438s R is free software and comes with ABSOLUTELY NO WARRANTY.
438s You are welcome to redistribute it under certain conditions.
438s Type 'license()' or 'licence()' for distribution details.
438s 
438s R is a collaborative project with many contributors.
438s Type 'contributors()' for more information and
438s 'citation()' on how to cite R or R packages in publications.
438s 
438s Type 'demo()' for some demos, 'help()' for on-line help, or
438s 'help.start()' for an HTML browser interface to help.
438s Type 'q()' to quit R.
438s 
438s > library("matrixStats")
438s > 
438s > rowIQRs_R <- function(x, na.rm = FALSE, ..., useNames = NA) {
438s +   quantile_na <- function(x, ..., na.rm = FALSE) {
438s +     if (!na.rm && anyMissing(x))
438s +       return(c(NA_real_, NA_real_))
438s +     quantile(x, ..., na.rm = na.rm)
438s +   }
438s +   q <- apply(x, MARGIN = 1L, FUN = quantile_na,
438s +              probs = c(0.25, 0.75), na.rm = na.rm)
438s +   rownames(q) <- NULL # Not needed anymore
438s +   
438s +   # Preserve names attribute
438s +   dim(q) <- c(2L, nrow(x))
438s +   colnames(q) <- if (isTRUE(useNames)) rownames(x) else NULL
438s +   
438s +   q[2L, , drop = TRUE] - q[1L, , drop = TRUE]
438s + }
438s > 
438s > 
438s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
438s > # Subsetted tests
438s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
438s > source("utils/validateIndicesFramework.R")
438s > x <- runif(6, min = -6, max = 6)
438s > for (idxs in index_cases) {
438s +   for (na.rm in c(TRUE, FALSE)) {
438s +     validateIndicesTestVector(x, idxs, ftest = iqr, fsure = function(x, na.rm) {
438s +       dim(x) <- c(1L, length(x))
438s +       rowIQRs_R(x, na.rm = na.rm)
438s +     }, na.rm = na.rm)
438s +   }
438s + }
438s > 
438s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
438s > 
438s > # To check names attribute
438s > dimnames <- list(letters[1:6], LETTERS[1:6])
438s > 
438s > # Test with and without dimnames on x
438s > for (setDimnames in c(TRUE, FALSE)) {
438s +   if (setDimnames) dimnames(x) <- dimnames
438s +   else dimnames(x) <- NULL
438s +   
438s +   count <- 0L
438s +   for (rows in index_cases) {
438s +     for (cols in index_cases) {
438s +       count <- count + 1L
438s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
438s +       useNames <- c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)
438s +       useNames <- useNames[count %% length(useNames) + 1]
438s +       
438s +       validateIndicesTestMatrix(x, rows, cols,
438s +                                 ftest = rowIQRs, fsure = rowIQRs_R,
438s +                                 na.rm = na.rm, useNames = useNames)
438s +       validateIndicesTestMatrix(x, rows, cols,
438s +                                 fcoltest = colIQRs, fsure = rowIQRs_R,
438s +                                 na.rm = na.rm, useNames = useNames)
438s +     }
438s +   }
438s + }
442s > 
442s 
442s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
442s Copyright (C) 2024 The R Foundation for Statistical Computing
442s Platform: arm-unknown-linux-gnueabihf (32-bit)
442s 
442s R is free software and comes with ABSOLUTELY NO WARRANTY.
442s You are welcome to redistribute it under certain conditions.
442s Type 'license()' or 'licence()' for distribution details.
442s 
442s R is a collaborative project with many contributors.
442s Type 'contributors()' for more information and
442s 'citation()' on how to cite R or R packages in publications.
442s 
442s Type 'demo()' for some demos, 'help()' for on-line help, or
442s 'help.start()' for an HTML browser interface to help.
442s Type 'q()' to quit R.
442s 
443s > # Test inspired by the harmonic mean example in R-help
443s > # thread '[R] Beyond double-precision?' on May 9, 2009.
443s > 
443s > library("matrixStats")
443s > library("stats")
443s > 
443s > logSumExp0 <- function(lx) {
443s +   idx_max <- which.max(lx)
443s +   log1p(sum(exp(lx[-idx_max] - lx[idx_max]))) + lx[idx_max]
443s + }
443s > 
443s > n <- 200L
443s > set.seed(1)
443s > 
443s > for (mode in c("integer", "double")) {
443s +   cat("mode: ", mode, "\n", sep = "")
443s +   x <- matrix(runif(n, min = 1.0, max = 3.0), nrow = 20L)
443s +   storage.mode(x) <- mode
443s +   str(x)
443s + 
443s +   # The logarithm of the harmonic mean by rows
443s +   y_h <- log(1 / rowMeans(1 / x))
443s +   str(y_h)
443s + 
443s +   lx_neg <- -log(x)
443s + 
443s +   y0 <- log(ncol(x)) - apply(lx_neg, MARGIN = 1L, FUN = logSumExp0)
443s +   stopifnot(all.equal(y0, y_h))
443s + 
443s +   y1 <- log(ncol(x)) - apply(lx_neg, MARGIN = 1L, FUN = logSumExp)
443s +   stopifnot(all.equal(y1, y0))
443s + 
443s +   y2 <- log(ncol(x)) - rowLogSumExps(lx_neg)
443s +   stopifnot(all.equal(y2, y0))
443s + 
443s +   y3 <- log(ncol(x)) - colLogSumExps(t(lx_neg))
443s +   stopifnot(all.equal(y3, y0))
443s + 
443s + 
443s +   # The logarithm of the harmonic mean by columns
443s +   y_h <- log(1 / colMeans(1 / x))
443s +   str(y_h)
443s + 
443s +   y0 <- log(nrow(x)) - apply(lx_neg, MARGIN = 2L, FUN = logSumExp0)
443s +   stopifnot(all.equal(y0, y_h))
443s + 
443s +   y1 <- log(nrow(x)) - apply(lx_neg, MARGIN = 2L, FUN = logSumExp)
443s +   stopifnot(all.equal(y1, y0))
443s + 
443s +   y2 <- log(nrow(x)) - colLogSumExps(lx_neg)
443s +   stopifnot(all.equal(y2, y0))
443s + 
443s +   y3 <- log(nrow(x)) - rowLogSumExps(t(lx_neg))
443s +   stopifnot(all.equal(y3, y0))
443s + 
443s +   # Testing names
443s +   rownames(lx_neg) <- seq_len(nrow(x))
443s +   colnames(lx_neg) <- seq_len(ncol(x))
443s +   y2 <- rowLogSumExps(lx_neg, useNames = TRUE)
443s +   stopifnot(identical(names(y2), rownames(lx_neg)))
443s +   y3 <- colLogSumExps(t(lx_neg), useNames = TRUE)
443s +   stopifnot(identical(names(y3), rownames(lx_neg)))
443s + } # for (mode ...)
443s mode: integer
443s  int [1:20, 1:10] 1 1 2 2 1 2 2 2 2 1 ...
443s  num [1:20] 0.357 0.223 0.223 0.288 0.511 ...
443s  num [1:10] 0.322 0.223 0.322 0.255 0.255 ...
443s mode: double
443s  num [1:20, 1:10] 1.54 1.44 2.03 1.54 1.36 ...
443s  num [1:20] 0.526 0.466 0.734 0.638 0.604 ...
443s  num [1:10] 0.627 0.582 0.617 0.474 0.418 ...
443s > 
443s > 
443s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
443s > # Corner cases
443s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
443s > ## Zero-size matrices
443s > lx <- matrix(numeric(0L), nrow = 0L, ncol = 0L)
443s > y <- rowLogSumExps(lx)
443s > print(y)
443s numeric(0)
443s > stopifnot(length(y) == nrow(lx))
443s > 
443s > y <- colLogSumExps(lx)
443s > print(y)
443s numeric(0)
443s > stopifnot(length(y) == ncol(lx))
443s > 
443s > ## Zero-height matrices
443s > lx <- matrix(numeric(0L), nrow = 0L, ncol = 5L)
443s > y <- rowLogSumExps(lx)
443s > print(y)
443s numeric(0)
443s > stopifnot(length(y) == nrow(lx))
443s > 
443s > y <- colLogSumExps(lx)
443s > print(y)
443s [1] -Inf -Inf -Inf -Inf -Inf
443s > stopifnot(length(y) == ncol(lx))
443s > stopifnot(all(y == -Inf))
443s > 
443s > ## Zero-width matrices
443s > lx <- matrix(numeric(0L), nrow = 5L, ncol = 0L)
443s > y <- colLogSumExps(lx)
443s > print(y)
443s numeric(0)
443s > stopifnot(length(y) == ncol(lx))
443s > 
443s > y <- rowLogSumExps(lx)
443s > print(y)
443s [1] -Inf -Inf -Inf -Inf -Inf
443s > stopifnot(length(y) == nrow(lx))
443s > stopifnot(all(y == -Inf))
443s > 
443s > 
443s > ## Matrices with one element
443s > lx <- matrix(1.0, nrow = 1L, ncol = 1L)
443s > y <- rowLogSumExps(lx)
443s > print(y)
443s [1] 1
443s > stopifnot(length(y) == nrow(lx))
443s > stopifnot(all(y == lx))
443s > 
443s > y <- colLogSumExps(lx)
443s > print(y)
443s [1] 1
443s > stopifnot(length(y) == ncol(lx))
443s > stopifnot(all(y == lx))
443s > 
443s > ## All missing values
443s > lx <- matrix(NA_real_, nrow = 1L, ncol = 1L)
443s > y <- rowLogSumExps(lx, na.rm = TRUE)
443s > print(y)
443s [1] -Inf
443s > stopifnot(length(y) == nrow(lx))
443s > stopifnot(identical(y, -Inf))
443s > 
443s > lx <- matrix(NA_real_, nrow = 1L, ncol = 1L)
443s > y <- colLogSumExps(lx, na.rm = TRUE)
443s > print(y)
443s [1] -Inf
443s > stopifnot(length(y) == ncol(lx))
443s > stopifnot(identical(y, -Inf))
443s > 
443s > lx <- matrix(NA_real_, nrow = 2L, ncol = 2L)
443s > y <- rowLogSumExps(lx, na.rm = TRUE)
443s > print(y)
443s [1] -Inf -Inf
443s > stopifnot(length(y) == nrow(lx))
443s > stopifnot(all(y == -Inf))
443s > 
443s > y <- rowLogSumExps(lx, na.rm = FALSE)
443s > print(y)
443s [1] NA NA
443s > stopifnot(length(y) == nrow(lx))
443s > stopifnot(all(is.na(y) & !is.nan(y)))
443s > 
443s > lx <- matrix(NA_real_, nrow = 2L, ncol = 2L)
443s > y <- colLogSumExps(lx, na.rm = TRUE)
443s > print(y)
443s [1] -Inf -Inf
443s > stopifnot(length(y) == ncol(lx))
443s > stopifnot(all(y == -Inf))
443s > 
443s > y <- colLogSumExps(lx, na.rm = FALSE)
443s > print(y)
443s [1] NA NA
443s > stopifnot(length(y) == ncol(lx))
443s > stopifnot(all(is.na(y) & !is.nan(y)))
443s > 
443s > ## +Inf values
443s > lx <- matrix(c(1, 2, +Inf), nrow = 3L, ncol = 2L)
443s > y <- colLogSumExps(lx, na.rm = TRUE)
443s > print(y)
443s [1] Inf Inf
443s > stopifnot(length(y) == ncol(lx))
443s > stopifnot(all(y == +Inf))
443s > 
443s > ## multiple -Inf values
443s > lx <- matrix(c(-Inf, -Inf), nrow = 2L, ncol = 3L)
443s > y <- rowLogSumExps(lx)
443s > print(y)
443s [1] -Inf -Inf
443s > stopifnot(length(y) == nrow(lx))
443s > stopifnot(all(y == -Inf))
443s > 
443s > lx <- matrix(c(-Inf, 5, -Inf), nrow = 2L, ncol = 3L, byrow = TRUE)
443s > y <- rowLogSumExps(lx)
443s > print(y)
443s [1] 5 5
443s > stopifnot(length(y) == nrow(lx))
443s > stopifnot(all(y == 5))
443s > 
443s > ## Bug report #104 (https://github.com/HenrikBengtsson/matrixStats/issues/104)
443s > ## (This would core dump on Windows)
443s > x <- matrix(0.0, nrow = 2L, ncol = 32762L)
443s > y <- colLogSumExps(x)
443s > str(y)
443s  num [1:32762] 0.693 0.693 0.693 0.693 0.693 ...
443s > 
443s > ## Bug report #120 (https://github.com/HenrikBengtsson/matrixStats/issues/120)
443s > ## (This would error if x had rownames/colnames and non-NULL rows/cols were
443s > ## used)
443s > x <- matrix(runif(6), nrow = 2L, ncol = 3L,
443s +             dimnames = list(c("A", "B"), c("a", "b", "c")))
443s > y <- colLogSumExps(x, cols = 3:1, useNames = TRUE)
443s > stopifnot(names(y) == c("c", "b", "a"))
443s > y <- rowLogSumExps(x, rows = 2, useNames = TRUE)
443s > stopifnot(names(y) == "B")
443s > 
443s > 
443s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
443s > # Check names attributes
443s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
443s > 
443s > ## Create isFALSE() if running on an old version of R
443s > if (!exists("isFALSE", mode="function")) {
443s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
443s + }
443s > 
443s > rowLogSumExps_R <- function(x, ..., useNames = NA) {
443s +   res <- apply(x, MARGIN = 1L, FUN = function(rx, ...) {
443s +     log(sum(exp(rx), ...))
443s +   }, ...)
443s +   if (isFALSE(useNames)) names(res) <- NULL
443s +   res
443s + }
443s > 
443s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6L, ncol = 6L)
443s > 
443s > # To check names attribute
443s > dimnames <- list(letters[1:6], LETTERS[1:6])
443s > 
443s > # Test with and without dimnames on x
443s > for (setDimnames in c(TRUE, FALSE)) {
443s +   if (setDimnames) dimnames(x) <- dimnames
443s +   else dimnames(x) <- NULL
443s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
443s +     y0 <- rowLogSumExps_R(x, useNames = useNames)
443s +     y1 <- rowLogSumExps(x, useNames = useNames)
443s +     y2 <- colLogSumExps(t(x), useNames = useNames)
443s +     stopifnot(all.equal(y1, y0))
443s +     stopifnot(all.equal(y2, y0))
443s +   }
443s + }
443s > 
443s 
443s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
443s Copyright (C) 2024 The R Foundation for Statistical Computing
443s Platform: arm-unknown-linux-gnueabihf (32-bit)
443s 
443s R is free software and comes with ABSOLUTELY NO WARRANTY.
443s You are welcome to redistribute it under certain conditions.
443s Type 'license()' or 'licence()' for distribution details.
443s 
443s R is a collaborative project with many contributors.
443s Type 'contributors()' for more information and
443s 'citation()' on how to cite R or R packages in publications.
443s 
443s Type 'demo()' for some demos, 'help()' for on-line help, or
443s 'help.start()' for an HTML browser interface to help.
443s Type 'q()' to quit R.
443s 
443s > library("matrixStats")
443s > 
443s > ## Create isFALSE() if running on an old version of R
443s > if (!exists("isFALSE", mode="function")) {
443s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
443s + }
443s > 
443s > rowLogSumExps_R <- function(x, ..., useNames = NA) {
443s +   res <- apply(x, MARGIN = 1L, FUN = function(rx, ...) {
443s +     log(sum(exp(rx), ...))
443s +   }, ...)
443s +   if (isFALSE(useNames)) names(res) <- NULL
443s +   res
443s + }
443s > 
443s > 
443s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
443s > # Subsetted tests
443s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
443s > source("utils/validateIndicesFramework.R")
443s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
443s > 
443s > # To check names attribute
443s > dimnames <- list(letters[1:6], LETTERS[1:6])
443s > 
443s > # Test with and without dimnames on x
443s > for (setDimnames in c(TRUE, FALSE)) {
443s +   if (setDimnames) dimnames(x) <- dimnames
443s +   else dimnames(x) <- NULL
443s +   for (rows in index_cases) {
443s +     for (cols in index_cases) {
443s +       for (na.rm in c(TRUE, FALSE)) {
443s +         for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
443s +           validateIndicesTestMatrix(x, rows, cols,
443s +                                     ftest = rowLogSumExps,
443s +                                     fsure = rowLogSumExps_R,
443s +                                     na.rm = na.rm, useNames = useNames)
443s +           validateIndicesTestMatrix(x, rows, cols,
443s +                                     fcoltest = colLogSumExps,
443s +                                     fsure = rowLogSumExps_R,
443s +                                     na.rm = na.rm, useNames = useNames)
443s +         }
443s +       }
443s +     }
443s +   }
443s + }
447s > 
447s 
447s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
447s Copyright (C) 2024 The R Foundation for Statistical Computing
447s Platform: arm-unknown-linux-gnueabihf (32-bit)
447s 
447s R is free software and comes with ABSOLUTELY NO WARRANTY.
447s You are welcome to redistribute it under certain conditions.
447s Type 'license()' or 'licence()' for distribution details.
447s 
447s R is a collaborative project with many contributors.
447s Type 'contributors()' for more information and
447s 'citation()' on how to cite R or R packages in publications.
447s 
447s Type 'demo()' for some demos, 'help()' for on-line help, or
447s 'help.start()' for an HTML browser interface to help.
447s Type 'q()' to quit R.
447s 
447s > library("matrixStats")
447s > 
447s > ## Always allow testing of the 'center' argument (as long as it's not defunct)
447s > options(matrixStats.center.onUse = "ignore")
447s > 
447s > rowMads_R <- function(x, na.rm = FALSE, ..., useNames = NA) {
447s +   suppressWarnings({
447s +     res <- apply(x, MARGIN = 1L, FUN = mad, na.rm = na.rm)
447s +   })
447s +   if (is.na(useNames) || !useNames) names(res) <- NULL
447s +   res
447s + }
447s > 
447s > colMads_R <- function(x, na.rm = FALSE, ..., useNames = NA) {
447s +   suppressWarnings({
447s +     res <- apply(x, MARGIN = 2L, FUN = mad, na.rm = na.rm)
447s +   })
447s +   if (is.na(useNames) || !useNames) names(res) <- NULL
447s +   res
447s + }
447s > 
447s > rowMads_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = NA) {
447s +   center <- rowMedians(x, cols = cols, na.rm = na.rm, useNames = FALSE)
447s +   rowMads(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
447s + }
447s > 
447s > colMads_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = NA) {
447s +   center <- colMedians(x, rows = rows, na.rm = na.rm, useNames = FALSE)
447s +   colMads(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
447s + }
447s > 
447s > 
447s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
447s > # A 3x3 matrix (no ties)
447s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
447s > for (mode in c("integer", "double")) {
447s +   x <- matrix(c(1, 2, 3, 2, 3, 4, 3, 4, 5) + 0.1, nrow = 3, ncol = 3)
447s +   cat("mode: ", mode, "\n", sep = "")
447s +   storage.mode(x) <- mode
447s +   str(x)
447s +   
447s +   # To check name attribute
447s +   dimnames <- list(letters[1:3], LETTERS[1:3])
447s +   
447s +   # Test with and without dimnames on x
447s +   for (setDimnames in c(TRUE, FALSE)) {
447s +     if (setDimnames) dimnames(x) <- dimnames
447s +     else dimnames(x) <- NULL
447s +     tx <- t(x)
447s +     # Check names attribute
447s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
447s +       cat("rowMads():\n")
447s +       center <- rowMedians(x, na.rm = TRUE, useNames = useNames)
447s +       r0 <- rowMads_R(x, na.rm = TRUE, useNames = useNames)
447s +       r1 <- rowMads(x, na.rm = TRUE, useNames = useNames)
447s +       r1b <- rowMads_center(x, na.rm = TRUE, useNames = useNames)
447s +       r1c <- rowMads(x, center = center, na.rm = TRUE, useNames = useNames)
447s +       r2 <- colMads(tx, na.rm = TRUE, useNames = useNames)
447s +       r2b <- colMads_center(tx, na.rm = TRUE, useNames = useNames)
447s +       stopifnot(all.equal(r1, r2))
447s +       stopifnot(all.equal(r1, r0))
447s +       stopifnot(all.equal(r1b, r1))
447s +       stopifnot(all.equal(r1c, r1))
447s +       stopifnot(all.equal(r2, r0))
447s +       stopifnot(all.equal(r2b, r2))
447s +       
447s +       cat("colMads():\n")
447s +       center <- colMedians(x, na.rm = TRUE, useNames = useNames)
447s +       r0 <- colMads_R(x, na.rm = TRUE, useNames = useNames)
447s +       r1 <- colMads(x, na.rm = TRUE, useNames = useNames)
447s +       r1b <- colMads_center(x, na.rm = TRUE, useNames = useNames)
447s +       r1c <- colMads(x, center = center, na.rm = TRUE, useNames = useNames)
447s +       r2 <- rowMads(tx, na.rm = TRUE, useNames = useNames)
447s +       r2b <- rowMads_center(tx, na.rm = TRUE, useNames = useNames)
447s +       stopifnot(all.equal(r1, r2))
447s +       stopifnot(all.equal(r1, r0))
447s +       stopifnot(all.equal(r1b, r1))
447s +       stopifnot(all.equal(r1c, r1))
447s +       stopifnot(all.equal(r2, r0))
447s +       stopifnot(all.equal(r2b, r2))
447s +     }
447s +   }
447s + }
447s mode: integer
447s  int [1:3, 1:3] 1 2 3 2 3 4 3 4 5
447s rowMads():
447s colMads():
447s rowMads():
447s colMads():
447s rowMads():
447s colMads():
447s rowMads():
447s colMads():
447s mode: double
447s  num [1:3, 1:3] 1.1 2.1 3.1 2.1 3.1 4.1 3.1 4.1 5.1
447s rowMads():
447s colMads():
447s rowMads():
447s colMads():
447s rowMads():
447s colMads():
447s rowMads():
447s colMads():
447s > 
447s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
447s > # Ties: a 4x4 matrix
447s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
447s > for (mode in c("integer", "double")) {
447s +   x <- matrix(c(1:4, 2:5, 3:6, 4:7) + 0.1, nrow = 4, ncol = 4)
447s +   cat("mode: ", mode, "\n", sep = "")
447s +   storage.mode(x) <- mode
447s +   str(x)
447s +   tx <- t(x)
447s +   
447s +   # To check name attribute
447s +   dimnames <- list(letters[1:4], LETTERS[1:4])
447s +   
447s +   # Test with and without dimnames on x
447s +   for (setDimnames in c(TRUE, FALSE)) {
447s +     if (setDimnames) dimnames(x) <- dimnames
447s +     else dimnames(x) <- NULL
447s +     tx <- t(x)
447s +     # Check names attribute
447s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
447s +       cat("rowMads():\n")
447s +       r0 <- rowMads_R(x, na.rm = TRUE, useNames = useNames)
447s +       r1 <- rowMads(x, na.rm = TRUE, useNames = useNames)
447s +       r2 <- colMads(tx, na.rm = TRUE, useNames = useNames)
447s +       stopifnot(all.equal(r1, r2))
447s +       stopifnot(all.equal(r1, r0))
447s +       stopifnot(all.equal(r2, r0))
447s +       
447s +       cat("colMads():\n")
447s +       r0 <- colMads_R(x, na.rm = TRUE, useNames = useNames)
447s +       r1 <- colMads(x, na.rm = TRUE, useNames = useNames)
447s +       r2 <- rowMads(tx, na.rm = TRUE, useNames = useNames)
447s +       stopifnot(all.equal(r1, r2))
447s +       stopifnot(all.equal(r1, r0))
447s +       stopifnot(all.equal(r2, r0))
447s +     }
447s +   }
447s + }
448s mode: integer
448s  int [1:4, 1:4] 1 2 3 4 2 3 4 5 3 4 ...
448s rowMads():
448s colMads():
448s rowMads():
448s colMads():
448s rowMads():
448s colMads():
448s rowMads():
448s colMads():
448s mode: double
448s  num [1:4, 1:4] 1.1 2.1 3.1 4.1 2.1 3.1 4.1 5.1 3.1 4.1 ...
448s rowMads():
448s colMads():
448s rowMads():
448s colMads():
448s rowMads():
448s colMads():
448s rowMads():
448s colMads():
448s > tx <- NULL
448s > 
448s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
448s > # No ties: a 3x3 matrix with an NA value
448s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
448s > for (mode in c("integer", "double")) {
448s +   x <- matrix(c(1, 2, 3, 2, 3, 4, 3, 4, 5) + 0.1, nrow = 3, ncol = 3)
448s +   x[2, 2] <- NA_real_
448s + 
448s +   cat("mode: ", mode, "\n", sep = "")
448s +   storage.mode(x) <- mode
448s +   str(x)
448s +   tx <- t(x)
448s +   
448s +   # To check name attribute
448s +   dimnames <- list(letters[1:3], LETTERS[1:3])
448s +   
448s +   # Test with and without dimnames on x
448s +   for (setDimnames in c(TRUE, FALSE)) {
448s +     if (setDimnames) dimnames(x) <- dimnames
448s +     else dimnames(x) <- NULL
448s +     tx <- t(x)
448s +     # Check names attribute
448s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
448s +       cat("rowMads():\n")
448s +       r0 <- rowMads_R(x, na.rm = TRUE, useNames = useNames)
448s +       r1 <- rowMads(x, na.rm = TRUE, useNames = useNames)
448s +       r2 <- colMads(tx, na.rm = TRUE, useNames = useNames)
448s +       stopifnot(all.equal(r1, r2))
448s +       stopifnot(all.equal(r1, r0))
448s +       stopifnot(all.equal(r2, r0))
448s +       
448s +       cat("colMads():\n")
448s +       r0 <- colMads_R(x, na.rm = TRUE, useNames = useNames)
448s +       r1 <- colMads(x, na.rm = TRUE, useNames = useNames)
448s +       r2 <- rowMads(tx, na.rm = TRUE, useNames = useNames)
448s +       stopifnot(all.equal(r1, r2))
448s +       stopifnot(all.equal(r1, r0))
448s +       stopifnot(all.equal(r2, r0))
448s +     }
448s +   }
448s + }
448s mode: integer
448s  int [1:3, 1:3] 1 2 3 2 NA 4 3 4 5
448s rowMads():
448s colMads():
448s rowMads():
448s colMads():
448s rowMads():
448s colMads():
448s rowMads():
448s colMads():
448s mode: double
448s  num [1:3, 1:3] 1.1 2.1 3.1 2.1 NA 4.1 3.1 4.1 5.1
448s rowMads():
448s colMads():
448s rowMads():
448s colMads():
448s rowMads():
448s colMads():
448s rowMads():
448s colMads():
448s > tx <- NULL
448s > 
448s > 
448s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
448s > # With and without some NAs
448s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
448s > for (add_na in c(FALSE, TRUE)) {
448s +   cat("add_na = ", add_na, "\n", sep = "")
448s + 
448s +   x <- matrix(1:50, nrow = 10L, ncol = 5L)
448s +   if (add_na) {
448s +     x[3:7, c(2, 4)] <- NA_real_
448s +   }
448s +   
448s +   # To check name attribute
448s +   dimnames <- list(letters[1:10], LETTERS[1:5])
448s +   
448s +   # Test with and without dimnames on x
448s +   for (setDimnames in c(TRUE, FALSE)) {
448s +     if (setDimnames) dimnames(x) <- dimnames
448s +     else dimnames(x) <- NULL
448s +     tx <- t(x)
448s +     # Row/column ranges
448s +     for (na.rm in c(FALSE, TRUE)) {
448s +       # Check names attribute
448s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
448s +       cat("na.rm = ", na.rm, "\n", sep = "")
448s +         cat("rowMads():\n")
448s +         center <- rowMedians(x, na.rm = na.rm, useNames = useNames)
448s +         r0 <- rowMads_R(x, na.rm = na.rm, useNames = useNames)
448s +         r1 <- rowMads(x, na.rm = na.rm, useNames = useNames)
448s +         r2 <- rowMads(x, center = center, na.rm = na.rm, useNames = useNames)
448s +         r3 <- colMads(tx, na.rm = na.rm, useNames = useNames)
448s +         stopifnot(all.equal(r1, r0))
448s +         stopifnot(all.equal(r2, r0))
448s +         stopifnot(all.equal(r2, r1))
448s +         stopifnot(all.equal(r3, r0))
448s +         stopifnot(all.equal(r3, r1))
448s +         stopifnot(all.equal(r3, r2))
448s +         
448s +         cat("colMads():\n")
448s +         center <- colMedians(x, na.rm = na.rm, useNames = useNames)
448s +         r0 <- colMads_R(x, na.rm = na.rm, useNames = useNames)
448s +         r1 <- colMads(x, na.rm = na.rm, useNames = useNames)
448s +         r2 <- colMads(x, center = center, na.rm = na.rm, useNames = useNames)
448s +         r3 <- rowMads(tx, na.rm = na.rm, useNames = useNames)
448s +         stopifnot(all.equal(r1, r0))
448s +         stopifnot(all.equal(r2, r0))
448s +         stopifnot(all.equal(r2, r1))
448s +         stopifnot(all.equal(r3, r0))
448s +         stopifnot(all.equal(r3, r1))
448s +         stopifnot(all.equal(r3, r2))
448s +       }
448s +     }
448s +   }
448s +   tx <- NULL
448s + } # for (add_na ...)
448s add_na = FALSE
448s na.rm = FALSE
448s rowMads():
448s colMads():
448s na.rm = FALSE
448s rowMads():
448s colMads():
448s na.rm = TRUE
448s rowMads():
448s colMads():
448s na.rm = TRUE
448s rowMads():
448s colMads():
448s na.rm = FALSE
448s rowMads():
448s colMads():
448s na.rm = FALSE
448s rowMads():
448s colMads():
448s na.rm = TRUE
448s rowMads():
448s colMads():
448s na.rm = TRUE
448s rowMads():
448s colMads():
448s add_na = TRUE
448s na.rm = FALSE
448s rowMads():
448s colMads():
448s na.rm = FALSE
448s rowMads():
448s colMads():
448s na.rm = TRUE
448s rowMads():
448s colMads():
448s na.rm = TRUE
448s rowMads():
448s colMads():
448s na.rm = FALSE
448s rowMads():
448s colMads():
448s na.rm = FALSE
448s rowMads():
448s colMads():
448s na.rm = TRUE
448s rowMads():
448s colMads():
448s na.rm = TRUE
448s rowMads():
448s colMads():
448s > 
448s > 
448s > 
448s > 
448s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
448s > # All NAs
448s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
448s > x <- matrix(NA_real_, nrow = 10L, ncol = 5L)
448s > # Test with and without dimnames on x
448s > for (setDimnames in c(TRUE, FALSE)) {
448s +   if (setDimnames) dimnames(x) <- dimnames
448s +   else dimnames(x) <- NULL
448s +   tx <- t(x)
448s +   # Row/column ranges
448s +   for (na.rm in c(FALSE, TRUE)) {
448s +     # Check names attribute
448s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
448s +       cat("na.rm = ", na.rm, "\n", sep = "")
448s +       r0 <- rowMads_R(x, na.rm = na.rm, useNames = useNames)
448s +       if (na.rm) r0[is.na(r0)] <- NaN
448s +       r1 <- rowMads(x, na.rm = na.rm, useNames = useNames)
448s +       r2 <- colMads(tx, na.rm = na.rm, useNames = useNames)
448s +       stopifnot(all.equal(r1, r0))
448s +       stopifnot(all.equal(r2, r0))
448s +       stopifnot(all.equal(r1, r2))
448s +     }
448s +   }
448s + }
448s na.rm = FALSE
448s na.rm = FALSE
448s na.rm = TRUE
448s na.rm = TRUE
448s na.rm = FALSE
448s na.rm = FALSE
448s na.rm = TRUE
448s na.rm = TRUE
448s > tx <- NULL
448s > 
448s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
448s > # A 1x1 matrix
448s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
448s > x <- matrix(0, nrow = 1L, ncol = 1L)
448s > dimnames <- list("a", "A")
448s > # Test with and without dimnames on x
448s > for (setDimnames in c(TRUE, FALSE)) {
448s +   if (setDimnames) dimnames(x) <- dimnames
448s +   else dimnames(x) <- NULL
448s +   tx <- t(x)
448s +   # Row/column ranges
448s +   for (na.rm in c(FALSE, TRUE)) {
448s +     # Check names attribute
448s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
448s +       cat("na.rm = ", na.rm, "\n", sep = "")
448s +       r0 <- rowMads_R(x, na.rm = na.rm, useNames = useNames)
448s +       r1 <- rowMads(x, na.rm = na.rm, useNames = useNames)
448s +       r2 <- colMads(tx, na.rm = na.rm, useNames = useNames)
448s +       stopifnot(all.equal(r1, r0))
448s +       stopifnot(all.equal(r2, r0))
448s +       stopifnot(all.equal(r1, r2))
448s +     }
448s +   }
448s + }
448s na.rm = FALSE
448s na.rm = FALSE
448s na.rm = TRUE
448s na.rm = TRUE
448s na.rm = FALSE
448s na.rm = FALSE
448s na.rm = TRUE
448s na.rm = TRUE
448s > 
448s > 
448s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
448s > # A 0x0 matrix
448s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
448s > x <- matrix(double(0), nrow = 0, ncol = 0)
448s > tx <- t(x)
448s > for (na.rm in c(FALSE, TRUE)) {
448s +   cat("na.rm = ", na.rm, "\n", sep = "")
448s +   r0 <- rowMads_R(x, na.rm = na.rm)
448s +   r1 <- rowMads(x, na.rm = na.rm)
448s +   r2 <- colMads(tx, na.rm = na.rm)
448s +   stopifnot(all.equal(r1, r2))
448s +   stopifnot(all.equal(r1, r0))
448s +   stopifnot(all.equal(r2, r0))
448s + }
448s na.rm = FALSE
448s na.rm = TRUE
448s > 
448s 
448s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
448s Copyright (C) 2024 The R Foundation for Statistical Computing
448s Platform: arm-unknown-linux-gnueabihf (32-bit)
448s 
448s R is free software and comes with ABSOLUTELY NO WARRANTY.
448s You are welcome to redistribute it under certain conditions.
448s Type 'license()' or 'licence()' for distribution details.
448s 
448s R is a collaborative project with many contributors.
448s Type 'contributors()' for more information and
448s 'citation()' on how to cite R or R packages in publications.
448s 
448s Type 'demo()' for some demos, 'help()' for on-line help, or
448s 'help.start()' for an HTML browser interface to help.
448s Type 'q()' to quit R.
448s 
449s > library("matrixStats")
449s > 
449s > ## Always allow testing of the 'center' argument (as long as it's not defunct)
449s > options(matrixStats.center.onUse = "ignore")
449s > 
449s > rowMads_R <- function(x, na.rm = FALSE, ..., useNames = NA) {
449s +   suppressWarnings({
449s +     res <- apply(x, MARGIN = 1L, FUN = mad, na.rm = na.rm)
449s +   })
449s +   if (is.na(useNames) || !useNames) names(res) <- NULL
449s +   res
449s + }
449s > 
449s > colMads_R <- function(x, na.rm = FALSE, ..., useNames = NA) {
449s +   suppressWarnings({
449s +     res <- apply(x, MARGIN = 2L, FUN = mad, na.rm = na.rm)
449s +   })
449s +   if (is.na(useNames) || !useNames) names(res) <- NULL
449s +   res
449s + }
449s > 
449s > rowMads_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = NA) {
449s +   center <- rowMedians(x, cols = cols, na.rm = na.rm, useNames = FALSE)
449s +   rowMads(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
449s + }
449s > 
449s > colMads_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = NA) {
449s +   center <- colMedians(x, rows = rows, na.rm = na.rm, useNames = FALSE)
449s +   colMads(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
449s + }
449s > 
449s > 
449s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
449s > # Subsetted tests
449s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
449s > source("utils/validateIndicesFramework.R")
449s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
449s > storage.mode(x) <- "integer"
449s > 
449s > # To check names attribute
449s > dimnames <- list(letters[1:6], LETTERS[1:6])
449s > 
449s > # Test with and without dimnames on x
449s > for (setDimnames in c(TRUE, FALSE)) {
449s +   if (setDimnames) dimnames(x) <- dimnames
449s +   else dimnames(x) <- NULL
449s + 
449s +   count <- 0L
449s +   for (rows in index_cases) {
449s +     for (cols in index_cases) {
449s +       count <- count + 1L
449s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
449s +       useNames <- c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)
449s +       useNames <- useNames[count %% length(useNames) + 1]
449s +       
449s +       validateIndicesTestMatrix(x, rows, cols,
449s +                                 ftest = rowMads, fsure = rowMads_R,
449s +                                 na.rm = na.rm, useNames = useNames)
449s +       validateIndicesTestMatrix(x, rows, cols,
449s +                                 ftest = rowMads_center, fsure = rowMads_R,
449s +                                 na.rm = na.rm, useNames = useNames)
449s + 
449s +       validateIndicesTestMatrix(x, rows, cols,
449s +                                 fcoltest = colMads, fsure = rowMads_R,
449s +                                 na.rm = na.rm, useNames = useNames)
449s +       validateIndicesTestMatrix(x, rows, cols,
449s +                                 fcoltest = colMads_center, fsure = rowMads_R,
449s +                                 na.rm = na.rm, useNames = useNames)
449s +     }
449s +   }
449s + }
452s > 
452s 
452s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
452s Copyright (C) 2024 The R Foundation for Statistical Computing
452s Platform: arm-unknown-linux-gnueabihf (32-bit)
452s 
452s R is free software and comes with ABSOLUTELY NO WARRANTY.
452s You are welcome to redistribute it under certain conditions.
452s Type 'license()' or 'licence()' for distribution details.
452s 
452s R is a collaborative project with many contributors.
452s Type 'contributors()' for more information and
452s 'citation()' on how to cite R or R packages in publications.
452s 
452s Type 'demo()' for some demos, 'help()' for on-line help, or
452s 'help.start()' for an HTML browser interface to help.
452s Type 'q()' to quit R.
452s 
453s > library("matrixStats")
453s > 
453s > rowMeans_R <- function(x, na.rm = FALSE, ..., useNames = NA) {
453s +   res <- rowMeans(x, na.rm = na.rm)
453s +   if (is.na(useNames) || !useNames) names(res) <- NULL
453s +   res
453s + }
453s > 
453s > colMeans_R <- function(x, na.rm = FALSE, ..., useNames = NA) {
453s +   res <- colMeans(x, na.rm = na.rm)
453s +   if (is.na(useNames) || !useNames) names(res) <- NULL
453s +   res
453s + }
453s > 
453s > for (mode in c("integer", "logical", "double")) {
453s +   x <- matrix(-4:4, nrow = 3, ncol = 3)
453s +   storage.mode(x) <- mode
453s +   if (mode == "double") x <- x + 0.1
453s +   
453s +   # To check names attribute
453s +   dimnames <- list(letters[1:3], LETTERS[1:3])
453s +   
453s +   # Test with and without dimnames on x
453s +   for (setDimnames in c(TRUE, FALSE)) {
453s +     if (setDimnames) dimnames(x) <- dimnames
453s +     else dimnames(x) <- NULL
453s +     # Check names attribute
453s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
453s +       y0 <- rowMeans_R(x, na.rm = FALSE, useNames = useNames)
453s +       y1 <- rowMeans2(x, na.rm = FALSE, useNames = useNames)
453s +       stopifnot(all.equal(y1, y0))
453s +       
453s +       y0 <- colMeans_R(x, na.rm = FALSE, useNames = useNames)
453s +       y1 <- colMeans2(x, na.rm = FALSE, useNames = useNames)
453s +       stopifnot(all.equal(y1, y0))
453s +     }
453s +   }
453s + }
453s > 
453s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
453s > # Special case: Single-element matrix
453s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
453s > cat("Special case: Single-element matrix:\n")
453s Special case: Single-element matrix:
453s > for (mode in c("integer", "logical", "double")) {
453s +   x <- matrix(1, nrow = 1, ncol = 1)
453s +   storage.mode(x) <- mode
453s +   
453s +   # To check names attribute
453s +   dimnames <- list("a", "A")
453s +   
453s +   # Test with and without dimnames on x
453s +   for (setDimnames in c(TRUE, FALSE)) {
453s +     if (setDimnames) dimnames(x) <- dimnames
453s +     else dimnames(x) <- NULL
453s +     # Check names attribute
453s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
453s +       y0 <- rowMeans_R(x, na.rm = FALSE, useNames = useNames)
453s +       y1 <- rowMeans2(x, na.rm = FALSE, useNames = useNames)
453s +       stopifnot(all.equal(y1, y0))
453s +       
453s +       y0 <- colMeans_R(x, na.rm = FALSE, useNames = useNames)
453s +       y1 <- colMeans2(x, na.rm = FALSE, useNames = useNames)
453s +       stopifnot(all.equal(y1, y0))
453s +     }
453s +   }
453s + }
453s > 
453s > 
453s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
453s > # Special case: Empty matrix
453s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
453s > cat("Special case: Empty matrix:\n")
453s Special case: Empty matrix:
453s > for (mode in c("integer", "logical", "double")) {
453s +   x <- matrix(integer(0), nrow = 0, ncol = 0)
453s +   storage.mode(x) <- mode
453s + 
453s +   y0 <- rowMeans(x, na.rm = FALSE)
453s +   y1 <- rowMeans2(x, na.rm = FALSE)
453s +   stopifnot(all.equal(y1, y0))
453s + 
453s +   y0 <- colMeans(x, na.rm = FALSE)
453s +   y1 <- colMeans2(x, na.rm = FALSE)
453s +   stopifnot(all.equal(y1, y0))
453s + }
453s > 
453s > 
453s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
453s > # Special case: All NAs
453s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
453s > cat("Special case: All NAs:\n")
453s Special case: All NAs:
453s > for (mode in c("integer", "logical", "double")) {
453s +   x <- matrix(NA_integer_, nrow = 3, ncol = 3)
453s +   storage.mode(x) <- mode
453s +   
453s +   # To check names attribute
453s +   dimnames <- list(letters[1:3], LETTERS[1:3])
453s +   
453s +   # Test with and without dimnames on x
453s +   for (setDimnames in c(TRUE, FALSE)) {
453s +     if (setDimnames) dimnames(x) <- dimnames
453s +     else dimnames(x) <- NULL
453s +     # Check names attribute
453s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
453s +       y0 <- rowMeans_R(x, na.rm = TRUE, useNames = useNames)
453s +       y1 <- rowMeans2(x, na.rm = TRUE, useNames = useNames)
453s +       stopifnot(all.equal(y1, y0))
453s +       
453s +       y0 <- colMeans_R(x, na.rm = TRUE, useNames = useNames)
453s +       y1 <- colMeans2(x, na.rm = TRUE, useNames = useNames)
453s +       stopifnot(all.equal(y1, y0))
453s +     }
453s +   }
453s + }
453s > 
453s > 
453s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
453s > # Special case: All NaNs
453s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
453s > cat("Special case: All NaNs:\n")
453s Special case: All NaNs:
453s > x <- matrix(NA_real_, nrow = 3, ncol = 3)
453s > 
453s > # Test with and without dimnames on x
453s > for (setDimnames in c(TRUE, FALSE)) {
453s +   if (setDimnames) dimnames(x) <- dimnames
453s +   else dimnames(x) <- NULL
453s +   # Check names attribute
453s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
453s +     y0 <- rowMeans_R(x, na.rm = TRUE, useNames = useNames)
453s +     y1 <- rowMeans2(x, na.rm = TRUE, useNames = useNames)
453s +     stopifnot(all.equal(y1, y0))
453s +     
453s +     y0 <- colMeans_R(x, na.rm = TRUE, useNames = useNames)
453s +     y1 <- colMeans2(x, na.rm = TRUE, useNames = useNames)
453s +     stopifnot(all.equal(y1, y0))
453s +   }
453s + }
453s > 
453s > 
453s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
453s > # Special case: All Infs
453s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
453s > cat("Special case: All Infs:\n")
453s Special case: All Infs:
453s > x <- matrix(Inf, nrow = 3, ncol = 3)
453s > 
453s > # Test with and without dimnames on x
453s > for (setDimnames in c(TRUE, FALSE)) {
453s +   if (setDimnames) dimnames(x) <- dimnames
453s +   else dimnames(x) <- NULL
453s +   # Check names attribute
453s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
453s +     y0 <- rowMeans_R(x, na.rm = FALSE, useNames = useNames)
453s +     y1 <- rowMeans2(x, na.rm = FALSE, useNames = useNames)
453s +     stopifnot(all.equal(y1, y0))
453s +     
453s +     y0 <- colMeans_R(x, na.rm = FALSE, useNames = useNames)
453s +     y1 <- colMeans2(x, na.rm = FALSE, useNames = useNames)
453s +     stopifnot(all.equal(y1, y0))
453s +   }
453s + }
453s > 
453s > 
453s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
453s > # Special case: All -Infs
453s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
453s > cat("Special case: All -Infs:\n")
453s Special case: All -Infs:
453s > x <- matrix(-Inf, nrow = 3, ncol = 3)
453s > 
453s > # Test with and without dimnames on x
453s > for (setDimnames in c(TRUE, FALSE)) {
453s +   if (setDimnames) dimnames(x) <- dimnames
453s +   else dimnames(x) <- NULL
453s +   # Check names attribute
453s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
453s +     y0 <- rowMeans_R(x, na.rm = FALSE, useNames = useNames)
453s +     y1 <- rowMeans2(x, na.rm = FALSE, useNames = useNames)
453s +     stopifnot(all.equal(y1, y0))
453s +     
453s +     y0 <- colMeans_R(x, na.rm = FALSE, useNames = useNames)
453s +     y1 <- colMeans2(x, na.rm = FALSE, useNames = useNames)
453s +     stopifnot(all.equal(y1, y0))
453s +   }
453s + }
453s > 
453s > 
453s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
453s > # Special case: Infs and -Infs
453s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
453s > cat("Special case: Infs and -Infs:\n")
453s Special case: Infs and -Infs:
453s > x <- matrix(c(-Inf, +Inf), nrow = 4, ncol = 4)
453s > 
453s > # To check names attribute
453s > dimnames <- list(letters[1:4], LETTERS[1:4])
453s > 
453s > # Test with and without dimnames on x
453s > for (setDimnames in c(TRUE, FALSE)) {
453s +   if (setDimnames) dimnames(x) <- dimnames
453s +   else dimnames(x) <- NULL
453s +   # Check names attribute
453s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
453s +     y0 <- rowMeans_R(x, na.rm = FALSE, useNames = useNames)
453s +     y1 <- rowMeans2(x, na.rm = FALSE, useNames = useNames)
453s +     stopifnot(all.equal(y1, y0))
453s +     
453s +     y0 <- colMeans_R(x, na.rm = FALSE, useNames = useNames)
453s +     y1 <- colMeans2(x, na.rm = FALSE, useNames = useNames)
453s +     stopifnot(all.equal(y1, y0))
453s +   }
453s + }
453s > 
453s > 
453s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
453s > # Special case: NaNs and NAs
453s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
453s > cat("Special case: NaNs and NAs:\n")
453s Special case: NaNs and NAs:
453s > x <- matrix(c(NaN, NA_real_), nrow = 4, ncol = 4)
453s > 
453s > # Test with and without dimnames on x
453s > for (setDimnames in c(TRUE, FALSE)) {
453s +   if (setDimnames) dimnames(x) <- dimnames
453s +   else dimnames(x) <- NULL
453s +   # Check names attribute
453s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
453s +     y0 <- rowMeans_R(x, na.rm = FALSE, useNames = useNames)
453s +     str(y0)
453s +     stopifnot(all(is.na(y0)), length(unique(y0)) >= 1L)
453s +     y1 <- rowMeans2(x, na.rm = FALSE, useNames = useNames)
453s +     str(y1)
453s +     stopifnot(all(is.na(y1)), length(unique(y1)) >= 1L)
453s +     stopifnot(all.equal(y1, y0))
453s +     
453s +     y0 <- colMeans_R(x, na.rm = FALSE, useNames = useNames)
453s +     stopifnot(all(is.na(y0)), length(unique(y0)) == 1L)
453s +     y1 <- colMeans2(x, na.rm = FALSE, useNames = useNames)
453s +     stopifnot(all(is.na(y1)), length(unique(y1)) == 1L)
453s +     stopifnot(all.equal(y1, y0))
453s +   }
453s + }
453s  Named num [1:4] NaN NA NaN NA
453s  - attr(*, "names")= chr [1:4] "a" "b" "c" "d"
453s  Named num [1:4] NaN NA NaN NA
453s  - attr(*, "names")= chr [1:4] "a" "b" "c" "d"
453s  num [1:4] NaN NA NaN NA
453s  num [1:4] NaN NA NaN NA
453s  num [1:4] NaN NA NaN NA
453s  num [1:4] NaN NA NaN NA
453s  num [1:4] NaN NA NaN NA
453s  num [1:4] NaN NA NaN NA
453s > ## NOTE, due to compiler optimization, it is not guaranteed that NA is
453s > ## returned here (as one would expect). NaN might very well be returned,
453s > ## when both NA and NaN are involved.  This is an accepted feature in R,
453s > ## which is documented in help("is.nan").  See also
453s > ## https://stat.ethz.ch/pipermail/r-devel/2017-April/074009.html.
453s > ## Thus, we cannot guarantee that y1 is identical to y0.
453s > 
453s > 
453s > 
453s > 
453s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
453s > # Special case: Integer overflow with ties
453s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
453s > cat("Special case: Integer overflow with ties:\n")
453s Special case: Integer overflow with ties:
453s > x <- matrix(.Machine$integer.max, nrow = 4, ncol = 4)
453s > 
453s > # Test with and without dimnames on x
453s > for (setDimnames in c(TRUE, FALSE)) {
453s +   if (setDimnames) dimnames(x) <- dimnames
453s +   else dimnames(x) <- NULL
453s +   # Check names attribute
453s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
453s +     y0 <- rowMeans_R(x, na.rm = FALSE, useNames = useNames)
453s +     y1 <- rowMeans2(x, na.rm = FALSE, useNames = useNames)
453s +     stopifnot(all.equal(y1, y0))
453s +     
453s +     y0 <- colMeans_R(x, na.rm = FALSE, useNames = useNames)
453s +     y1 <- colMeans2(x, na.rm = FALSE, useNames = useNames)
453s +     stopifnot(all.equal(y1, y0))
453s +   }
453s + }
453s > 
453s > 
453s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
453s > # Consistency checks
453s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
453s > set.seed(1)
453s > 
453s > cat("Consistency checks:\n")
453s Consistency checks:
453s > n_sims <- if (Sys.getenv("_R_CHECK_USE_VALGRIND_") != "") 4L else 20L
453s > for (kk in seq_len(n_sims)) {
453s +   cat("Random test #", kk, "\n", sep = "")
453s + 
453s +   # Simulate data in a matrix of any shape
453s +   dim <- sample(50:200, size = 2)
453s +   n <- prod(dim)
453s +   x <- rnorm(n, sd = 100)
453s +   dim(x) <- dim
453s + 
453s +   # Add NAs?
453s +   if ((kk %% 4) %in% c(3, 0)) {
453s +     cat("Adding NAs\n")
453s +     nna <- sample(n, size = 1)
453s +     na_values <- c(NA_real_, NaN)
453s +     t <- sample(na_values, size = nna, replace = TRUE)
453s +     x[sample(length(x), size = nna)] <- t
453s +   }
453s + 
453s +   # Mode?
453s +   modes <- "double"
453s +   if ((kk %% 4) %in% c(2, 0)) {
453s +     modes <- c("integer", "logical")
453s +   }
453s + 
453s +   for (mode in modes) {
453s +     if (mode != "double") {
453s +       cat(sprintf("Coercing from %s to %s\n", storage.mode(x), mode))
453s +       storage.mode(x) <- mode
453s +     }
453s + 
453s +     na.rm <- sample(c(TRUE, FALSE), size = 1)
453s +   
453s +     # rowMeans2():
453s +     y0 <- rowMeans(x, na.rm = na.rm)
453s +     y1 <- rowMeans2(x, na.rm = na.rm)
453s +     stopifnot(all.equal(y1, y0))
453s +     y2 <- colMeans2(t(x), na.rm = na.rm)
453s +     stopifnot(all.equal(y2, y0))
453s +   
453s +     # colMeans2():
453s +     y0 <- colMeans(x, na.rm = na.rm)
453s +     y1 <- colMeans2(x, na.rm = na.rm)
453s +     stopifnot(all.equal(y1, y0))
453s +     y2 <- rowMeans2(t(x), na.rm = na.rm)
453s +     stopifnot(all.equal(y2, y0))
453s +   }
453s + } # for (kk ...)
453s Random test #1
453s Random test #2
453s Coercing from double to integer
453s Coercing from integer to logical
453s Random test #3
453s Adding NAs
453s Random test #4
453s Adding NAs
453s Coercing from double to integer
453s Coercing from integer to logical
453s Random test #5
453s Random test #6
453s Coercing from double to integer
453s Coercing from integer to logical
453s Random test #7
453s Adding NAs
453s Random test #8
453s Adding NAs
453s Coercing from double to integer
453s Coercing from integer to logical
453s Random test #9
453s Random test #10
453s Coercing from double to integer
453s Coercing from integer to logical
453s Random test #11
453s Adding NAs
453s Random test #12
453s Adding NAs
453s Coercing from double to integer
453s Coercing from integer to logical
453s Random test #13
453s Random test #14
453s Coercing from double to integer
453s Coercing from integer to logical
453s Random test #15
453s Adding NAs
453s Random test #16
453s Adding NAs
453s Coercing from double to integer
453s Coercing from integer to logical
453s Random test #17
453s Random test #18
453s Coercing from double to integer
453s Coercing from integer to logical
453s Random test #19
453s Adding NAs
453s Random test #20
453s Adding NAs
453s Coercing from double to integer
453s Coercing from integer to logical
453s > 
454s 
454s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
454s Copyright (C) 2024 The R Foundation for Statistical Computing
454s Platform: arm-unknown-linux-gnueabihf (32-bit)
454s 
454s R is free software and comes with ABSOLUTELY NO WARRANTY.
454s You are welcome to redistribute it under certain conditions.
454s Type 'license()' or 'licence()' for distribution details.
454s 
454s R is a collaborative project with many contributors.
454s Type 'contributors()' for more information and
454s 'citation()' on how to cite R or R packages in publications.
454s 
454s Type 'demo()' for some demos, 'help()' for on-line help, or
454s 'help.start()' for an HTML browser interface to help.
454s Type 'q()' to quit R.
454s 
454s > library("matrixStats")
454s > 
454s > rowMeans_R <- function(x, na.rm = FALSE, ..., useNames = NA) {
454s +   res <- rowMeans(x, na.rm = na.rm)
454s +   if (is.na(useNames) || !useNames) names(res) <- NULL
454s +   res
454s + }
454s > 
454s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
454s > # Subsetted tests
454s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
454s > source("utils/validateIndicesFramework.R")
454s > x <- matrix(runif(6 * 6, min = -3, max = 3), nrow = 6, ncol = 6)
454s > storage.mode(x) <- "integer"
454s > 
454s > # To check names attribute
454s > dimnames <- list(letters[1:6], LETTERS[1:6])
454s > 
454s > # Test with and without dimnames on x
454s > for (setDimnames in c(TRUE, FALSE)) {
454s +   if (setDimnames) dimnames(x) <- dimnames
454s +   else dimnames(x) <- NULL
454s +   
454s +   count <- 0L
454s +   for (rows in index_cases) {
454s +     for (cols in index_cases) {
454s +       count <- count + 1L
454s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
454s +       useNames <- c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)
454s +       useNames <- useNames[count %% length(useNames) + 1]
454s +       
454s +       validateIndicesTestMatrix(x, rows, cols,
454s +                                 ftest = rowMeans2, fsure = rowMeans_R,
454s +                                 na.rm = na.rm, useNames = useNames)
454s +       validateIndicesTestMatrix(x, rows, cols,
454s +                                 fcoltest = colMeans2, fsure = rowMeans_R,
454s +                                 na.rm = na.rm, useNames = useNames)
454s +     }
454s +   }
454s + }
455s > 
455s 
455s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
455s Copyright (C) 2024 The R Foundation for Statistical Computing
455s Platform: arm-unknown-linux-gnueabihf (32-bit)
455s 
455s R is free software and comes with ABSOLUTELY NO WARRANTY.
455s You are welcome to redistribute it under certain conditions.
455s Type 'license()' or 'licence()' for distribution details.
455s 
455s R is a collaborative project with many contributors.
455s Type 'contributors()' for more information and
455s 'citation()' on how to cite R or R packages in publications.
455s 
455s Type 'demo()' for some demos, 'help()' for on-line help, or
455s 'help.start()' for an HTML browser interface to help.
455s Type 'q()' to quit R.
455s 
455s > library("matrixStats")
455s > 
455s > rowMedians_R <- function(x, na.rm = FALSE, ..., useNames = NA) {
455s +   res <- apply(x, MARGIN = 1L, FUN = median, na.rm = na.rm)
455s +   if (is.na(useNames) || !useNames) names(res) <- NULL
455s +   res
455s + }
455s > 
455s > colMedians_R <- function(x, na.rm = FALSE, ..., useNames = NA) {
455s +   res <- apply(x, MARGIN = 2L, FUN = median, na.rm = na.rm)
455s +   if (is.na(useNames) || !useNames) names(res) <- NULL
455s +   res
455s + }
455s > 
455s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
455s > # Special case: Non-ties
455s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
455s > cat("Special case: Non-ties:\n")
455s Special case: Non-ties:
455s > for (mode in c("integer", "double")) {
455s +   x <- matrix(1:9 + 0.1, nrow = 3, ncol = 3)
455s +   storage.mode(x) <- mode
455s +   
455s +   # To check names attribute
455s +   dimnames <- list(letters[1:3], LETTERS[1:3])
455s +   
455s +   # Test with and without dimnames on x
455s +   for (setDimnames in c(TRUE, FALSE)) {
455s +     if (setDimnames) dimnames(x) <- dimnames
455s +     else dimnames(x) <- NULL
455s +     # Check names attribute
455s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
455s +       y0 <- rowMedians_R(x, na.rm = FALSE, useNames = useNames)
455s +       y1 <- rowMedians(x, na.rm = FALSE, useNames = useNames)
455s +       stopifnot(all.equal(y1, y0))
455s +       
455s +       y0 <- colMedians_R(x, na.rm = FALSE, useNames = useNames)
455s +       y1 <- colMedians(x, na.rm = FALSE, useNames = useNames)
455s +       stopifnot(all.equal(y1, y0))
455s +     }
455s +   }
455s + }
455s > 
455s > 
455s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
455s > # Special case: Ties
455s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
455s > cat("Special case: Ties:\n")
455s Special case: Ties:
455s > for (mode in c("integer", "double")) {
455s +   x <- matrix(1:16 + 0.1, nrow = 4, ncol = 4)
455s +   storage.mode(x) <- mode
455s +   
455s +   # To check names attribute
455s +   dimnames <- list(letters[1:4], LETTERS[1:4])
455s + 
455s +   # Test with and without dimnames on x
455s +   for (setDimnames in c(TRUE, FALSE)) {
455s +     if (setDimnames) dimnames(x) <- dimnames
455s +     else dimnames(x) <- NULL
455s +     # Check names attribute
455s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
455s +       y0 <- rowMedians_R(x, na.rm = FALSE, useNames = useNames)
455s +       y1 <- rowMedians(x, na.rm = FALSE, useNames = useNames)
455s +       stopifnot(all.equal(y1, y0))
455s +       
455s +       y0 <- colMedians_R(x, na.rm = FALSE, useNames = useNames)
455s +       y1 <- colMedians(x, na.rm = FALSE, useNames = useNames)
455s +       stopifnot(all.equal(y1, y0))
455s +     }
455s +   }
455s + }
455s > 
455s > 
455s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
455s > # Special case: Single-element matrix
455s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
455s > cat("Special case: Single-element matrix:\n")
455s Special case: Single-element matrix:
455s > for (mode in c("integer", "double")) {
455s +   x <- matrix(1, nrow = 1, ncol = 1)
455s +   storage.mode(x) <- mode
455s +   
455s +   # To check names attribute
455s +   dimnames <- list("a", "A")
455s + 
455s +   # Test with and without dimnames on x
455s +   for (setDimnames in c(TRUE, FALSE)) {
455s +     if (setDimnames) dimnames(x) <- dimnames
455s +     else dimnames(x) <- NULL
455s +     # Check names attribute
455s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
455s +       y0 <- rowMedians_R(x, na.rm = FALSE, useNames = useNames)
455s +       y1 <- rowMedians(x, na.rm = FALSE, useNames = useNames)
455s +       stopifnot(all.equal(y1, y0))
455s +       
455s +       y0 <- colMedians_R(x, na.rm = FALSE, useNames = useNames)
455s +       y1 <- colMedians(x, na.rm = FALSE, useNames = useNames)
455s +       stopifnot(all.equal(y1, y0))
455s +     }
455s +   }
455s + }
455s > 
455s > 
455s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
455s > # Special case: Empty matrix
455s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
455s > cat("Special case: Empty matrix:\n")
455s Special case: Empty matrix:
455s > for (mode in c("integer", "double")) {
455s +   x <- matrix(integer(0), nrow = 0, ncol = 0)
455s +   storage.mode(x) <- mode
455s + 
455s +   y0 <- rowMedians_R(x, na.rm = FALSE)
455s +   y1 <- rowMedians(x, na.rm = FALSE)
455s +   stopifnot(all.equal(y1, y0))
455s + 
455s +   y0 <- colMedians_R(x, na.rm = FALSE)
455s +   y1 <- colMedians(x, na.rm = FALSE)
455s +   stopifnot(all.equal(y1, y0))
455s + }
455s > 
455s > 
455s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
455s > # Special case: All NAs
455s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
455s > cat("Special case: All NAs:\n")
455s Special case: All NAs:
455s > for (mode in c("integer", "double")) {
455s +   x <- matrix(NA_integer_, nrow = 3, ncol = 3)
455s +   storage.mode(x) <- mode
455s +   
455s +   # To check names attribute
455s +   dimnames <- list(letters[1:3], LETTERS[1:3])
455s + 
455s +   # Test with and without dimnames on x
455s +   for (setDimnames in c(TRUE, FALSE)) {
455s +     if (setDimnames) dimnames(x) <- dimnames
455s +     else dimnames(x) <- NULL
455s +     # Check names attribute
455s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
455s +       y0 <- rowMedians_R(x, na.rm = TRUE, useNames = useNames)
455s +       y1 <- rowMedians(x, na.rm = TRUE, useNames = useNames)
455s +       stopifnot(all.equal(y1, y0))
455s +       
455s +       y0 <- colMedians_R(x, na.rm = TRUE, useNames = useNames)
455s +       y1 <- colMedians(x, na.rm = TRUE, useNames = useNames)
455s +       stopifnot(all.equal(y1, y0))
455s +     }
455s +   }
455s + }
456s > 
456s > 
456s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
456s > # Special case: All NaNs
456s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
456s > cat("Special case: All NaNs:\n")
456s Special case: All NaNs:
456s > x <- matrix(NA_real_, nrow = 3, ncol = 3)
456s > 
456s > # Test with and without dimnames on x
456s > for (setDimnames in c(TRUE, FALSE)) {
456s +   if (setDimnames) dimnames(x) <- dimnames
456s +   else dimnames(x) <- NULL
456s +   # Check names attribute
456s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
456s +     y0 <- rowMedians_R(x, na.rm = TRUE, useNames = useNames)
456s +     y1 <- rowMedians(x, na.rm = TRUE, useNames = useNames)
456s +     stopifnot(all.equal(y1, y0))
456s +     
456s +     y0 <- colMedians_R(x, na.rm = TRUE, useNames = useNames)
456s +     y1 <- colMedians(x, na.rm = TRUE, useNames = useNames)
456s +     stopifnot(all.equal(y1, y0))
456s +   }
456s + }
456s > 
456s > 
456s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
456s > # Special case: All Infs
456s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
456s > cat("Special case: All Infs:\n")
456s Special case: All Infs:
456s > x <- matrix(Inf, nrow = 3, ncol = 3)
456s > 
456s > # Test with and without dimnames on x
456s > for (setDimnames in c(TRUE, FALSE)) {
456s +   if (setDimnames) dimnames(x) <- dimnames
456s +   else dimnames(x) <- NULL
456s +   # Check names attribute
456s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
456s +     y0 <- rowMedians_R(x, na.rm = FALSE, useNames = useNames)
456s +     y1 <- rowMedians(x, na.rm = FALSE, useNames = useNames)
456s +     stopifnot(all.equal(y1, y0))
456s +     
456s +     y0 <- colMedians_R(x, na.rm = FALSE, useNames = useNames)
456s +     y1 <- colMedians(x, na.rm = FALSE, useNames = useNames)
456s +     stopifnot(all.equal(y1, y0))
456s +   }
456s + }
456s > 
456s > 
456s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
456s > # Special case: All -Infs
456s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
456s > cat("Special case: All -Infs:\n")
456s Special case: All -Infs:
456s > x <- matrix(-Inf, nrow = 3, ncol = 3)
456s > 
456s > # Test with and without dimnames on x
456s > for (setDimnames in c(TRUE, FALSE)) {
456s +   if (setDimnames) dimnames(x) <- dimnames
456s +   else dimnames(x) <- NULL
456s +   # Check names attribute
456s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
456s +     y0 <- rowMedians_R(x, na.rm = FALSE, useNames = useNames)
456s +     y1 <- rowMedians(x, na.rm = FALSE, useNames = useNames)
456s +     stopifnot(all.equal(y1, y0))
456s +     
456s +     y0 <- colMedians_R(x, na.rm = FALSE, useNames = useNames)
456s +     y1 <- colMedians(x, na.rm = FALSE, useNames = useNames)
456s +     stopifnot(all.equal(y1, y0))
456s +   }
456s + }
456s > 
456s > 
456s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
456s > # Special case: Infs and -Infs
456s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
456s > cat("Special case: Infs and -Infs:\n")
456s Special case: Infs and -Infs:
456s > x <- matrix(c(-Inf, +Inf), nrow = 4, ncol = 4)
456s > 
456s > # To check names attribute
456s > dimnames <- list(letters[1:4], LETTERS[1:4])
456s > 
456s > # Test with and without dimnames on x
456s > for (setDimnames in c(TRUE, FALSE)) {
456s +   if (setDimnames) dimnames(x) <- dimnames
456s +   else dimnames(x) <- NULL
456s +   # Check names attribute
456s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
456s +     y0 <- rowMedians_R(x, na.rm = FALSE, useNames = useNames)
456s +     y1 <- rowMedians(x, na.rm = FALSE, useNames = useNames)
456s +     stopifnot(all.equal(y1, y0))
456s +     
456s +     y0 <- colMedians_R(x, na.rm = FALSE, useNames = useNames)
456s +     y1 <- colMedians(x, na.rm = FALSE, useNames = useNames)
456s +     stopifnot(all.equal(y1, y0))
456s +   }
456s + }
456s > 
456s > 
456s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
456s > # Special case: Integer overflow with ties
456s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
456s > cat("Special case: Integer overflow with ties:\n")
456s Special case: Integer overflow with ties:
456s > x <- matrix(.Machine$integer.max, nrow = 4, ncol = 4)
456s > 
456s > # Test with and without dimnames on x
456s > for (setDimnames in c(TRUE, FALSE)) {
456s +   if (setDimnames) dimnames(x) <- dimnames
456s +   else dimnames(x) <- NULL
456s +   # Check names attribute
456s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
456s +     y0 <- rowMedians_R(x, na.rm = FALSE, useNames = useNames)
456s +     y1 <- rowMedians(x, na.rm = FALSE, useNames = useNames)
456s +     stopifnot(all.equal(y1, y0))
456s +     
456s +     y0 <- colMedians_R(x, na.rm = FALSE, useNames = useNames)
456s +     y1 <- colMedians(x, na.rm = FALSE, useNames = useNames)
456s +     stopifnot(all.equal(y1, y0))
456s +   }
456s + }
456s > 
456s > 
456s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
456s > # Consistency checks
456s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
456s > set.seed(1)
456s > 
456s > cat("Consistency checks:\n")
456s Consistency checks:
456s > n_sims <- if (Sys.getenv("_R_CHECK_USE_VALGRIND_") != "") 4L else 20L
456s > for (kk in seq_len(n_sims)) {
456s +   cat("Random test #", kk, "\n", sep = "")
456s + 
456s +   # Simulate data in a matrix of any shape
456s +   dim <- sample(50:200, size = 2)
456s +   n <- prod(dim)
456s +   x <- rnorm(n, sd = 100)
456s +   dim(x) <- dim
456s + 
456s +   # Add NAs?
456s +   if ((kk %% 4) %in% c(3, 0)) {
456s +     cat("Adding NAs\n")
456s +     nna <- sample(n, size = 1)
456s +     na_values <- c(NA_real_, NaN)
456s +     t <- sample(na_values, size = nna, replace = TRUE)
456s +     x[sample(length(x), size = nna)] <- t
456s +   }
456s + 
456s +   # Integer or double?
456s +   if ((kk %% 4) %in% c(2, 0)) {
456s +     cat("Coercing to integers\n")
456s +     storage.mode(x) <- "integer"
456s +   }
456s + 
456s +   na.rm <- sample(c(TRUE, FALSE), size = 1)
456s + 
456s +   # rowMedians():
456s +   y0 <- rowMedians_R(x, na.rm = na.rm)
456s +   y1 <- rowMedians(x, na.rm = na.rm)
456s +   stopifnot(all.equal(y1, y0))
456s +   y2 <- colMedians(t(x), na.rm = na.rm)
456s +   stopifnot(all.equal(y2, y0))
456s + 
456s +   # colMedians():
456s +   y0 <- colMedians_R(x, na.rm = na.rm)
456s +   y1 <- colMedians(x, na.rm = na.rm)
456s +   stopifnot(all.equal(y1, y0))
456s +   y2 <- rowMedians(t(x), na.rm = na.rm)
456s +   stopifnot(all.equal(y2, y0))
456s + } # for (kk ...)
456s Random test #1
456s Random test #2
456s Coercing to integers
456s Random test #3
456s Adding NAs
456s Random test #4
456s Adding NAs
456s Coercing to integers
456s Random test #5
456s Random test #6
456s Coercing to integers
456s Random test #7
456s Adding NAs
456s Random test #8
456s Adding NAs
456s Coercing to integers
456s Random test #9
456s Random test #10
456s Coercing to integers
456s Random test #11
456s Adding NAs
456s Random test #12
456s Adding NAs
456s Coercing to integers
456s Random test #13
456s Random test #14
456s Coercing to integers
456s Random test #15
456s Adding NAs
456s Random test #16
456s Adding NAs
456s Coercing to integers
456s Random test #17
456s Random test #18
456s Coercing to integers
457s Random test #19
457s Adding NAs
457s Random test #20
457s Adding NAs
457s Coercing to integers
457s > 
457s 
457s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
457s Copyright (C) 2024 The R Foundation for Statistical Computing
457s Platform: arm-unknown-linux-gnueabihf (32-bit)
457s 
457s R is free software and comes with ABSOLUTELY NO WARRANTY.
457s You are welcome to redistribute it under certain conditions.
457s Type 'license()' or 'licence()' for distribution details.
457s 
457s R is a collaborative project with many contributors.
457s Type 'contributors()' for more information and
457s 'citation()' on how to cite R or R packages in publications.
457s 
457s Type 'demo()' for some demos, 'help()' for on-line help, or
457s 'help.start()' for an HTML browser interface to help.
457s Type 'q()' to quit R.
457s 
457s > library("matrixStats")
457s > 
457s > rowMedians_R <- function(x, na.rm = FALSE, ..., useNames = NA) {
457s +   res <- apply(x, MARGIN = 1L, FUN = median, na.rm = na.rm)
457s +   if (is.na(useNames) || !useNames) names(res) <- NULL
457s +   res
457s + }
457s > 
457s > colMedians_R <- function(x, na.rm = FALSE, ..., useNames = NA) {
457s +   res <- apply(x, MARGIN = 2L, FUN = median, na.rm = na.rm)
457s +   if (is.na(useNames) || !useNames) names(res) <- NULL
457s +   res
457s + }
457s > 
457s > 
457s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
457s > # Subsetted tests
457s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
457s > source("utils/validateIndicesFramework.R")
457s > x <- matrix(runif(6 * 6, min = -3, max = 3), nrow = 6, ncol = 6)
457s > storage.mode(x) <- "integer"
457s > 
457s > # To check names attribute
457s > dimnames <- list(letters[1:6], LETTERS[1:6])
457s > 
457s > # Test with and without dimnames on x
457s > for (setDimnames in c(TRUE, FALSE)) {
457s +   if (setDimnames) dimnames(x) <- dimnames
457s +   else dimnames(x) <- NULL
457s + 
457s +   count <- 0L
457s +   for (rows in index_cases) {
457s +     for (cols in index_cases) {
457s +       count <- count + 1L
457s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
457s +       useNames <- c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)
457s +       useNames <- useNames[count %% length(useNames) + 1]
457s +       
457s +       validateIndicesTestMatrix(x, rows, cols,
457s +                                 ftest = rowMedians, fsure = rowMedians_R,
457s +                                 na.rm = na.rm, useNames = useNames)
457s +       validateIndicesTestMatrix(x, rows, cols,
457s +                                 fcoltest = colMedians, fsure = rowMedians_R,
457s +                                 na.rm = na.rm, useNames = useNames)
457s +     }
457s +   }
457s + }
458s > 
458s 
458s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
458s Copyright (C) 2024 The R Foundation for Statistical Computing
458s Platform: arm-unknown-linux-gnueabihf (32-bit)
458s 
458s R is free software and comes with ABSOLUTELY NO WARRANTY.
458s You are welcome to redistribute it under certain conditions.
458s Type 'license()' or 'licence()' for distribution details.
458s 
458s R is a collaborative project with many contributors.
458s Type 'contributors()' for more information and
458s 'citation()' on how to cite R or R packages in publications.
458s 
458s Type 'demo()' for some demos, 'help()' for on-line help, or
458s 'help.start()' for an HTML browser interface to help.
458s Type 'q()' to quit R.
458s 
459s > library("matrixStats")
459s > library("stats")
459s > 
459s > asWhich <- function(probs, max) {
459s +   idx <- as.integer(round(probs * max))
459s +   if (idx < 1L) {
459s +     idx <- 1L
459s +   } else if (idx > max) {
459s +     idx <- max
459s +   }
459s +   idx
459s + } # asWhich()
459s > 
459s > rowOrderStats_R <- function(x, probs, ..., useNames = NA) {
459s +   ans <- apply(x, MARGIN = 1L, FUN = quantile, probs = probs, type = 3L)
459s +   
459s +   # Remove Attributes
459s +   if (is.na(useNames) || !useNames || length(ans) == 0L) attributes(ans) <- NULL
459s +   ans
459s + } # rowOrderStats_R()
459s > 
459s > 
459s > set.seed(1)
459s > 
459s > 
459s > # Simulate data in a matrix of any shape
459s > nrow <- 60L
459s > ncol <- 30L
459s > x <- rnorm(nrow * ncol)
459s > dim(x) <- c(nrow, ncol)
459s > probs <- 0.3
459s > which <- asWhich(probs, max = ncol)
459s > 
459s > y0 <- rowOrderStats_R(x, probs = probs)
459s > y1 <- rowOrderStats(x, which = which)
459s > stopifnot(all.equal(y1, y0))
459s > y2 <- colOrderStats(t(x), which = which)
459s > stopifnot(all.equal(y2, y0))
459s > 
459s > 
459s > 
459s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
459s > # Consistency checks
459s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
459s > for (mode in c("integer", "double")) {
459s +   cat("Consistency checks without NAs:\n")
459s +   for (kk in 1:3) {
459s +     cat("Random test #", kk, "\n", sep = "")
459s + 
459s +     # Simulate data in a matrix of any shape
459s +     nrow <- sample(20L, size = 1L)
459s +     ncol <- sample(20L, size = 1L)
459s +     x <- rnorm(nrow * ncol)
459s +     dim(x) <- c(nrow, ncol)
459s + 
459s +     cat("mode: ", mode, "\n", sep = "")
459s +     storage.mode(x) <- mode
459s +     str(x)
459s + 
459s +     probs <- runif(1)
459s +     which <- asWhich(probs, max = ncol)
459s + 
459s +     y0 <- rowOrderStats_R(x, probs = probs)
459s +     y1 <- rowOrderStats(x, which = which)
459s +     stopifnot(all.equal(y1, y0))
459s +     y2 <- colOrderStats(t(x), which = which)
459s +     stopifnot(all.equal(y2, y0))
459s +   } # for (kk in ...)
459s + } # for (mode ...)
459s Consistency checks without NAs:
459s Random test #1
459s mode: integer
459s  int [1:14, 1:6] 0 0 1 0 2 -1 1 0 0 0 ...
459s Random test #2
459s mode: integer
459s  int [1:8, 1:13] 0 0 1 -2 0 0 0 0 1 0 ...
459s Random test #3
459s mode: integer
459s  int [1:20, 1:17] 0 0 0 0 1 0 1 0 0 -1 ...
459s Consistency checks without NAs:
459s Random test #1
459s mode: double
459s  num [1:9, 1:5] -1.4286 -0.00386 -0.70456 -0.29242 -0.49607 ...
459s Random test #2
459s mode: double
459s  num [1:11, 1:20] -0.796 0.482 -0.952 0.5 1.242 ...
459s Random test #3
459s mode: double
459s  num [1:7, 1:18] 1.553 -2.405 0.167 -0.403 -1.746 ...
459s > 
459s > 
459s > # Check names attribute
459s > x <- matrix(1:9 + 0.1, nrow = 3L, ncol = 3L)
459s > 
459s > probs <- runif(1)
459s > which <- asWhich(probs, max = ncol(x))
459s > 
459s > dimnames <- list(letters[1:3], LETTERS[1:3])
459s > 
459s > # Test with and without dimnames on x
459s > for (setDimnames in c(TRUE, FALSE)) {
459s +   if (setDimnames) dimnames(x) <- dimnames
459s +   else dimnames(x) <- NULL
459s +   # Check names attribute
459s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
459s +     y0 <- rowOrderStats_R(x, probs = probs, useNames = useNames)
459s +     y1 <- rowOrderStats(x, which = which, useNames = useNames)
459s +     stopifnot(all.equal(y1, y0))
459s +     y2 <- colOrderStats(t(x), which = which, useNames = useNames)
459s +     stopifnot(all.equal(y2, y0))    
459s +   }
459s + }
459s > 
459s 
459s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
459s Copyright (C) 2024 The R Foundation for Statistical Computing
459s Platform: arm-unknown-linux-gnueabihf (32-bit)
459s 
459s R is free software and comes with ABSOLUTELY NO WARRANTY.
459s You are welcome to redistribute it under certain conditions.
459s Type 'license()' or 'licence()' for distribution details.
459s 
459s R is a collaborative project with many contributors.
459s Type 'contributors()' for more information and
459s 'citation()' on how to cite R or R packages in publications.
459s 
459s Type 'demo()' for some demos, 'help()' for on-line help, or
459s 'help.start()' for an HTML browser interface to help.
459s Type 'q()' to quit R.
459s 
459s > library("matrixStats")
459s > 
459s > rowOrderStats_R <- function(x, probs, ..., useNames = NA) {
459s +   ans <- apply(x, MARGIN = 1L, FUN = quantile, probs = probs, type = 3L)
459s + 
459s +   # Remove Attributes
459s +   if (is.na(useNames) || !useNames || length(ans) == 0L) attributes(ans) <- NULL
459s +   ans
459s + } # rowOrderStats_R()
459s > 
459s > 
459s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
459s > # Subsetted tests
459s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
459s > source("utils/validateIndicesFramework.R")
459s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
459s > storage.mode(x) <- "integer"
459s > 
459s > # To check names attribute
459s > dimnames <- list(letters[1:6], LETTERS[1:6])
459s > 
459s > probs <- 0.3
459s > # Test with and without dimnames on x
459s > for (setDimnames in c(TRUE, FALSE)) {
459s +   if (setDimnames) dimnames(x) <- dimnames
459s +   else dimnames(x) <- NULL
459s +   for (rows in index_cases) {
459s +     for (cols in index_cases) {
459s +       # Check names attribute
459s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
459s +         if (is.null(cols)) which <- round(probs * ncol(x))
459s +         else {
459s +           xxrows <- rows
459s +           suppressWarnings({
459s +             xx <- tryCatch(x[, cols, drop = FALSE], error = function(c) "error")
459s +             if (identical(xx, "error")) which <- 0L
459s +             else which <- round(probs * ncol(xx))
459s +           })
459s +         }
459s +         if (which == 0L) next
459s +     
459s +         validateIndicesTestMatrix(x, rows, cols,
459s +                                   ftest = rowOrderStats, fsure = rowOrderStats_R,
459s +                                   which = which, probs = probs, useNames = useNames)
459s +         validateIndicesTestMatrix(x, rows, cols,
459s +                                   fcoltest = colOrderStats, fsure = rowOrderStats_R,
459s +                                   which = which, probs = probs, useNames = useNames)
459s +       }
459s +     }
459s +   }
459s + }
462s > 
463s 
463s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
463s Copyright (C) 2024 The R Foundation for Statistical Computing
463s Platform: arm-unknown-linux-gnueabihf (32-bit)
463s 
463s R is free software and comes with ABSOLUTELY NO WARRANTY.
463s You are welcome to redistribute it under certain conditions.
463s Type 'license()' or 'licence()' for distribution details.
463s 
463s R is a collaborative project with many contributors.
463s Type 'contributors()' for more information and
463s 'citation()' on how to cite R or R packages in publications.
463s 
463s Type 'demo()' for some demos, 'help()' for on-line help, or
463s 'help.start()' for an HTML browser interface to help.
463s Type 'q()' to quit R.
463s 
463s > library("matrixStats")
463s > 
463s > rowProds_R <- function(x, FUN = prod, na.rm = FALSE, ..., useNames = NA) {
463s +   res <- apply(x, MARGIN = 1L, FUN = FUN, na.rm = na.rm)
463s +   if (is.na(useNames) || !useNames) names(res) <- NULL
463s +   res
463s + }
463s > 
463s > all.equal.na <- function(target, current, ...) {
463s +   # Computations involving NaN may return NaN or NA, cf. ?is.nan
463s +   current[is.nan(current)] <- NA_real_
463s +   target[is.nan(target)] <- NA_real_
463s +   all.equal(target, current, ...)
463s + }
463s > 
463s > for (mode in c("integer", "double")) {
463s +   # Missing values
463s +   x <- matrix(c(1, NA, NaN, 1, 1, 0, 1, 0), nrow = 4, ncol = 2)
463s +   cat("mode: ", mode, "\n", sep = "")
463s +   storage.mode(x) <- mode
463s +   str(x)
463s +   
463s +   # To check names attribute
463s +   dimnames <- list(letters[1:4], LETTERS[1:2])
463s +   
463s +   # Test with and without dimnames on x
463s +   for (setDimnames in c(TRUE, FALSE)) {
463s +     if (setDimnames) dimnames(x) <- dimnames
463s +     else dimnames(x) <- NULL
463s +     # Check names attribute
463s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
463s +       y0 <- rowProds_R(x, na.rm = TRUE, useNames = useNames)
463s +       print(y0)
463s +       y1 <- rowProds(x, na.rm = TRUE, useNames = useNames)
463s +       print(y1)
463s +       y2 <- colProds(t(x), na.rm = TRUE, useNames = useNames)
463s +       print(y2)
463s +       stopifnot(all.equal(y1, y0))
463s +       stopifnot(all.equal(y2, y1))
463s +       
463s +       # Missing values
463s +       y0 <- rowProds_R(x, na.rm = FALSE, useNames = useNames)
463s +       print(y0)
463s +       y1 <- rowProds(x, na.rm = FALSE, useNames = useNames)
463s +       print(y1)
463s +       y2 <- colProds(t(x), na.rm = FALSE, useNames = useNames)
463s +       print(y2)
463s +       stopifnot(all.equal(y1, y0))
463s +       stopifnot(all.equal(y2, y1))
463s +       
463s +       # "Empty" rows
463s +       y0 <- rowProds_R(x[integer(0), , drop = FALSE], na.rm = FALSE, useNames = useNames)
463s +       print(y0)
463s +       y1 <- rowProds(x[integer(0), , drop = FALSE], na.rm = FALSE, useNames = useNames)
463s +       print(y1)
463s +       y2 <- colProds(t(x[integer(0), , drop = FALSE]), na.rm = FALSE, useNames = useNames)
463s +       print(y2)
463s +       stopifnot(all.equal.na(y1, y0))
463s +       stopifnot(all.equal(y2, y1))
463s +       stopifnot(length(y1) == 0L)
463s +       
463s +       # Using product()
463s +       y1 <- rowProds(x, method = "expSumLog", na.rm = FALSE, useNames = useNames)
463s +       print(y1)
463s +       y2 <- colProds(t(x), method = "expSumLog", na.rm = FALSE, useNames = useNames)
463s +       print(y2)
463s +       stopifnot(all.equal(y2, y1))
463s +     }
463s +   }
463s + } # for (mode ...)
463s mode: integer
463s  int [1:4, 1:2] 1 NA NA 1 1 0 1 0
463s a b c d 
463s 1 0 1 0 
463s a b c d 
463s 1 0 1 0 
463s a b c d 
463s 1 0 1 0 
463s  a  b  c  d 
463s  1 NA NA  0 
463s  a  b  c  d 
463s  1 NA NA  0 
463s  a  b  c  d 
463s  1 NA NA  0 
463s numeric(0)
463s numeric(0)
463s numeric(0)
463s  a  b  c  d 
463s  1 NA NA  0 
463s  a  b  c  d 
463s  1 NA NA  0 
463s [1] 1 0 1 0
463s [1] 1 0 1 0
463s [1] 1 0 1 0
463s [1]  1 NA NA  0
463s [1]  1 NA NA  0
463s [1]  1 NA NA  0
463s numeric(0)
463s numeric(0)
463s numeric(0)
463s [1]  1 NA NA  0
463s [1]  1 NA NA  0
463s [1] 1 0 1 0
463s [1] 1 0 1 0
463s [1] 1 0 1 0
463s [1]  1 NA NA  0
463s [1]  1 NA NA  0
463s [1]  1 NA NA  0
463s numeric(0)
463s numeric(0)
463s numeric(0)
463s [1]  1 NA NA  0
463s [1]  1 NA NA  0
463s [1] 1 0 1 0
463s [1] 1 0 1 0
463s [1] 1 0 1 0
463s [1]  1 NA NA  0
463s [1]  1 NA NA  0
463s [1]  1 NA NA  0
463s numeric(0)
463s numeric(0)
463s numeric(0)
463s [1]  1 NA NA  0
463s [1]  1 NA NA  0
463s mode: double
463s  num [1:4, 1:2] 1 NA NaN 1 1 0 1 0
463s a b c d 
463s 1 0 1 0 
463s a b c d 
463s 1 0 1 0 
463s a b c d 
463s 1 0 1 0 
463s   a   b   c   d 
463s   1  NA NaN   0 
463s   a   b   c   d 
463s   1  NA NaN   0 
463s   a   b   c   d 
463s   1  NA NaN   0 
463s numeric(0)
463s numeric(0)
463s numeric(0)
463s  a  b  c  d 
463s  1 NA NA  0 
463s  a  b  c  d 
463s  1 NA NA  0 
463s [1] 1 0 1 0
463s [1] 1 0 1 0
463s [1] 1 0 1 0
463s [1]   1  NA NaN   0
463s [1]   1  NA NaN   0
463s [1]   1  NA NaN   0
463s numeric(0)
463s numeric(0)
463s numeric(0)
463s [1]  1 NA NA  0
463s [1]  1 NA NA  0
463s [1] 1 0 1 0
463s [1] 1 0 1 0
463s [1] 1 0 1 0
463s [1]   1  NA NaN   0
463s [1]   1  NA NaN   0
463s [1]   1  NA NaN   0
463s numeric(0)
463s numeric(0)
463s numeric(0)
463s [1]  1 NA NA  0
463s [1]  1 NA NA  0
463s [1] 1 0 1 0
463s [1] 1 0 1 0
463s [1] 1 0 1 0
463s [1]   1  NA NaN   0
463s [1]   1  NA NaN   0
463s [1]   1  NA NaN   0
463s numeric(0)
463s numeric(0)
463s numeric(0)
463s [1]  1 NA NA  0
463s [1]  1 NA NA  0
463s > 
463s > 
463s > # Bug report 2012-06-25
463s > x <- matrix(c(1, 1, 1, 1, 1, 0, 1, 0), nrow = 4, ncol = 2)
463s > y0 <- rowProds_R(x)
463s > print(y0)
463s [1] 1 0 1 0
463s > y1 <- rowProds(x)
463s > print(y1)
463s [1] 1 0 1 0
463s > y2 <- colProds(t(x))
463s > print(y2)
463s [1] 1 0 1 0
463s > stopifnot(all.equal.na(y1, y0))
463s > stopifnot(all.equal.na(y1, x[, 1] * x[, 2]))
463s > stopifnot(all.equal.na(y2, y1))
463s > # Check names attribute
463s > dimnames(x) <- dimnames
463s > y0 <- rowProds_R(x, useNames = TRUE)
463s > print(y0)
463s a b c d 
463s 1 0 1 0 
463s > y1 <- rowProds(x, useNames = TRUE)
463s > print(y1)
463s a b c d 
463s 1 0 1 0 
463s > y2 <- colProds(t(x), useNames = TRUE)
463s > print(y2)
463s a b c d 
463s 1 0 1 0 
463s > stopifnot(all.equal.na(y1, y0))
463s > stopifnot(all.equal.na(y1, x[, 1] * x[, 2]))
463s > stopifnot(all.equal.na(y2, y1))
463s > 
463s > # Bug report 2014-03-25 ("all rows contains a zero")
463s > x <- matrix(c(0, 1, 1, 0), nrow = 2, ncol = 2)
463s > # To check names attribute
463s > dimnames <- list(letters[1:2], LETTERS[1:2])
463s > y0 <- rowProds_R(x)
463s > print(y0)
463s [1] 0 0
463s > y1 <- rowProds(x)
463s > print(y1)
463s [1] 0 0
463s > y2 <- colProds(t(x))
463s > print(y2)
463s [1] 0 0
463s > stopifnot(all.equal.na(y1, y0))
463s > stopifnot(all.equal.na(y1, c(0, 0)))
463s > stopifnot(all.equal.na(y2, y1))
463s > # Check names attribute
463s > dimnames(x) <- dimnames
463s > y0 <- rowProds_R(x, useNames = TRUE)
463s > print(y0)
463s a b 
463s 0 0 
463s > y1 <- rowProds(x, useNames = TRUE)
463s > print(y1)
463s a b 
463s 0 0 
463s > y2 <- colProds(t(x), useNames = TRUE)
463s > print(y2)
463s a b 
463s 0 0 
463s > stopifnot(all.equal.na(y1, y0))
463s > stopifnot(all.equal.na(y2, y1))
463s > 
463s 
463s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
463s Copyright (C) 2024 The R Foundation for Statistical Computing
463s Platform: arm-unknown-linux-gnueabihf (32-bit)
463s 
463s R is free software and comes with ABSOLUTELY NO WARRANTY.
463s You are welcome to redistribute it under certain conditions.
463s Type 'license()' or 'licence()' for distribution details.
463s 
463s R is a collaborative project with many contributors.
463s Type 'contributors()' for more information and
463s 'citation()' on how to cite R or R packages in publications.
463s 
463s Type 'demo()' for some demos, 'help()' for on-line help, or
463s 'help.start()' for an HTML browser interface to help.
463s Type 'q()' to quit R.
463s 
464s > library("matrixStats")
464s > 
464s > rowProds_R <- function(x, FUN = prod, na.rm = FALSE, ..., useNames = NA) {
464s +   res <- apply(x, MARGIN = 1L, FUN = FUN, na.rm = na.rm)
464s +   if (is.na(useNames) || !useNames) names(res) <- NULL
464s +   res
464s + }
464s > 
464s > 
464s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
464s > # Subsetted tests
464s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
464s > source("utils/validateIndicesFramework.R")
464s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
464s > storage.mode(x) <- "integer"
464s > 
464s > # To check names attribute
464s > dimnames <- list(letters[1:6], LETTERS[1:6])
464s > 
464s > # Test with and without dimnames on x
464s > for (setDimnames in c(TRUE, FALSE)) {
464s +   if (setDimnames) dimnames(x) <- dimnames
464s +   else dimnames(x) <- NULL
464s +   for (rows in index_cases) {
464s +     for (cols in index_cases) {
464s +       for (na.rm in c(TRUE, FALSE)) {
464s +         for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
464s +           validateIndicesTestMatrix(x, rows, cols,
464s +                                     ftest = rowProds, fsure = rowProds_R,
464s +                                     method = "expSumLog",
464s +                                     FUN = product, na.rm = na.rm, useNames = useNames)
464s +           validateIndicesTestMatrix(x, rows, cols,
464s +                                     fcoltest = colProds, fsure = rowProds_R,
464s +                                     method = "expSumLog",
464s +                                     FUN = product, na.rm = na.rm, useNames = useNames)
464s +         }
464s +       }
464s +     }
464s +   }
464s + }
467s > 
467s 
467s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
467s Copyright (C) 2024 The R Foundation for Statistical Computing
467s Platform: arm-unknown-linux-gnueabihf (32-bit)
467s 
467s R is free software and comes with ABSOLUTELY NO WARRANTY.
467s You are welcome to redistribute it under certain conditions.
467s Type 'license()' or 'licence()' for distribution details.
467s 
467s R is a collaborative project with many contributors.
467s Type 'contributors()' for more information and
467s 'citation()' on how to cite R or R packages in publications.
467s 
467s Type 'demo()' for some demos, 'help()' for on-line help, or
467s 'help.start()' for an HTML browser interface to help.
467s Type 'q()' to quit R.
467s 
468s > library("matrixStats")
468s > 
468s > ## Create isFALSE() if running on an old version of R
468s > if (!exists("isFALSE", mode="function")) {
468s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
468s + }
468s > 
468s > rowQuantiles_R <- function(x, probs = c(0, 0.25, 0.50, 0.75, 1), na.rm = FALSE, drop = TRUE, type = 7L, ..., useNames = NA) {
468s +   q <- apply(x, MARGIN = 1L, FUN = function(x, probs, na.rm) {
468s +     if (!na.rm && any(is.na(x))) {
468s +       na_value <- NA_real_
468s +       if (type != 7L) storage.mode(na_value) <- storage.mode(x)
468s +       rep(na_value, times = length(probs))
468s +     } else {
468s +       as.vector(quantile(x, probs = probs, na.rm = na.rm, type = type, names = FALSE, ...))
468s +     }
468s +   }, probs = probs, na.rm = na.rm)
468s + 
468s +   if (!is.null(dim(q))) q <- t(q)
468s +   else dim(q) <- c(nrow(x), length(probs))
468s + 
468s +   colnames(q) <- matrixStats:::quantile_probs_names(probs)
468s +   rownames(q) <- rownames(x)
468s +   if (isFALSE(useNames)) dimnames(q) <- NULL
468s + 
468s +   if (drop) q <- drop(q)
468s +   q
468s + }
468s > 
468s > 
468s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
468s > # Test with multiple quantiles
468s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
468s > for (mode in c("logical", "integer", "double")) {
468s +   cat("mode: ", mode, "\n", sep = "")
468s +   x <- matrix(1:40 + 0.1, nrow = 8, ncol = 5)
468s +   storage.mode(x) <- mode
468s +   dimnames <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
468s +   str(x)
468s + 
468s +   probs <- c(0, 0.5, 1)
468s +   # Test with and without dimnames on x
468s +   for (setDimnames in c(TRUE, FALSE)) {
468s +     if (setDimnames) dimnames(x) <- dimnames
468s +     else dimnames(x) <- NULL    
468s +     # Check names attribute
468s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
468s +       q0 <- rowQuantiles_R(x, probs = probs, useNames = useNames)
468s +       print(q0)
468s +       q1 <- rowQuantiles(x, probs = probs, useNames = useNames)
468s +       print(q1)
468s +       ## FIXME: Workaround for R (< 3.0.0)
468s +       if (getRversion() < "3.0.0" && mode == "logical") storage.mode(q1) <- storage.mode(q0)
468s +       stopifnot(all.equal(q1, q0))
468s +       q2 <- colQuantiles(t(x), probs = probs, useNames = useNames)
468s +       ## FIXME: Workaround for R (< 3.0.0)
468s +       if (getRversion() < "3.0.0" && mode == "logical") storage.mode(q2) <- storage.mode(q0)
468s +       stopifnot(all.equal(q2, q0))      
468s +     }
468s +   }
468s + } # for (mode ...)
468s mode: logical
468s  logi [1:8, 1:5] TRUE TRUE TRUE TRUE TRUE TRUE ...
468s   0% 50% 100%
468s a  1   1    1
468s b  1   1    1
468s c  1   1    1
468s d  1   1    1
468s e  1   1    1
468s f  1   1    1
468s g  1   1    1
468s h  1   1    1
468s   0% 50% 100%
468s a  1   1    1
468s b  1   1    1
468s c  1   1    1
468s d  1   1    1
468s e  1   1    1
468s f  1   1    1
468s g  1   1    1
468s h  1   1    1
468s      [,1] [,2] [,3]
468s [1,]    1    1    1
468s [2,]    1    1    1
468s [3,]    1    1    1
468s [4,]    1    1    1
468s [5,]    1    1    1
468s [6,]    1    1    1
468s [7,]    1    1    1
468s [8,]    1    1    1
468s      [,1] [,2] [,3]
468s [1,]    1    1    1
468s [2,]    1    1    1
468s [3,]    1    1    1
468s [4,]    1    1    1
468s [5,]    1    1    1
468s [6,]    1    1    1
468s [7,]    1    1    1
468s [8,]    1    1    1
468s      0% 50% 100%
468s [1,]  1   1    1
468s [2,]  1   1    1
468s [3,]  1   1    1
468s [4,]  1   1    1
468s [5,]  1   1    1
468s [6,]  1   1    1
468s [7,]  1   1    1
468s [8,]  1   1    1
468s      0% 50% 100%
468s [1,]  1   1    1
468s [2,]  1   1    1
468s [3,]  1   1    1
468s [4,]  1   1    1
468s [5,]  1   1    1
468s [6,]  1   1    1
468s [7,]  1   1    1
468s [8,]  1   1    1
468s      [,1] [,2] [,3]
468s [1,]    1    1    1
468s [2,]    1    1    1
468s [3,]    1    1    1
468s [4,]    1    1    1
468s [5,]    1    1    1
468s [6,]    1    1    1
468s [7,]    1    1    1
468s [8,]    1    1    1
468s      [,1] [,2] [,3]
468s [1,]    1    1    1
468s [2,]    1    1    1
468s [3,]    1    1    1
468s [4,]    1    1    1
468s [5,]    1    1    1
468s [6,]    1    1    1
468s [7,]    1    1    1
468s [8,]    1    1    1
468s mode: integer
468s  int [1:8, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
468s   0% 50% 100%
468s a  1  17   33
468s b  2  18   34
468s c  3  19   35
468s d  4  20   36
468s e  5  21   37
468s f  6  22   38
468s g  7  23   39
468s h  8  24   40
468s   0% 50% 100%
468s a  1  17   33
468s b  2  18   34
468s c  3  19   35
468s d  4  20   36
468s e  5  21   37
468s f  6  22   38
468s g  7  23   39
468s h  8  24   40
468s      [,1] [,2] [,3]
468s [1,]    1   17   33
468s [2,]    2   18   34
468s [3,]    3   19   35
468s [4,]    4   20   36
468s [5,]    5   21   37
468s [6,]    6   22   38
468s [7,]    7   23   39
468s [8,]    8   24   40
468s      [,1] [,2] [,3]
468s [1,]    1   17   33
468s [2,]    2   18   34
468s [3,]    3   19   35
468s [4,]    4   20   36
468s [5,]    5   21   37
468s [6,]    6   22   38
468s [7,]    7   23   39
468s [8,]    8   24   40
468s      0% 50% 100%
468s [1,]  1  17   33
468s [2,]  2  18   34
468s [3,]  3  19   35
468s [4,]  4  20   36
468s [5,]  5  21   37
468s [6,]  6  22   38
468s [7,]  7  23   39
468s [8,]  8  24   40
468s      0% 50% 100%
468s [1,]  1  17   33
468s [2,]  2  18   34
468s [3,]  3  19   35
468s [4,]  4  20   36
468s [5,]  5  21   37
468s [6,]  6  22   38
468s [7,]  7  23   39
468s [8,]  8  24   40
468s      [,1] [,2] [,3]
468s [1,]    1   17   33
468s [2,]    2   18   34
468s [3,]    3   19   35
468s [4,]    4   20   36
468s [5,]    5   21   37
468s [6,]    6   22   38
468s [7,]    7   23   39
468s [8,]    8   24   40
468s      [,1] [,2] [,3]
468s [1,]    1   17   33
468s [2,]    2   18   34
468s [3,]    3   19   35
468s [4,]    4   20   36
468s [5,]    5   21   37
468s [6,]    6   22   38
468s [7,]    7   23   39
468s [8,]    8   24   40
468s mode: double
468s  num [1:8, 1:5] 1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1 10.1 ...
468s    0%  50% 100%
468s a 1.1 17.1 33.1
468s b 2.1 18.1 34.1
468s c 3.1 19.1 35.1
468s d 4.1 20.1 36.1
468s e 5.1 21.1 37.1
468s f 6.1 22.1 38.1
468s g 7.1 23.1 39.1
468s h 8.1 24.1 40.1
468s    0%  50% 100%
468s a 1.1 17.1 33.1
468s b 2.1 18.1 34.1
468s c 3.1 19.1 35.1
468s d 4.1 20.1 36.1
468s e 5.1 21.1 37.1
468s f 6.1 22.1 38.1
468s g 7.1 23.1 39.1
468s h 8.1 24.1 40.1
468s      [,1] [,2] [,3]
468s [1,]  1.1 17.1 33.1
468s [2,]  2.1 18.1 34.1
468s [3,]  3.1 19.1 35.1
468s [4,]  4.1 20.1 36.1
468s [5,]  5.1 21.1 37.1
468s [6,]  6.1 22.1 38.1
468s [7,]  7.1 23.1 39.1
468s [8,]  8.1 24.1 40.1
468s      [,1] [,2] [,3]
468s [1,]  1.1 17.1 33.1
468s [2,]  2.1 18.1 34.1
468s [3,]  3.1 19.1 35.1
468s [4,]  4.1 20.1 36.1
468s [5,]  5.1 21.1 37.1
468s [6,]  6.1 22.1 38.1
468s [7,]  7.1 23.1 39.1
468s [8,]  8.1 24.1 40.1
468s       0%  50% 100%
468s [1,] 1.1 17.1 33.1
468s [2,] 2.1 18.1 34.1
468s [3,] 3.1 19.1 35.1
468s [4,] 4.1 20.1 36.1
468s [5,] 5.1 21.1 37.1
468s [6,] 6.1 22.1 38.1
468s [7,] 7.1 23.1 39.1
468s [8,] 8.1 24.1 40.1
468s       0%  50% 100%
468s [1,] 1.1 17.1 33.1
468s [2,] 2.1 18.1 34.1
468s [3,] 3.1 19.1 35.1
468s [4,] 4.1 20.1 36.1
468s [5,] 5.1 21.1 37.1
468s [6,] 6.1 22.1 38.1
468s [7,] 7.1 23.1 39.1
468s [8,] 8.1 24.1 40.1
468s      [,1] [,2] [,3]
468s [1,]  1.1 17.1 33.1
468s [2,]  2.1 18.1 34.1
468s [3,]  3.1 19.1 35.1
468s [4,]  4.1 20.1 36.1
468s [5,]  5.1 21.1 37.1
468s [6,]  6.1 22.1 38.1
468s [7,]  7.1 23.1 39.1
468s [8,]  8.1 24.1 40.1
468s      [,1] [,2] [,3]
468s [1,]  1.1 17.1 33.1
468s [2,]  2.1 18.1 34.1
468s [3,]  3.1 19.1 35.1
468s [4,]  4.1 20.1 36.1
468s [5,]  5.1 21.1 37.1
468s [6,]  6.1 22.1 38.1
468s [7,]  7.1 23.1 39.1
468s [8,]  8.1 24.1 40.1
468s > 
468s > 
468s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
468s > # Test with a single quantile
468s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
468s > for (mode in c("logical", "integer", "double")) {
468s +   cat("mode: ", mode, "\n", sep = "")
468s +   x <- matrix(1:40, nrow = 8, ncol = 5)
468s +   storage.mode(x) <- mode
468s +   dimnames <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
468s +   str(x)
468s + 
468s +   probs <- c(0.5)
468s +   # Test with and without dimnames on x
468s +   for (setDimnames in c(TRUE, FALSE)) {
468s +     if (setDimnames) dimnames(x) <- dimnames
468s +     else dimnames(x) <- NULL    
468s +     # Check names attribute
468s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
468s +       q0 <- rowQuantiles_R(x, probs = probs, useNames = useNames)
468s +       print(q0)
468s +       q1 <- rowQuantiles(x, probs = probs, useNames = useNames)
468s +       ## FIXME: Workaround for R (< 3.0.0)
468s +       if (getRversion() < "3.0.0" && mode == "logical") storage.mode(q1) <- storage.mode(q0)
468s +       print(q1)
468s +       stopifnot(all.equal(q1, q0))
468s +       q2 <- colQuantiles(t(x), probs = probs, useNames = useNames)
468s +       ## FIXME: Workaround for R (< 3.0.0)
468s +       if (getRversion() < "3.0.0" && mode == "logical") storage.mode(q2) <- storage.mode(q0)
468s +       stopifnot(all.equal(q2, q0))      
468s +     }
468s +   }
468s + } # for (mode ...)
468s mode: logical
468s  logi [1:8, 1:5] TRUE TRUE TRUE TRUE TRUE TRUE ...
468s a b c d e f g h 
468s 1 1 1 1 1 1 1 1 
468s a b c d e f g h 
468s 1 1 1 1 1 1 1 1 
468s [1] 1 1 1 1 1 1 1 1
468s [1] 1 1 1 1 1 1 1 1
468s [1] 1 1 1 1 1 1 1 1
468s [1] 1 1 1 1 1 1 1 1
468s [1] 1 1 1 1 1 1 1 1
468s [1] 1 1 1 1 1 1 1 1
468s mode: integer
468s  int [1:8, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
468s  a  b  c  d  e  f  g  h 
468s 17 18 19 20 21 22 23 24 
468s  a  b  c  d  e  f  g  h 
468s 17 18 19 20 21 22 23 24 
468s [1] 17 18 19 20 21 22 23 24
468s [1] 17 18 19 20 21 22 23 24
468s [1] 17 18 19 20 21 22 23 24
468s [1] 17 18 19 20 21 22 23 24
468s [1] 17 18 19 20 21 22 23 24
468s [1] 17 18 19 20 21 22 23 24
468s mode: double
468s  num [1:8, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
468s  a  b  c  d  e  f  g  h 
468s 17 18 19 20 21 22 23 24 
468s  a  b  c  d  e  f  g  h 
468s 17 18 19 20 21 22 23 24 
468s [1] 17 18 19 20 21 22 23 24
468s [1] 17 18 19 20 21 22 23 24
468s [1] 17 18 19 20 21 22 23 24
468s [1] 17 18 19 20 21 22 23 24
468s [1] 17 18 19 20 21 22 23 24
468s [1] 17 18 19 20 21 22 23 24
468s > 
468s > 
468s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
468s > # Consistency checks
468s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
468s > set.seed(1)
468s > 
468s > probs <- seq(from = 0, to = 1, by = 0.25)
468s > 
468s > cat("Consistency checks:\n")
468s Consistency checks:
468s > n_sims <- if (Sys.getenv("_R_CHECK_USE_VALGRIND_") != "") 6L else 24L
468s > for (kk in seq_len(n_sims)) {
468s +   cat("Random test #", kk, "\n", sep = "")
468s + 
468s +   # Simulate data in a matrix of any shape
468s +   dim <- sample(20:60, size = 2L)
468s +   n <- prod(dim)
468s +   x <- rnorm(n, sd = 100)
468s +   dim(x) <- dim
468s +   dimnames <- lapply(dim(x), FUN = function(n) rep(letters, length.out = n))
468s + 
468s +   # Add NAs?
468s +   has_na <- ((kk %% 2) == 0L)
468s +   if (has_na) {
468s +     cat("Adding NAs\n")
468s +     nna <- sample(n, size = 1)
468s +     na_values <- c(NA_real_, NaN)
468s +     t <- sample(na_values, size = nna, replace = TRUE)
468s +     x[sample(length(x), size = nna)] <- t
468s +   }
468s + 
468s +   # Logical, integer, or double?
468s +   mode <- "numeric"
468s +   if ((kk %% 6) %in% 1:2) {
468s +     cat("Coercing to logical\n")
468s +     mode <- "logical"
468s +   } else if ((kk %% 6) %in% 3:4) {
468s +     cat("Coercing to integers\n")
468s +     mode <- "integer"
468s +   }
468s +   storage.mode(x) <- mode
468s +   
468s +   str(x)
468s + 
468s +   # rowQuantiles():
468s +   for (type in 1:9) {
468s +     cat(sprintf("type=%d, has_na=%s:\n", type, has_na))
468s +     # Test with and without dimnames on x
468s +     for (setDimnames in c(TRUE, FALSE)) {
468s +       if (setDimnames) dimnames(x) <- dimnames
468s +       else dimnames(x) <- NULL    
468s +       # Check names attribute
468s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
468s +         q0 <- rowQuantiles_R(x, probs = probs, na.rm = has_na, type = type, useNames = useNames)
468s +         q1 <- rowQuantiles(x, probs = probs, na.rm = has_na, type = type, useNames = useNames)
468s +         ## FIXME: Workaround for R (< 3.0.0)
468s +         if (getRversion() < "3.0.0" && mode == "logical" && !has_na && type == 7L) storage.mode(q1) <- storage.mode(q0)
468s +         stopifnot(all.equal(q1, q0))
468s +         q2 <- colQuantiles(t(x), probs = probs, na.rm = has_na, type = type, useNames = useNames)
468s +         ## FIXME: Workaround for R (< 3.0.0)
468s +         if (getRversion() < "3.0.0" && mode == "logical" && !has_na && type == 7L) storage.mode(q2) <- storage.mode(q0)
468s +         stopifnot(all.equal(q2, q0))
468s +       }
468s +     }
468s +   }
468s + } # for (kk ...)
468s Random test #1
468s Coercing to logical
468s  logi [1:23, 1:58] TRUE TRUE TRUE TRUE TRUE TRUE ...
468s type=1, has_na=FALSE:
468s type=2, has_na=FALSE:
468s type=3, has_na=FALSE:
469s type=4, has_na=FALSE:
469s type=5, has_na=FALSE:
469s type=6, has_na=FALSE:
469s type=7, has_na=FALSE:
469s type=8, has_na=FALSE:
469s type=9, has_na=FALSE:
469s Random test #2
469s Adding NAs
469s Coercing to logical
469s  logi [1:58, 1:33] TRUE TRUE TRUE TRUE TRUE NA ...
469s type=1, has_na=TRUE:
469s type=2, has_na=TRUE:
469s type=3, has_na=TRUE:
470s type=4, has_na=TRUE:
470s type=5, has_na=TRUE:
470s type=6, has_na=TRUE:
470s type=7, has_na=TRUE:
471s type=8, has_na=TRUE:
471s type=9, has_na=TRUE:
471s Random test #3
471s Coercing to integers
471s  int [1:28, 1:60] 119 -164 115 -129 209 -175 2 -32 120 -28 ...
471s type=1, has_na=FALSE:
471s type=2, has_na=FALSE:
471s type=3, has_na=FALSE:
471s type=4, has_na=FALSE:
471s type=5, has_na=FALSE:
472s type=6, has_na=FALSE:
472s type=7, has_na=FALSE:
472s type=8, has_na=FALSE:
472s type=9, has_na=FALSE:
472s Random test #4
472s Adding NAs
472s Coercing to integers
472s  int [1:54, 1:35] 147 11 116 -50 NA -69 132 NA 114 NA ...
472s type=1, has_na=TRUE:
472s type=2, has_na=TRUE:
472s type=3, has_na=TRUE:
473s type=4, has_na=TRUE:
473s type=5, has_na=TRUE:
473s type=6, has_na=TRUE:
473s type=7, has_na=TRUE:
474s type=8, has_na=TRUE:
474s type=9, has_na=TRUE:
474s Random test #5
474s  num [1:39, 1:53] 5.94 -27.16 -30.78 173 126.05 ...
474s type=1, has_na=FALSE:
474s type=2, has_na=FALSE:
474s type=3, has_na=FALSE:
474s type=4, has_na=FALSE:
475s type=5, has_na=FALSE:
475s type=6, has_na=FALSE:
475s type=7, has_na=FALSE:
475s type=8, has_na=FALSE:
475s type=9, has_na=FALSE:
475s Random test #6
475s Adding NAs
475s  num [1:46, 1:22] 197 -107 15 148 -110 ...
475s type=1, has_na=TRUE:
475s type=2, has_na=TRUE:
476s type=3, has_na=TRUE:
476s type=4, has_na=TRUE:
476s type=5, has_na=TRUE:
476s type=6, has_na=TRUE:
476s type=7, has_na=TRUE:
477s type=8, has_na=TRUE:
477s type=9, has_na=TRUE:
477s Random test #7
477s Coercing to logical
477s  logi [1:21, 1:51] TRUE TRUE TRUE TRUE TRUE TRUE ...
477s type=1, has_na=FALSE:
477s type=2, has_na=FALSE:
477s type=3, has_na=FALSE:
477s type=4, has_na=FALSE:
477s type=5, has_na=FALSE:
477s type=6, has_na=FALSE:
478s type=7, has_na=FALSE:
478s type=8, has_na=FALSE:
478s type=9, has_na=FALSE:
478s Random test #8
478s Adding NAs
478s Coercing to logical
478s  logi [1:33, 1:53] NA NA TRUE TRUE TRUE TRUE ...
478s type=1, has_na=TRUE:
478s type=2, has_na=TRUE:
478s type=3, has_na=TRUE:
478s type=4, has_na=TRUE:
478s type=5, has_na=TRUE:
478s type=6, has_na=TRUE:
479s type=7, has_na=TRUE:
479s type=8, has_na=TRUE:
479s type=9, has_na=TRUE:
479s Random test #9
479s Coercing to integers
479s  int [1:53, 1:24] -73 10 -73 -5 44 -107 -100 95 58 -50 ...
479s type=1, has_na=FALSE:
479s type=2, has_na=FALSE:
479s type=3, has_na=FALSE:
480s type=4, has_na=FALSE:
480s type=5, has_na=FALSE:
480s type=6, has_na=FALSE:
480s type=7, has_na=FALSE:
480s type=8, has_na=FALSE:
481s type=9, has_na=FALSE:
481s Random test #10
481s Adding NAs
481s Coercing to integers
481s  int [1:44, 1:20] NA -140 NA -57 -252 NA NA 20 NA NA ...
481s type=1, has_na=TRUE:
481s type=2, has_na=TRUE:
481s type=3, has_na=TRUE:
481s type=4, has_na=TRUE:
482s type=5, has_na=TRUE:
482s type=6, has_na=TRUE:
482s type=7, has_na=TRUE:
482s type=8, has_na=TRUE:
482s type=9, has_na=TRUE:
482s Random test #11
482s  num [1:54, 1:23] -160.87 74.13 196.08 7.27 4.92 ...
482s type=1, has_na=FALSE:
483s type=2, has_na=FALSE:
483s type=3, has_na=FALSE:
483s type=4, has_na=FALSE:
483s type=5, has_na=FALSE:
483s type=6, has_na=FALSE:
484s type=7, has_na=FALSE:
484s type=8, has_na=FALSE:
484s type=9, has_na=FALSE:
484s Random test #12
484s Adding NAs
484s  num [1:59, 1:27] -139.2 -86.3 NA -40.7 NA ...
484s type=1, has_na=TRUE:
484s type=2, has_na=TRUE:
485s type=3, has_na=TRUE:
485s type=4, has_na=TRUE:
485s type=5, has_na=TRUE:
485s type=6, has_na=TRUE:
486s type=7, has_na=TRUE:
486s type=8, has_na=TRUE:
486s type=9, has_na=TRUE:
486s Random test #13
486s Coercing to logical
486s  logi [1:53, 1:60] TRUE TRUE TRUE TRUE TRUE TRUE ...
486s type=1, has_na=FALSE:
487s type=2, has_na=FALSE:
487s type=3, has_na=FALSE:
487s type=4, has_na=FALSE:
487s type=5, has_na=FALSE:
487s type=6, has_na=FALSE:
488s type=7, has_na=FALSE:
488s type=8, has_na=FALSE:
488s type=9, has_na=FALSE:
488s Random test #14
488s Adding NAs
488s Coercing to logical
488s  logi [1:22, 1:57] TRUE TRUE TRUE TRUE TRUE TRUE ...
488s type=1, has_na=TRUE:
488s type=2, has_na=TRUE:
488s type=3, has_na=TRUE:
488s type=4, has_na=TRUE:
488s type=5, has_na=TRUE:
489s type=6, has_na=TRUE:
489s type=7, has_na=TRUE:
489s type=8, has_na=TRUE:
489s type=9, has_na=TRUE:
489s Random test #15
489s Coercing to integers
489s  int [1:20, 1:34] 78 -41 183 190 -71 37 0 -4 -86 27 ...
489s type=1, has_na=FALSE:
489s type=2, has_na=FALSE:
489s type=3, has_na=FALSE:
489s type=4, has_na=FALSE:
489s type=5, has_na=FALSE:
489s type=6, has_na=FALSE:
490s type=7, has_na=FALSE:
490s type=8, has_na=FALSE:
490s type=9, has_na=FALSE:
490s Random test #16
490s Adding NAs
490s Coercing to integers
490s  int [1:42, 1:37] NA 12 -15 41 -28 17 NA -74 NA NA ...
490s type=1, has_na=TRUE:
490s type=2, has_na=TRUE:
490s type=3, has_na=TRUE:
490s type=4, has_na=TRUE:
491s type=5, has_na=TRUE:
491s type=6, has_na=TRUE:
491s type=7, has_na=TRUE:
491s type=8, has_na=TRUE:
491s type=9, has_na=TRUE:
491s Random test #17
491s  num [1:42, 1:29] -50.51 -6.51 -117.59 135.58 226.87 ...
491s type=1, has_na=FALSE:
492s type=2, has_na=FALSE:
492s type=3, has_na=FALSE:
492s type=4, has_na=FALSE:
492s type=5, has_na=FALSE:
492s type=6, has_na=FALSE:
492s type=7, has_na=FALSE:
492s type=8, has_na=FALSE:
493s type=9, has_na=FALSE:
493s Random test #18
493s Adding NAs
493s  num [1:57, 1:39] 223 156.8 -44.6 -127.5 -147.7 ...
493s type=1, has_na=TRUE:
493s type=2, has_na=TRUE:
493s type=3, has_na=TRUE:
494s type=4, has_na=TRUE:
494s type=5, has_na=TRUE:
494s type=6, has_na=TRUE:
494s type=7, has_na=TRUE:
494s type=8, has_na=TRUE:
495s type=9, has_na=TRUE:
495s Random test #19
495s Coercing to logical
495s  logi [1:52, 1:57] TRUE TRUE TRUE TRUE TRUE TRUE ...
495s type=1, has_na=FALSE:
495s type=2, has_na=FALSE:
495s type=3, has_na=FALSE:
495s type=4, has_na=FALSE:
496s type=5, has_na=FALSE:
496s type=6, has_na=FALSE:
496s type=7, has_na=FALSE:
496s type=8, has_na=FALSE:
496s type=9, has_na=FALSE:
497s Random test #20
497s Adding NAs
497s Coercing to logical
497s  logi [1:25, 1:48] NA TRUE NA NA NA NA ...
497s type=1, has_na=TRUE:
497s type=2, has_na=TRUE:
497s type=3, has_na=TRUE:
497s type=4, has_na=TRUE:
497s type=5, has_na=TRUE:
497s type=6, has_na=TRUE:
497s type=7, has_na=TRUE:
497s type=8, has_na=TRUE:
497s type=9, has_na=TRUE:
498s Random test #21
498s Coercing to integers
498s  int [1:53, 1:27] 3 -30 203 -49 19 -45 -138 28 46 -44 ...
498s type=1, has_na=FALSE:
498s type=2, has_na=FALSE:
498s type=3, has_na=FALSE:
498s type=4, has_na=FALSE:
498s type=5, has_na=FALSE:
499s type=6, has_na=FALSE:
499s type=7, has_na=FALSE:
499s type=8, has_na=FALSE:
499s type=9, has_na=FALSE:
499s Random test #22
499s Adding NAs
499s Coercing to integers
499s  int [1:48, 1:36] -131 NA NA -201 45 -17 NA 57 NA NA ...
499s type=1, has_na=TRUE:
500s type=2, has_na=TRUE:
500s type=3, has_na=TRUE:
500s type=4, has_na=TRUE:
500s type=5, has_na=TRUE:
500s type=6, has_na=TRUE:
500s type=7, has_na=TRUE:
501s type=8, has_na=TRUE:
501s type=9, has_na=TRUE:
501s Random test #23
501s  num [1:23, 1:43] -99.2 -68.8 -86.7 -104.2 48 ...
501s type=1, has_na=FALSE:
501s type=2, has_na=FALSE:
501s type=3, has_na=FALSE:
501s type=4, has_na=FALSE:
502s type=5, has_na=FALSE:
502s type=6, has_na=FALSE:
502s type=7, has_na=FALSE:
502s type=8, has_na=FALSE:
502s type=9, has_na=FALSE:
502s Random test #24
502s Adding NAs
502s  num [1:53, 1:29] NaN -67.6 10.8 -88.4 130.1 ...
502s type=1, has_na=TRUE:
502s type=2, has_na=TRUE:
502s type=3, has_na=TRUE:
503s type=4, has_na=TRUE:
503s type=5, has_na=TRUE:
503s type=6, has_na=TRUE:
503s type=7, has_na=TRUE:
504s type=8, has_na=TRUE:
504s type=9, has_na=TRUE:
504s > 
504s > 
504s > 
504s > for (mode in c("logical", "integer", "double")) {
504s +   naValue <- NA_real_
504s +   storage.mode(naValue) <- mode
504s + 
504s +   someValue <- 1
504s +   storage.mode(someValue) <- mode
504s + 
504s +   for (type in 1:9) {
504s +     # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
504s +     # All NA
504s +     # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
504s +     x <- matrix(naValue, nrow = 3L, ncol = 4L)
504s +     dimnames <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
504s +     # Test with and without dimnames on x
504s +     for (setDimnames in c(TRUE, FALSE)) {
504s +       if (setDimnames) dimnames(x) <- dimnames
504s +       else dimnames(x) <- NULL    
504s +       # Check names attribute
504s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
504s +         qr0 <- rowQuantiles_R(x, type = type, useNames = useNames)
504s +         
504s +         qr <- rowQuantiles(x, type = type, useNames = useNames)
504s +         stopifnot(identical(qr, qr0))
504s +         
504s +         # x <- matrix(naValue, nrow = 4L, ncol = 3L)
504s +         qc <- colQuantiles(t(x), type = type, useNames = useNames)
504s +         
504s +         stopifnot(identical(qc, qr))
504s +       }
504s +     }
504s + 
504s + 
504s +     # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
504s +     # Empty matrices
504s +     # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
504s +     probs <- c(0, 0.25, 0.75, 1)
504s +     x <- matrix(naValue, nrow = 0L, ncol = 0L)
504s +     dimnames(x) <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
504s +     q <- rowQuantiles(x, probs = probs, type = type, useNames = TRUE)
504s +     stopifnot(identical(dim(q), c(nrow(x), length(probs))))
504s +     q <- colQuantiles(x, probs = probs, type = type, useNames = TRUE)
504s +     stopifnot(identical(dim(q), c(ncol(x), length(probs))))
504s +     
504s +     x <- matrix(naValue, nrow = 2L, ncol = 0L)
504s +     dimnames(x) <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
504s +     q <- rowQuantiles(x, probs = probs, type = type, useNames = TRUE)
504s +     stopifnot(identical(dim(q), c(nrow(x), length(probs))))
504s +     
504s +     x <- matrix(naValue, nrow = 0L, ncol = 2L)
504s +     dimnames(x) <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
504s +     q <- colQuantiles(x, probs = probs, type = type, useNames = TRUE)
504s +     stopifnot(identical(dim(q), c(ncol(x), length(probs))))
504s + 
504s + 
504s +     # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
504s +     # Single column matrices
504s +     # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
504s +     probs <- c(0, 0.25, 0.75, 1)
504s +     x <- matrix(someValue, nrow = 2L, ncol = 1L)
504s +     dimnames(x) <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
504s +     qr <- rowQuantiles(x, probs = probs, type = type, useNames = TRUE)
504s +     print(qr)
504s +     
504s +     x <- matrix(someValue, nrow = 1L, ncol = 2L)
504s +     dimnames(x) <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
504s +     qc <- colQuantiles(x, probs = probs, type = type, useNames = TRUE)
504s +     print(qc)
504s +     
504s +     stopifnot(identical(qc, qr))
504s +   }
504s + }
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
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504s   0% 25% 75% 100%
504s a  1   1   1    1
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504s   0% 25% 75% 100%
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504s   0% 25% 75% 100%
504s a  1   1   1    1
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504s   0% 25% 75% 100%
504s a  1   1   1    1
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504s   0% 25% 75% 100%
504s a  1   1   1    1
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504s   0% 25% 75% 100%
504s a  1   1   1    1
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504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s   0% 25% 75% 100%
504s a  1   1   1    1
504s b  1   1   1    1
504s > 
505s 
505s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
505s Copyright (C) 2024 The R Foundation for Statistical Computing
505s Platform: arm-unknown-linux-gnueabihf (32-bit)
505s 
505s R is free software and comes with ABSOLUTELY NO WARRANTY.
505s You are welcome to redistribute it under certain conditions.
505s Type 'license()' or 'licence()' for distribution details.
505s 
505s R is a collaborative project with many contributors.
505s Type 'contributors()' for more information and
505s 'citation()' on how to cite R or R packages in publications.
505s 
505s Type 'demo()' for some demos, 'help()' for on-line help, or
505s 'help.start()' for an HTML browser interface to help.
505s Type 'q()' to quit R.
505s 
505s > library("matrixStats")
505s > 
505s > ## Create isFALSE() if running on an old version of R
505s > if (!exists("isFALSE", mode="function")) {
505s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
505s + }
505s > 
505s > rowQuantiles_R <- function(x, probs, na.rm = FALSE, drop = TRUE, ..., useNames = NA) {
505s +   q <- apply(x, MARGIN = 1L, FUN = function(x, probs, na.rm) {
505s +     if (!na.rm && any(is.na(x))) {
505s +       na_value <- NA_real_
505s +       storage.mode(na_value) <- storage.mode(x)
505s +       rep(na_value, times = length(probs))
505s + 
505s +     } else {
505s +       as.vector(quantile(x, probs = probs, na.rm = na.rm, names = FALSE, ...))
505s +     }
505s +   }, probs = probs, na.rm = na.rm)
505s + 
505s +   if (!is.null(dim(q))) q <- t(q)
505s +   else dim(q) <- c(nrow(x), length(probs))
505s + 
505s +   colnames(q) <- matrixStats:::quantile_probs_names(probs)
505s +   rownames(q) <- rownames(x)
505s +   if (isFALSE(useNames)) dimnames(q) <- NULL
505s + 
505s +   if (drop) q <- drop(q)
505s +   q
505s + }
505s > 
505s > 
505s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
505s > # Subsetted tests
505s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
505s > source("utils/validateIndicesFramework.R")
505s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
505s > dimnames <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
505s > probs <- c(0, 0.25, 0.75, 1)
505s > # Test with and without dimnames on x
505s > for (setDimnames in c(TRUE, FALSE)) {
505s +   if (setDimnames) dimnames(x) <- dimnames
505s +   else dimnames(x) <- NULL
505s +   
505s +   count <- 0L
505s +   for (rows in index_cases) {
505s +     for (cols in index_cases) {
505s +       count <- count + 1L
505s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
505s +       useNames <- c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)
505s +       useNames <- useNames[count %% length(useNames) + 1]
505s + 
505s +       validateIndicesTestMatrix(x, rows, cols,
505s +                                 ftest = rowQuantiles, fsure = rowQuantiles_R,
505s +                                 probs = probs, na.rm = na.rm, drop = FALSE, useNames = useNames)
505s +       validateIndicesTestMatrix(x, rows, cols,
505s +                                 fcoltest = colQuantiles, fsure = rowQuantiles_R,
505s +                                 probs = probs, na.rm = na.rm, drop = FALSE, useNames = useNames)
505s +     }
505s +   }
505s + }
509s > 
509s > 
509s 
509s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
509s Copyright (C) 2024 The R Foundation for Statistical Computing
509s Platform: arm-unknown-linux-gnueabihf (32-bit)
509s 
509s R is free software and comes with ABSOLUTELY NO WARRANTY.
509s You are welcome to redistribute it under certain conditions.
509s Type 'license()' or 'licence()' for distribution details.
509s 
509s R is a collaborative project with many contributors.
509s Type 'contributors()' for more information and
509s 'citation()' on how to cite R or R packages in publications.
509s 
509s Type 'demo()' for some demos, 'help()' for on-line help, or
509s 'help.start()' for an HTML browser interface to help.
509s Type 'q()' to quit R.
509s 
509s > library("matrixStats")
509s > 
509s > rowMins_R <- function(x, ..., useNames = NA) {
509s +   suppressWarnings({
509s +     res <- apply(x, MARGIN = 1L, FUN = min, ...)
509s +   })
509s +   if (is.na(useNames) || !useNames) names(res) <- NULL
509s +   res
509s + } # rowMins_R()
509s > 
509s > rowMaxs_R <- function(x, ..., useNames = NA) {
509s +   suppressWarnings({
509s +     res <- apply(x, MARGIN = 1L, FUN = max, ...)
509s +   })
509s +   if (is.na(useNames) || !useNames) names(res) <- NULL
509s +   res
509s + } # rowMaxs_R()
509s > 
509s > rowRanges_R <- function(x, ..., useNames = NA) {
509s +   suppressWarnings({
509s +     ans <- t(apply(x, MARGIN = 1L, FUN = range, ...))
509s +   })
509s +   
509s +   # Preserve rownames attribute
509s +   dim <- c(dim(x)[1], 2L)
509s +   if (!isTRUE(all.equal(dim(ans), dim))) {
509s +     dim(ans) <- dim
509s +     rownames <- rownames(x)
509s +     if (!is.null(dimnames)) rownames(ans) <- rownames
509s +   }
509s +   if (is.na(useNames) || !useNames) dimnames(ans) <- NULL
509s +   ans
509s + } # rowRanges_R()
509s > 
509s > 
509s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
509s > # With and without some NAs
509s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
509s > for (mode in c("integer", "double")) {
509s +   cat("mode: ", mode, "\n", sep = "")
509s + 
509s +   for (add_na in c(FALSE, TRUE)) {
509s +     cat("add_na = ", add_na, "\n", sep = "")
509s + 
509s +     x <- matrix(1:50 + 0.1, nrow = 10L, ncol = 5L)
509s +     if (add_na) {
509s +       x[3:7, c(2, 4)] <- NA_real_
509s +     }
509s +     storage.mode(x) <- mode
509s +     str(x)
509s +     
509s +     # To check names attribute
509s +     dimnames <- list(letters[1:10], LETTERS[1:5])
509s +     
509s +     # Test with and without dimnames on x
509s +     for (setDimnames in c(TRUE, FALSE)) {
509s +       if (setDimnames) dimnames(x) <- dimnames
509s +       else dimnames(x) <- NULL
509s +       # Row/column extremes
509s +       for (na.rm in c(FALSE, TRUE)) {
509s +         # Check names attribute
509s +         for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
509s +           cat("na.rm = ", na.rm, "\n", sep = "")
509s +           
509s +           # Ranges
509s +           cat("range:\n")
509s +           r0 <- rowRanges_R(x, na.rm = na.rm, useNames = useNames)
509s +           r1 <- rowRanges(x, na.rm = na.rm, useNames = useNames)
509s +           r2 <- colRanges(t(x), na.rm = na.rm, useNames = useNames)
509s +           stopifnot(all.equal(r1, r2))
509s +           stopifnot(all.equal(r1, r0))
509s +           
509s +           # Min
509s +           cat("min:\n")
509s +           m0 <- rowMins_R(x, na.rm = na.rm, useNames = useNames)
509s +           m1 <- rowMins(x, na.rm = na.rm, useNames = useNames)
509s +           m2 <- colMins(t(x), na.rm = na.rm, useNames = useNames)
509s +           stopifnot(all.equal(m1, m2))
509s +           stopifnot(all.equal(m1, m0))
509s +           
509s +           # Max
509s +           cat("max:\n")
509s +           m0 <- rowMaxs_R(x, na.rm = na.rm, useNames = useNames)
509s +           m1 <- rowMaxs(x, na.rm = na.rm, useNames = useNames)
509s +           m2 <- colMaxs(t(x), na.rm = na.rm, useNames = useNames)
509s +           stopifnot(all.equal(m1, m2))
509s +           stopifnot(all.equal(m1, m0))
509s +         }
509s +       }
509s +     }
509s +   } # for (add_na ...)
509s + } # for (mode ...)
509s mode: integer
509s add_na = FALSE
509s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
509s na.rm = FALSE
509s range:
509s min:
509s max:
509s na.rm = FALSE
509s range:
509s min:
510s max:
510s na.rm = TRUE
510s range:
510s min:
510s max:
510s na.rm = TRUE
510s range:
510s min:
510s max:
510s na.rm = FALSE
510s range:
510s min:
510s max:
510s na.rm = FALSE
510s range:
510s min:
510s max:
510s na.rm = TRUE
510s range:
510s min:
510s max:
510s na.rm = TRUE
510s range:
510s min:
510s max:
510s add_na = TRUE
510s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
510s na.rm = FALSE
510s range:
510s min:
510s max:
510s na.rm = FALSE
510s range:
510s min:
510s max:
510s na.rm = TRUE
510s range:
510s min:
510s max:
510s na.rm = TRUE
510s range:
510s min:
510s max:
510s na.rm = FALSE
510s range:
510s min:
510s max:
510s na.rm = FALSE
510s range:
510s min:
510s max:
510s na.rm = TRUE
510s range:
510s min:
510s max:
510s na.rm = TRUE
510s range:
510s min:
510s max:
510s mode: double
510s add_na = FALSE
510s  num [1:10, 1:5] 1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1 10.1 ...
510s na.rm = FALSE
510s range:
510s min:
510s max:
510s na.rm = FALSE
510s range:
510s min:
510s max:
510s na.rm = TRUE
510s range:
510s min:
510s max:
510s na.rm = TRUE
510s range:
510s min:
510s max:
510s na.rm = FALSE
510s range:
510s min:
510s max:
510s na.rm = FALSE
510s range:
510s min:
510s max:
510s na.rm = TRUE
510s range:
510s min:
510s max:
510s na.rm = TRUE
510s range:
510s min:
510s max:
510s add_na = TRUE
510s  num [1:10, 1:5] 1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1 10.1 ...
510s na.rm = FALSE
510s range:
510s min:
510s max:
510s na.rm = FALSE
510s range:
510s min:
510s max:
510s na.rm = TRUE
510s range:
510s min:
510s max:
510s na.rm = TRUE
510s range:
510s min:
510s max:
510s na.rm = FALSE
510s range:
510s min:
510s max:
510s na.rm = FALSE
510s range:
510s min:
510s max:
510s na.rm = TRUE
510s range:
510s min:
510s max:
510s na.rm = TRUE
510s range:
510s min:
510s max:
510s > 
510s > 
510s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
510s > # All NAs
510s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
510s > for (mode in c("integer", "double")) {
510s +   cat("mode: ", mode, "\n", sep = "")
510s +   x <- matrix(NA_real_, nrow = 10L, ncol = 5L)
510s +   storage.mode(x) <- mode
510s +   str(x)
510s +   
510s +   # Test with and without dimnames on x
510s +   for (setDimnames in c(TRUE, FALSE)) {
510s +     if (setDimnames) dimnames(x) <- dimnames
510s +     else dimnames(x) <- NULL
510s +     for (na.rm in c(FALSE, TRUE)) {
510s +       # Check names attribute
510s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
510s +         cat("na.rm = ", na.rm, "\n", sep = "")
510s +         r0 <- rowRanges_R(x, na.rm = na.rm, useNames = useNames)
510s +         r1 <- rowRanges(x, na.rm = na.rm, useNames = useNames)
510s +         r2 <- colRanges(t(x), na.rm = na.rm, useNames = useNames)
510s +         stopifnot(all.equal(r1, r2))
510s +         stopifnot(all.equal(r1, r0))
510s +       }
510s +     }
510s +   }
510s + } # for (mode ...)
510s mode: integer
510s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
510s na.rm = FALSE
510s na.rm = FALSE
510s na.rm = TRUE
510s na.rm = TRUE
510s na.rm = FALSE
510s na.rm = FALSE
510s na.rm = TRUE
510s na.rm = TRUE
510s mode: double
510s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
510s na.rm = FALSE
510s na.rm = FALSE
510s na.rm = TRUE
510s na.rm = TRUE
510s na.rm = FALSE
510s na.rm = FALSE
510s na.rm = TRUE
510s na.rm = TRUE
510s > 
510s > 
510s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
510s > # Special cases
510s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
510s > # Nx0 matrix
510s > x <- matrix(double(0L), nrow = 5L, ncol = 0L)
510s > r0 <- rowRanges_R(x)
510s > #r1 <- rowRanges(x)
510s > #r_truth <- matrix(c(Inf, -Inf), nrow = nrow(x), ncol = 2L, byrow = TRUE)
510s > #stopifnot(all.equal(r1, r_truth))
510s > 
510s > # 0xN matrix
510s > x <- t(x)
510s > #r1 <- colRanges(x)
510s > #stopifnot(all.equal(r1, r_truth))
510s > 
510s > # Nx1 matrix
510s > x <- matrix(1:5, nrow = 5L, ncol = 1L)
510s > # To check names attribute
510s > dimnames <- list(letters[1:5], "A")
510s > r1 <- rowRanges(x)
510s > r_truth <- matrix(1:5, nrow = nrow(x), ncol = 2L, byrow = FALSE)
510s > stopifnot(all.equal(r1, r_truth))
510s > # Check names attribute
510s > dimnames(x) <- dimnames
510s > r0 <- rowRanges_R(x, useNames = TRUE)
510s > r1 <- rowRanges(x, useNames = TRUE)
510s > stopifnot(all.equal(r1, r0))
510s > dimnames(x) <- NULL
510s > 
510s > # 1xN matrix
510s > x <- t(x)
510s > r1 <- colRanges(x)
510s > stopifnot(all.equal(r1, r_truth))
510s > # Check names attribute
510s > dimnames(x) <- list("a", LETTERS[1:5])
510s > r1 <- colRanges(x, useNames = TRUE)
510s > stopifnot(identical(rownames(r1), colnames(x)))
510s > 
510s > 
510s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
510s > # Additional tests with NA_integer_, NA_real, NaN, -Inf, +Inf
510s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
510s > x <- matrix(1:12, nrow = 4L, ncol = 3L)
510s > 
510s > na_list <- list(
510s +   "integer"       = matrix(1:12, nrow = 4L, ncol = 3L),
510s +   "integer w/ NA" = matrix(NA_integer_, nrow = 4L, ncol = 3L),
510s +   "real"          = matrix(as.double(1:12), nrow = 4L, ncol = 3L),
510s +   "real w/ NA"    = matrix(NA_real_, nrow = 4L, ncol = 3L)
510s + )
510s > 
510s > na <- na_list[["real"]]
510s > na[2, 2] <- NA
510s > na_list[["real + NA cell"]] <- na
510s > 
510s > na <- na_list[["real"]]
510s > na[2, ] <- NA
510s > na_list[["real + NA row"]] <- na
510s > 
510s > na <- na_list[["real"]]
510s > na[2, ] <- NaN
510s > na_list[["real + NaN row"]] <- na
510s > 
510s > na <- na_list[["real"]]
510s > na[2, 2] <- Inf
510s > na_list[["real + Inf cell"]] <- na
510s > 
510s > na <- na_list[["real"]]
510s > na[2, ] <- Inf
510s > na_list[["real + Inf row"]] <- na
510s > 
510s > na <- na_list[["real"]]
510s > na[2, 2] <- NaN
510s > na_list[["real + NaN cell"]] <- na
510s > 
510s > na <- na_list[["real w/ NA"]]
510s > na[2, 2] <- NaN
510s > na_list[["real w/ NA + NaN cell"]] <- na
510s > 
510s > na <- na_list[["real w/ NA"]]
510s > na[2, ] <- NaN
510s > na_list[["real w/ NA + NaN row"]] <- na
510s > 
510s > # To check names attribute
510s > dimnames <- list(letters[1:4], LETTERS[1:3])
510s > 
510s > # Test with and without dimnames on x
510s > for (setDimnames in c(TRUE, FALSE)) {
510s +   if (setDimnames) dimnames(x) <- dimnames
510s +   else dimnames(x) <- NULL
510s +   for (na.rm in c(FALSE, TRUE)) {
510s +     for (name in names(na_list)) {
510s +       # Check names attribute
510s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
510s +         na <- na_list[[name]]
510s +         cat(sprintf("%s (%s) w/ na.rm = %s:\n", name, typeof(na), na.rm))
510s +         print(na)
510s +         
510s +         cat("  min:\n")
510s +         y0 <- rowMins_R(na, na.rm = na.rm, useNames = useNames)
510s +         str(y0)
510s +         y1 <- rowMins(na, na.rm = na.rm, useNames = useNames)
510s +         str(y1)
510s +         stopifnot(all.equal(y1, y0))
510s +         y1c <- colMins(t(na), na.rm = na.rm, useNames = useNames)
510s +         str(y1c)
510s +         stopifnot(all.equal(y1c, y1))
510s +         
510s +         cat("  max:\n")
510s +         y0 <- rowMaxs_R(na, na.rm = na.rm, useNames = useNames)
510s +         str(y0)
510s +         y1 <- rowMaxs(na, na.rm = na.rm, useNames = useNames)
510s +         str(y1)
510s +         stopifnot(all.equal(y1, y0))
510s +         y1c <- colMaxs(t(na), na.rm = na.rm, useNames = useNames)
510s +         str(y1c)
510s +         stopifnot(all.equal(y1c, y1))
510s +         
510s +         cat("  range:\n")
510s +         y0 <- rowRanges_R(na, na.rm = na.rm, useNames = useNames)
510s +         str(y0)
510s +         y1 <- rowRanges(na, na.rm = na.rm, useNames = useNames)
510s +         str(y1)
510s +         stopifnot(all.equal(y1, y0))
510s +         y1c <- colRanges(t(na), na.rm = na.rm, useNames = useNames)
510s +         str(y1c)
510s +         stopifnot(all.equal(y1c, y1))
510s +       }
510s +     } # for (name ...)
510s +   } # for (na.rm ...)
510s + }
510s integer (integer) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2    6   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  int [1:4] 1 2 3 4
510s  int [1:4] 1 2 3 4
510s  int [1:4] 1 2 3 4
510s   max:
510s  int [1:4] 9 10 11 12
510s  int [1:4] 9 10 11 12
510s  int [1:4] 9 10 11 12
510s   range:
510s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
510s integer (integer) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2    6   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  int [1:4] 1 2 3 4
510s  int [1:4] 1 2 3 4
510s  int [1:4] 1 2 3 4
510s   max:
510s  int [1:4] 9 10 11 12
510s  int [1:4] 9 10 11 12
510s  int [1:4] 9 10 11 12
510s   range:
510s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
510s integer w/ NA (integer) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]   NA   NA   NA
510s [2,]   NA   NA   NA
510s [3,]   NA   NA   NA
510s [4,]   NA   NA   NA
510s   min:
510s  int [1:4] NA NA NA NA
510s  int [1:4] NA NA NA NA
510s  int [1:4] NA NA NA NA
510s   max:
510s  int [1:4] NA NA NA NA
510s  int [1:4] NA NA NA NA
510s  int [1:4] NA NA NA NA
510s   range:
510s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
510s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
510s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
510s integer w/ NA (integer) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]   NA   NA   NA
510s [2,]   NA   NA   NA
510s [3,]   NA   NA   NA
510s [4,]   NA   NA   NA
510s   min:
510s  int [1:4] NA NA NA NA
510s  int [1:4] NA NA NA NA
510s  int [1:4] NA NA NA NA
510s   max:
510s  int [1:4] NA NA NA NA
510s  int [1:4] NA NA NA NA
510s  int [1:4] NA NA NA NA
510s   range:
510s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
510s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
510s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
510s real (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2    6   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s   max:
510s  num [1:4] 9 10 11 12
510s  num [1:4] 9 10 11 12
510s  num [1:4] 9 10 11 12
510s   range:
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s real (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2    6   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s   max:
510s  num [1:4] 9 10 11 12
510s  num [1:4] 9 10 11 12
510s  num [1:4] 9 10 11 12
510s   range:
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s real w/ NA (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]   NA   NA   NA
510s [2,]   NA   NA   NA
510s [3,]   NA   NA   NA
510s [4,]   NA   NA   NA
510s   min:
510s  num [1:4] NA NA NA NA
510s  num [1:4] NA NA NA NA
510s  num [1:4] NA NA NA NA
510s   max:
510s  num [1:4] NA NA NA NA
510s  num [1:4] NA NA NA NA
510s  num [1:4] NA NA NA NA
510s   range:
510s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
510s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
510s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
510s real w/ NA (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]   NA   NA   NA
510s [2,]   NA   NA   NA
510s [3,]   NA   NA   NA
510s [4,]   NA   NA   NA
510s   min:
510s  num [1:4] NA NA NA NA
510s  num [1:4] NA NA NA NA
510s  num [1:4] NA NA NA NA
510s   max:
510s  num [1:4] NA NA NA NA
510s  num [1:4] NA NA NA NA
510s  num [1:4] NA NA NA NA
510s   range:
510s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
510s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
510s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
510s real + NA cell (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2   NA   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 NA 3 4
510s  num [1:4] 1 NA 3 4
510s  num [1:4] 1 NA 3 4
510s   max:
510s  num [1:4] 9 NA 11 12
510s  num [1:4] 9 NA 11 12
510s  num [1:4] 9 NA 11 12
510s   range:
510s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
510s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
510s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
510s real + NA cell (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2   NA   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 NA 3 4
510s  num [1:4] 1 NA 3 4
510s  num [1:4] 1 NA 3 4
510s   max:
510s  num [1:4] 9 NA 11 12
510s  num [1:4] 9 NA 11 12
510s  num [1:4] 9 NA 11 12
510s   range:
510s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
510s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
510s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
510s real + NA row (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]   NA   NA   NA
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 NA 3 4
510s  num [1:4] 1 NA 3 4
510s  num [1:4] 1 NA 3 4
510s   max:
510s  num [1:4] 9 NA 11 12
510s  num [1:4] 9 NA 11 12
510s  num [1:4] 9 NA 11 12
510s   range:
510s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
510s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
510s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
510s real + NA row (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]   NA   NA   NA
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 NA 3 4
510s  num [1:4] 1 NA 3 4
510s  num [1:4] 1 NA 3 4
510s   max:
510s  num [1:4] 9 NA 11 12
510s  num [1:4] 9 NA 11 12
510s  num [1:4] 9 NA 11 12
510s   range:
510s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
510s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
510s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
510s real + NaN row (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]  NaN  NaN  NaN
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 NaN 3 4
510s  num [1:4] 1 NaN 3 4
510s  num [1:4] 1 NaN 3 4
510s   max:
510s  num [1:4] 9 NaN 11 12
510s  num [1:4] 9 NaN 11 12
510s  num [1:4] 9 NaN 11 12
510s   range:
510s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
510s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
510s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
510s real + NaN row (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]  NaN  NaN  NaN
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 NaN 3 4
510s  num [1:4] 1 NaN 3 4
510s  num [1:4] 1 NaN 3 4
510s   max:
510s  num [1:4] 9 NaN 11 12
510s  num [1:4] 9 NaN 11 12
510s  num [1:4] 9 NaN 11 12
510s   range:
510s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
510s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
510s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
510s real + Inf cell (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2  Inf   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s   max:
510s  num [1:4] 9 Inf 11 12
510s  num [1:4] 9 Inf 11 12
510s  num [1:4] 9 Inf 11 12
510s   range:
510s  num [1:4, 1:2] 1 2 3 4 9 ...
510s  num [1:4, 1:2] 1 2 3 4 9 ...
510s  num [1:4, 1:2] 1 2 3 4 9 ...
510s real + Inf cell (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2  Inf   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s   max:
510s  num [1:4] 9 Inf 11 12
510s  num [1:4] 9 Inf 11 12
510s  num [1:4] 9 Inf 11 12
510s   range:
510s  num [1:4, 1:2] 1 2 3 4 9 ...
510s  num [1:4, 1:2] 1 2 3 4 9 ...
510s  num [1:4, 1:2] 1 2 3 4 9 ...
510s real + Inf row (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]  Inf  Inf  Inf
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 Inf 3 4
510s  num [1:4] 1 Inf 3 4
510s  num [1:4] 1 Inf 3 4
510s   max:
510s  num [1:4] 9 Inf 11 12
510s  num [1:4] 9 Inf 11 12
510s  num [1:4] 9 Inf 11 12
510s   range:
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s real + Inf row (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]  Inf  Inf  Inf
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 Inf 3 4
510s  num [1:4] 1 Inf 3 4
510s  num [1:4] 1 Inf 3 4
510s   max:
510s  num [1:4] 9 Inf 11 12
510s  num [1:4] 9 Inf 11 12
510s  num [1:4] 9 Inf 11 12
510s   range:
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s real + NaN cell (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2  NaN   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 NaN 3 4
510s  num [1:4] 1 NaN 3 4
510s  num [1:4] 1 NaN 3 4
510s   max:
510s  num [1:4] 9 NaN 11 12
510s  num [1:4] 9 NaN 11 12
510s  num [1:4] 9 NaN 11 12
510s   range:
510s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
510s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
510s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
510s real + NaN cell (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2  NaN   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 NaN 3 4
510s  num [1:4] 1 NaN 3 4
510s  num [1:4] 1 NaN 3 4
510s   max:
510s  num [1:4] 9 NaN 11 12
510s  num [1:4] 9 NaN 11 12
510s  num [1:4] 9 NaN 11 12
510s   range:
510s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
510s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
510s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
510s real w/ NA + NaN cell (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]   NA   NA   NA
510s [2,]   NA  NaN   NA
510s [3,]   NA   NA   NA
510s [4,]   NA   NA   NA
510s   min:
510s  num [1:4] NA NA NA NA
510s  num [1:4] NA NA NA NA
510s  num [1:4] NA NA NA NA
510s   max:
510s  num [1:4] NA NA NA NA
510s  num [1:4] NA NA NA NA
510s  num [1:4] NA NA NA NA
510s   range:
510s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
510s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
510s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
510s real w/ NA + NaN cell (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]   NA   NA   NA
510s [2,]   NA  NaN   NA
510s [3,]   NA   NA   NA
510s [4,]   NA   NA   NA
510s   min:
510s  num [1:4] NA NA NA NA
510s  num [1:4] NA NA NA NA
510s  num [1:4] NA NA NA NA
510s   max:
510s  num [1:4] NA NA NA NA
510s  num [1:4] NA NA NA NA
510s  num [1:4] NA NA NA NA
510s   range:
510s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
510s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
510s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
510s real w/ NA + NaN row (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]   NA   NA   NA
510s [2,]  NaN  NaN  NaN
510s [3,]   NA   NA   NA
510s [4,]   NA   NA   NA
510s   min:
510s  num [1:4] NA NaN NA NA
510s  num [1:4] NA NaN NA NA
510s  num [1:4] NA NaN NA NA
510s   max:
510s  num [1:4] NA NaN NA NA
510s  num [1:4] NA NaN NA NA
510s  num [1:4] NA NaN NA NA
510s   range:
510s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
510s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
510s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
510s real w/ NA + NaN row (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]   NA   NA   NA
510s [2,]  NaN  NaN  NaN
510s [3,]   NA   NA   NA
510s [4,]   NA   NA   NA
510s   min:
510s  num [1:4] NA NaN NA NA
510s  num [1:4] NA NaN NA NA
510s  num [1:4] NA NaN NA NA
510s   max:
510s  num [1:4] NA NaN NA NA
510s  num [1:4] NA NaN NA NA
510s  num [1:4] NA NaN NA NA
510s   range:
510s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
510s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
510s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
510s integer (integer) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2    6   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  int [1:4] 1 2 3 4
510s  int [1:4] 1 2 3 4
510s  int [1:4] 1 2 3 4
510s   max:
510s  int [1:4] 9 10 11 12
510s  int [1:4] 9 10 11 12
510s  int [1:4] 9 10 11 12
510s   range:
510s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
510s integer (integer) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2    6   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  int [1:4] 1 2 3 4
510s  int [1:4] 1 2 3 4
510s  int [1:4] 1 2 3 4
510s   max:
510s  int [1:4] 9 10 11 12
510s  int [1:4] 9 10 11 12
510s  int [1:4] 9 10 11 12
510s   range:
510s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
510s integer w/ NA (integer) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]   NA   NA   NA
510s [2,]   NA   NA   NA
510s [3,]   NA   NA   NA
510s [4,]   NA   NA   NA
510s   min:
510s  num [1:4] Inf Inf Inf Inf
510s  num [1:4] Inf Inf Inf Inf
510s  num [1:4] Inf Inf Inf Inf
510s   max:
510s  num [1:4] -Inf -Inf -Inf -Inf
510s  num [1:4] -Inf -Inf -Inf -Inf
510s  num [1:4] -Inf -Inf -Inf -Inf
510s   range:
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s integer w/ NA (integer) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]   NA   NA   NA
510s [2,]   NA   NA   NA
510s [3,]   NA   NA   NA
510s [4,]   NA   NA   NA
510s   min:
510s  num [1:4] Inf Inf Inf Inf
510s  num [1:4] Inf Inf Inf Inf
510s  num [1:4] Inf Inf Inf Inf
510s   max:
510s  num [1:4] -Inf -Inf -Inf -Inf
510s  num [1:4] -Inf -Inf -Inf -Inf
510s  num [1:4] -Inf -Inf -Inf -Inf
510s   range:
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s real (double) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2    6   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s   max:
510s  num [1:4] 9 10 11 12
510s  num [1:4] 9 10 11 12
510s  num [1:4] 9 10 11 12
510s   range:
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s real (double) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2    6   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s   max:
510s  num [1:4] 9 10 11 12
510s  num [1:4] 9 10 11 12
510s  num [1:4] 9 10 11 12
510s   range:
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s real w/ NA (double) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]   NA   NA   NA
510s [2,]   NA   NA   NA
510s [3,]   NA   NA   NA
510s [4,]   NA   NA   NA
510s   min:
510s  num [1:4] Inf Inf Inf Inf
510s  num [1:4] Inf Inf Inf Inf
510s  num [1:4] Inf Inf Inf Inf
510s   max:
510s  num [1:4] -Inf -Inf -Inf -Inf
510s  num [1:4] -Inf -Inf -Inf -Inf
510s  num [1:4] -Inf -Inf -Inf -Inf
510s   range:
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s real w/ NA (double) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]   NA   NA   NA
510s [2,]   NA   NA   NA
510s [3,]   NA   NA   NA
510s [4,]   NA   NA   NA
510s   min:
510s  num [1:4] Inf Inf Inf Inf
510s  num [1:4] Inf Inf Inf Inf
510s  num [1:4] Inf Inf Inf Inf
510s   max:
510s  num [1:4] -Inf -Inf -Inf -Inf
510s  num [1:4] -Inf -Inf -Inf -Inf
510s  num [1:4] -Inf -Inf -Inf -Inf
510s   range:
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s real + NA cell (double) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2   NA   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s   max:
510s  num [1:4] 9 10 11 12
510s  num [1:4] 9 10 11 12
510s  num [1:4] 9 10 11 12
510s   range:
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s real + NA cell (double) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2   NA   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s   max:
510s  num [1:4] 9 10 11 12
510s  num [1:4] 9 10 11 12
510s  num [1:4] 9 10 11 12
510s   range:
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s real + NA row (double) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]   NA   NA   NA
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 Inf 3 4
510s  num [1:4] 1 Inf 3 4
510s  num [1:4] 1 Inf 3 4
510s   max:
510s  num [1:4] 9 -Inf 11 12
510s  num [1:4] 9 -Inf 11 12
510s  num [1:4] 9 -Inf 11 12
510s   range:
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s real + NA row (double) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]   NA   NA   NA
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 Inf 3 4
510s  num [1:4] 1 Inf 3 4
510s  num [1:4] 1 Inf 3 4
510s   max:
510s  num [1:4] 9 -Inf 11 12
510s  num [1:4] 9 -Inf 11 12
510s  num [1:4] 9 -Inf 11 12
510s   range:
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s real + NaN row (double) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]  NaN  NaN  NaN
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 Inf 3 4
510s  num [1:4] 1 Inf 3 4
510s  num [1:4] 1 Inf 3 4
510s   max:
510s  num [1:4] 9 -Inf 11 12
510s  num [1:4] 9 -Inf 11 12
510s  num [1:4] 9 -Inf 11 12
510s   range:
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s real + NaN row (double) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]  NaN  NaN  NaN
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 Inf 3 4
510s  num [1:4] 1 Inf 3 4
510s  num [1:4] 1 Inf 3 4
510s   max:
510s  num [1:4] 9 -Inf 11 12
510s  num [1:4] 9 -Inf 11 12
510s  num [1:4] 9 -Inf 11 12
510s   range:
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s real + Inf cell (double) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2  Inf   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s   max:
510s  num [1:4] 9 Inf 11 12
510s  num [1:4] 9 Inf 11 12
510s  num [1:4] 9 Inf 11 12
510s   range:
510s  num [1:4, 1:2] 1 2 3 4 9 ...
510s  num [1:4, 1:2] 1 2 3 4 9 ...
510s  num [1:4, 1:2] 1 2 3 4 9 ...
510s real + Inf cell (double) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2  Inf   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s   max:
510s  num [1:4] 9 Inf 11 12
510s  num [1:4] 9 Inf 11 12
510s  num [1:4] 9 Inf 11 12
510s   range:
510s  num [1:4, 1:2] 1 2 3 4 9 ...
510s  num [1:4, 1:2] 1 2 3 4 9 ...
510s  num [1:4, 1:2] 1 2 3 4 9 ...
510s real + Inf row (double) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]  Inf  Inf  Inf
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 Inf 3 4
510s  num [1:4] 1 Inf 3 4
510s  num [1:4] 1 Inf 3 4
510s   max:
510s  num [1:4] 9 Inf 11 12
510s  num [1:4] 9 Inf 11 12
510s  num [1:4] 9 Inf 11 12
510s   range:
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s real + Inf row (double) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]  Inf  Inf  Inf
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 Inf 3 4
510s  num [1:4] 1 Inf 3 4
510s  num [1:4] 1 Inf 3 4
510s   max:
510s  num [1:4] 9 Inf 11 12
510s  num [1:4] 9 Inf 11 12
510s  num [1:4] 9 Inf 11 12
510s   range:
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s  num [1:4, 1:2] 1 Inf 3 4 9 ...
510s real + NaN cell (double) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2  NaN   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s   max:
510s  num [1:4] 9 10 11 12
510s  num [1:4] 9 10 11 12
510s  num [1:4] 9 10 11 12
510s   range:
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s real + NaN cell (double) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2  NaN   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s   max:
510s  num [1:4] 9 10 11 12
510s  num [1:4] 9 10 11 12
510s  num [1:4] 9 10 11 12
510s   range:
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s real w/ NA + NaN cell (double) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]   NA   NA   NA
510s [2,]   NA  NaN   NA
510s [3,]   NA   NA   NA
510s [4,]   NA   NA   NA
510s   min:
510s  num [1:4] Inf Inf Inf Inf
510s  num [1:4] Inf Inf Inf Inf
510s  num [1:4] Inf Inf Inf Inf
510s   max:
510s  num [1:4] -Inf -Inf -Inf -Inf
510s  num [1:4] -Inf -Inf -Inf -Inf
510s  num [1:4] -Inf -Inf -Inf -Inf
510s   range:
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s real w/ NA + NaN cell (double) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]   NA   NA   NA
510s [2,]   NA  NaN   NA
510s [3,]   NA   NA   NA
510s [4,]   NA   NA   NA
510s   min:
510s  num [1:4] Inf Inf Inf Inf
510s  num [1:4] Inf Inf Inf Inf
510s  num [1:4] Inf Inf Inf Inf
510s   max:
510s  num [1:4] -Inf -Inf -Inf -Inf
510s  num [1:4] -Inf -Inf -Inf -Inf
510s  num [1:4] -Inf -Inf -Inf -Inf
510s   range:
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s real w/ NA + NaN row (double) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]   NA   NA   NA
510s [2,]  NaN  NaN  NaN
510s [3,]   NA   NA   NA
510s [4,]   NA   NA   NA
510s   min:
510s  num [1:4] Inf Inf Inf Inf
510s  num [1:4] Inf Inf Inf Inf
510s  num [1:4] Inf Inf Inf Inf
510s   max:
510s  num [1:4] -Inf -Inf -Inf -Inf
510s  num [1:4] -Inf -Inf -Inf -Inf
510s  num [1:4] -Inf -Inf -Inf -Inf
510s   range:
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s real w/ NA + NaN row (double) w/ na.rm = TRUE:
510s      [,1] [,2] [,3]
510s [1,]   NA   NA   NA
510s [2,]  NaN  NaN  NaN
510s [3,]   NA   NA   NA
510s [4,]   NA   NA   NA
510s   min:
510s  num [1:4] Inf Inf Inf Inf
510s  num [1:4] Inf Inf Inf Inf
510s  num [1:4] Inf Inf Inf Inf
510s   max:
510s  num [1:4] -Inf -Inf -Inf -Inf
510s  num [1:4] -Inf -Inf -Inf -Inf
510s  num [1:4] -Inf -Inf -Inf -Inf
510s   range:
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
510s integer (integer) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2    6   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  int [1:4] 1 2 3 4
510s  int [1:4] 1 2 3 4
510s  int [1:4] 1 2 3 4
510s   max:
510s  int [1:4] 9 10 11 12
510s  int [1:4] 9 10 11 12
510s  int [1:4] 9 10 11 12
510s   range:
510s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
510s integer (integer) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2    6   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  int [1:4] 1 2 3 4
510s  int [1:4] 1 2 3 4
510s  int [1:4] 1 2 3 4
510s   max:
510s  int [1:4] 9 10 11 12
510s  int [1:4] 9 10 11 12
510s  int [1:4] 9 10 11 12
510s   range:
510s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
510s integer w/ NA (integer) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]   NA   NA   NA
510s [2,]   NA   NA   NA
510s [3,]   NA   NA   NA
510s [4,]   NA   NA   NA
510s   min:
510s  int [1:4] NA NA NA NA
510s  int [1:4] NA NA NA NA
510s  int [1:4] NA NA NA NA
510s   max:
510s  int [1:4] NA NA NA NA
510s  int [1:4] NA NA NA NA
510s  int [1:4] NA NA NA NA
510s   range:
510s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
510s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
510s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
510s integer w/ NA (integer) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]   NA   NA   NA
510s [2,]   NA   NA   NA
510s [3,]   NA   NA   NA
510s [4,]   NA   NA   NA
510s   min:
510s  int [1:4] NA NA NA NA
510s  int [1:4] NA NA NA NA
510s  int [1:4] NA NA NA NA
510s   max:
510s  int [1:4] NA NA NA NA
510s  int [1:4] NA NA NA NA
510s  int [1:4] NA NA NA NA
510s   range:
510s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
510s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
510s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
510s real (double) w/ na.rm = FALSE:
510s      [,1] [,2] [,3]
510s [1,]    1    5    9
510s [2,]    2    6   10
510s [3,]    3    7   11
510s [4,]    4    8   12
510s   min:
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s  num [1:4] 1 2 3 4
510s   max:
510s  num [1:4] 9 10 11 12
510s  num [1:4] 9 10 11 12
510s  num [1:4] 9 10 11 12
510s   range:
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
510s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s real (double) w/ na.rm = FALSE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]    2    6   10
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s   max:
511s  num [1:4] 9 10 11 12
511s  num [1:4] 9 10 11 12
511s  num [1:4] 9 10 11 12
511s   range:
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s real w/ NA (double) w/ na.rm = FALSE:
511s      [,1] [,2] [,3]
511s [1,]   NA   NA   NA
511s [2,]   NA   NA   NA
511s [3,]   NA   NA   NA
511s [4,]   NA   NA   NA
511s   min:
511s  num [1:4] NA NA NA NA
511s  num [1:4] NA NA NA NA
511s  num [1:4] NA NA NA NA
511s   max:
511s  num [1:4] NA NA NA NA
511s  num [1:4] NA NA NA NA
511s  num [1:4] NA NA NA NA
511s   range:
511s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
511s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
511s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
511s real w/ NA (double) w/ na.rm = FALSE:
511s      [,1] [,2] [,3]
511s [1,]   NA   NA   NA
511s [2,]   NA   NA   NA
511s [3,]   NA   NA   NA
511s [4,]   NA   NA   NA
511s   min:
511s  num [1:4] NA NA NA NA
511s  num [1:4] NA NA NA NA
511s  num [1:4] NA NA NA NA
511s   max:
511s  num [1:4] NA NA NA NA
511s  num [1:4] NA NA NA NA
511s  num [1:4] NA NA NA NA
511s   range:
511s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
511s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
511s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
511s real + NA cell (double) w/ na.rm = FALSE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]    2   NA   10
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 NA 3 4
511s  num [1:4] 1 NA 3 4
511s  num [1:4] 1 NA 3 4
511s   max:
511s  num [1:4] 9 NA 11 12
511s  num [1:4] 9 NA 11 12
511s  num [1:4] 9 NA 11 12
511s   range:
511s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
511s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
511s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
511s real + NA cell (double) w/ na.rm = FALSE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]    2   NA   10
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 NA 3 4
511s  num [1:4] 1 NA 3 4
511s  num [1:4] 1 NA 3 4
511s   max:
511s  num [1:4] 9 NA 11 12
511s  num [1:4] 9 NA 11 12
511s  num [1:4] 9 NA 11 12
511s   range:
511s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
511s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
511s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
511s real + NA row (double) w/ na.rm = FALSE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]   NA   NA   NA
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 NA 3 4
511s  num [1:4] 1 NA 3 4
511s  num [1:4] 1 NA 3 4
511s   max:
511s  num [1:4] 9 NA 11 12
511s  num [1:4] 9 NA 11 12
511s  num [1:4] 9 NA 11 12
511s   range:
511s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
511s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
511s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
511s real + NA row (double) w/ na.rm = FALSE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]   NA   NA   NA
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 NA 3 4
511s  num [1:4] 1 NA 3 4
511s  num [1:4] 1 NA 3 4
511s   max:
511s  num [1:4] 9 NA 11 12
511s  num [1:4] 9 NA 11 12
511s  num [1:4] 9 NA 11 12
511s   range:
511s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
511s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
511s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
511s real + NaN row (double) w/ na.rm = FALSE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]  NaN  NaN  NaN
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 NaN 3 4
511s  num [1:4] 1 NaN 3 4
511s  num [1:4] 1 NaN 3 4
511s   max:
511s  num [1:4] 9 NaN 11 12
511s  num [1:4] 9 NaN 11 12
511s  num [1:4] 9 NaN 11 12
511s   range:
511s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
511s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
511s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
511s real + NaN row (double) w/ na.rm = FALSE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]  NaN  NaN  NaN
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 NaN 3 4
511s  num [1:4] 1 NaN 3 4
511s  num [1:4] 1 NaN 3 4
511s   max:
511s  num [1:4] 9 NaN 11 12
511s  num [1:4] 9 NaN 11 12
511s  num [1:4] 9 NaN 11 12
511s   range:
511s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
511s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
511s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
511s real + Inf cell (double) w/ na.rm = FALSE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]    2  Inf   10
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s   max:
511s  num [1:4] 9 Inf 11 12
511s  num [1:4] 9 Inf 11 12
511s  num [1:4] 9 Inf 11 12
511s   range:
511s  num [1:4, 1:2] 1 2 3 4 9 ...
511s  num [1:4, 1:2] 1 2 3 4 9 ...
511s  num [1:4, 1:2] 1 2 3 4 9 ...
511s real + Inf cell (double) w/ na.rm = FALSE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]    2  Inf   10
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s   max:
511s  num [1:4] 9 Inf 11 12
511s  num [1:4] 9 Inf 11 12
511s  num [1:4] 9 Inf 11 12
511s   range:
511s  num [1:4, 1:2] 1 2 3 4 9 ...
511s  num [1:4, 1:2] 1 2 3 4 9 ...
511s  num [1:4, 1:2] 1 2 3 4 9 ...
511s real + Inf row (double) w/ na.rm = FALSE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]  Inf  Inf  Inf
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 Inf 3 4
511s  num [1:4] 1 Inf 3 4
511s  num [1:4] 1 Inf 3 4
511s   max:
511s  num [1:4] 9 Inf 11 12
511s  num [1:4] 9 Inf 11 12
511s  num [1:4] 9 Inf 11 12
511s   range:
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s real + Inf row (double) w/ na.rm = FALSE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]  Inf  Inf  Inf
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 Inf 3 4
511s  num [1:4] 1 Inf 3 4
511s  num [1:4] 1 Inf 3 4
511s   max:
511s  num [1:4] 9 Inf 11 12
511s  num [1:4] 9 Inf 11 12
511s  num [1:4] 9 Inf 11 12
511s   range:
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s real + NaN cell (double) w/ na.rm = FALSE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]    2  NaN   10
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 NaN 3 4
511s  num [1:4] 1 NaN 3 4
511s  num [1:4] 1 NaN 3 4
511s   max:
511s  num [1:4] 9 NaN 11 12
511s  num [1:4] 9 NaN 11 12
511s  num [1:4] 9 NaN 11 12
511s   range:
511s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
511s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
511s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
511s real + NaN cell (double) w/ na.rm = FALSE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]    2  NaN   10
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 NaN 3 4
511s  num [1:4] 1 NaN 3 4
511s  num [1:4] 1 NaN 3 4
511s   max:
511s  num [1:4] 9 NaN 11 12
511s  num [1:4] 9 NaN 11 12
511s  num [1:4] 9 NaN 11 12
511s   range:
511s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
511s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
511s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
511s real w/ NA + NaN cell (double) w/ na.rm = FALSE:
511s      [,1] [,2] [,3]
511s [1,]   NA   NA   NA
511s [2,]   NA  NaN   NA
511s [3,]   NA   NA   NA
511s [4,]   NA   NA   NA
511s   min:
511s  num [1:4] NA NA NA NA
511s  num [1:4] NA NA NA NA
511s  num [1:4] NA NA NA NA
511s   max:
511s  num [1:4] NA NA NA NA
511s  num [1:4] NA NA NA NA
511s  num [1:4] NA NA NA NA
511s   range:
511s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
511s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
511s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
511s real w/ NA + NaN cell (double) w/ na.rm = FALSE:
511s      [,1] [,2] [,3]
511s [1,]   NA   NA   NA
511s [2,]   NA  NaN   NA
511s [3,]   NA   NA   NA
511s [4,]   NA   NA   NA
511s   min:
511s  num [1:4] NA NA NA NA
511s  num [1:4] NA NA NA NA
511s  num [1:4] NA NA NA NA
511s   max:
511s  num [1:4] NA NA NA NA
511s  num [1:4] NA NA NA NA
511s  num [1:4] NA NA NA NA
511s   range:
511s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
511s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
511s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
511s real w/ NA + NaN row (double) w/ na.rm = FALSE:
511s      [,1] [,2] [,3]
511s [1,]   NA   NA   NA
511s [2,]  NaN  NaN  NaN
511s [3,]   NA   NA   NA
511s [4,]   NA   NA   NA
511s   min:
511s  num [1:4] NA NaN NA NA
511s  num [1:4] NA NaN NA NA
511s  num [1:4] NA NaN NA NA
511s   max:
511s  num [1:4] NA NaN NA NA
511s  num [1:4] NA NaN NA NA
511s  num [1:4] NA NaN NA NA
511s   range:
511s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
511s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
511s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
511s real w/ NA + NaN row (double) w/ na.rm = FALSE:
511s      [,1] [,2] [,3]
511s [1,]   NA   NA   NA
511s [2,]  NaN  NaN  NaN
511s [3,]   NA   NA   NA
511s [4,]   NA   NA   NA
511s   min:
511s  num [1:4] NA NaN NA NA
511s  num [1:4] NA NaN NA NA
511s  num [1:4] NA NaN NA NA
511s   max:
511s  num [1:4] NA NaN NA NA
511s  num [1:4] NA NaN NA NA
511s  num [1:4] NA NaN NA NA
511s   range:
511s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
511s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
511s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
511s integer (integer) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]    2    6   10
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  int [1:4] 1 2 3 4
511s  int [1:4] 1 2 3 4
511s  int [1:4] 1 2 3 4
511s   max:
511s  int [1:4] 9 10 11 12
511s  int [1:4] 9 10 11 12
511s  int [1:4] 9 10 11 12
511s   range:
511s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
511s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
511s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
511s integer (integer) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]    2    6   10
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  int [1:4] 1 2 3 4
511s  int [1:4] 1 2 3 4
511s  int [1:4] 1 2 3 4
511s   max:
511s  int [1:4] 9 10 11 12
511s  int [1:4] 9 10 11 12
511s  int [1:4] 9 10 11 12
511s   range:
511s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
511s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
511s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
511s integer w/ NA (integer) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]   NA   NA   NA
511s [2,]   NA   NA   NA
511s [3,]   NA   NA   NA
511s [4,]   NA   NA   NA
511s   min:
511s  num [1:4] Inf Inf Inf Inf
511s  num [1:4] Inf Inf Inf Inf
511s  num [1:4] Inf Inf Inf Inf
511s   max:
511s  num [1:4] -Inf -Inf -Inf -Inf
511s  num [1:4] -Inf -Inf -Inf -Inf
511s  num [1:4] -Inf -Inf -Inf -Inf
511s   range:
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s integer w/ NA (integer) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]   NA   NA   NA
511s [2,]   NA   NA   NA
511s [3,]   NA   NA   NA
511s [4,]   NA   NA   NA
511s   min:
511s  num [1:4] Inf Inf Inf Inf
511s  num [1:4] Inf Inf Inf Inf
511s  num [1:4] Inf Inf Inf Inf
511s   max:
511s  num [1:4] -Inf -Inf -Inf -Inf
511s  num [1:4] -Inf -Inf -Inf -Inf
511s  num [1:4] -Inf -Inf -Inf -Inf
511s   range:
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s real (double) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]    2    6   10
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s   max:
511s  num [1:4] 9 10 11 12
511s  num [1:4] 9 10 11 12
511s  num [1:4] 9 10 11 12
511s   range:
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s real (double) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]    2    6   10
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s   max:
511s  num [1:4] 9 10 11 12
511s  num [1:4] 9 10 11 12
511s  num [1:4] 9 10 11 12
511s   range:
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s real w/ NA (double) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]   NA   NA   NA
511s [2,]   NA   NA   NA
511s [3,]   NA   NA   NA
511s [4,]   NA   NA   NA
511s   min:
511s  num [1:4] Inf Inf Inf Inf
511s  num [1:4] Inf Inf Inf Inf
511s  num [1:4] Inf Inf Inf Inf
511s   max:
511s  num [1:4] -Inf -Inf -Inf -Inf
511s  num [1:4] -Inf -Inf -Inf -Inf
511s  num [1:4] -Inf -Inf -Inf -Inf
511s   range:
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s real w/ NA (double) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]   NA   NA   NA
511s [2,]   NA   NA   NA
511s [3,]   NA   NA   NA
511s [4,]   NA   NA   NA
511s   min:
511s  num [1:4] Inf Inf Inf Inf
511s  num [1:4] Inf Inf Inf Inf
511s  num [1:4] Inf Inf Inf Inf
511s   max:
511s  num [1:4] -Inf -Inf -Inf -Inf
511s  num [1:4] -Inf -Inf -Inf -Inf
511s  num [1:4] -Inf -Inf -Inf -Inf
511s   range:
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s real + NA cell (double) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]    2   NA   10
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s   max:
511s  num [1:4] 9 10 11 12
511s  num [1:4] 9 10 11 12
511s  num [1:4] 9 10 11 12
511s   range:
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s real + NA cell (double) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]    2   NA   10
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s   max:
511s  num [1:4] 9 10 11 12
511s  num [1:4] 9 10 11 12
511s  num [1:4] 9 10 11 12
511s   range:
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s real + NA row (double) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]   NA   NA   NA
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 Inf 3 4
511s  num [1:4] 1 Inf 3 4
511s  num [1:4] 1 Inf 3 4
511s   max:
511s  num [1:4] 9 -Inf 11 12
511s  num [1:4] 9 -Inf 11 12
511s  num [1:4] 9 -Inf 11 12
511s   range:
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s real + NA row (double) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]   NA   NA   NA
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 Inf 3 4
511s  num [1:4] 1 Inf 3 4
511s  num [1:4] 1 Inf 3 4
511s   max:
511s  num [1:4] 9 -Inf 11 12
511s  num [1:4] 9 -Inf 11 12
511s  num [1:4] 9 -Inf 11 12
511s   range:
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s real + NaN row (double) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]  NaN  NaN  NaN
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 Inf 3 4
511s  num [1:4] 1 Inf 3 4
511s  num [1:4] 1 Inf 3 4
511s   max:
511s  num [1:4] 9 -Inf 11 12
511s  num [1:4] 9 -Inf 11 12
511s  num [1:4] 9 -Inf 11 12
511s   range:
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s real + NaN row (double) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]  NaN  NaN  NaN
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 Inf 3 4
511s  num [1:4] 1 Inf 3 4
511s  num [1:4] 1 Inf 3 4
511s   max:
511s  num [1:4] 9 -Inf 11 12
511s  num [1:4] 9 -Inf 11 12
511s  num [1:4] 9 -Inf 11 12
511s   range:
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s real + Inf cell (double) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]    2  Inf   10
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s   max:
511s  num [1:4] 9 Inf 11 12
511s  num [1:4] 9 Inf 11 12
511s  num [1:4] 9 Inf 11 12
511s   range:
511s  num [1:4, 1:2] 1 2 3 4 9 ...
511s  num [1:4, 1:2] 1 2 3 4 9 ...
511s  num [1:4, 1:2] 1 2 3 4 9 ...
511s real + Inf cell (double) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]    2  Inf   10
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s   max:
511s  num [1:4] 9 Inf 11 12
511s  num [1:4] 9 Inf 11 12
511s  num [1:4] 9 Inf 11 12
511s   range:
511s  num [1:4, 1:2] 1 2 3 4 9 ...
511s  num [1:4, 1:2] 1 2 3 4 9 ...
511s  num [1:4, 1:2] 1 2 3 4 9 ...
511s real + Inf row (double) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]  Inf  Inf  Inf
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 Inf 3 4
511s  num [1:4] 1 Inf 3 4
511s  num [1:4] 1 Inf 3 4
511s   max:
511s  num [1:4] 9 Inf 11 12
511s  num [1:4] 9 Inf 11 12
511s  num [1:4] 9 Inf 11 12
511s   range:
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s real + Inf row (double) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]  Inf  Inf  Inf
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 Inf 3 4
511s  num [1:4] 1 Inf 3 4
511s  num [1:4] 1 Inf 3 4
511s   max:
511s  num [1:4] 9 Inf 11 12
511s  num [1:4] 9 Inf 11 12
511s  num [1:4] 9 Inf 11 12
511s   range:
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s  num [1:4, 1:2] 1 Inf 3 4 9 ...
511s real + NaN cell (double) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]    2  NaN   10
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s   max:
511s  num [1:4] 9 10 11 12
511s  num [1:4] 9 10 11 12
511s  num [1:4] 9 10 11 12
511s   range:
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s real + NaN cell (double) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]    1    5    9
511s [2,]    2  NaN   10
511s [3,]    3    7   11
511s [4,]    4    8   12
511s   min:
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s  num [1:4] 1 2 3 4
511s   max:
511s  num [1:4] 9 10 11 12
511s  num [1:4] 9 10 11 12
511s  num [1:4] 9 10 11 12
511s   range:
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
511s real w/ NA + NaN cell (double) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]   NA   NA   NA
511s [2,]   NA  NaN   NA
511s [3,]   NA   NA   NA
511s [4,]   NA   NA   NA
511s   min:
511s  num [1:4] Inf Inf Inf Inf
511s  num [1:4] Inf Inf Inf Inf
511s  num [1:4] Inf Inf Inf Inf
511s   max:
511s  num [1:4] -Inf -Inf -Inf -Inf
511s  num [1:4] -Inf -Inf -Inf -Inf
511s  num [1:4] -Inf -Inf -Inf -Inf
511s   range:
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s real w/ NA + NaN cell (double) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]   NA   NA   NA
511s [2,]   NA  NaN   NA
511s [3,]   NA   NA   NA
511s [4,]   NA   NA   NA
511s   min:
511s  num [1:4] Inf Inf Inf Inf
511s  num [1:4] Inf Inf Inf Inf
511s  num [1:4] Inf Inf Inf Inf
511s   max:
511s  num [1:4] -Inf -Inf -Inf -Inf
511s  num [1:4] -Inf -Inf -Inf -Inf
511s  num [1:4] -Inf -Inf -Inf -Inf
511s   range:
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s real w/ NA + NaN row (double) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]   NA   NA   NA
511s [2,]  NaN  NaN  NaN
511s [3,]   NA   NA   NA
511s [4,]   NA   NA   NA
511s   min:
511s  num [1:4] Inf Inf Inf Inf
511s  num [1:4] Inf Inf Inf Inf
511s  num [1:4] Inf Inf Inf Inf
511s   max:
511s  num [1:4] -Inf -Inf -Inf -Inf
511s  num [1:4] -Inf -Inf -Inf -Inf
511s  num [1:4] -Inf -Inf -Inf -Inf
511s   range:
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s real w/ NA + NaN row (double) w/ na.rm = TRUE:
511s      [,1] [,2] [,3]
511s [1,]   NA   NA   NA
511s [2,]  NaN  NaN  NaN
511s [3,]   NA   NA   NA
511s [4,]   NA   NA   NA
511s   min:
511s  num [1:4] Inf Inf Inf Inf
511s  num [1:4] Inf Inf Inf Inf
511s  num [1:4] Inf Inf Inf Inf
511s   max:
511s  num [1:4] -Inf -Inf -Inf -Inf
511s  num [1:4] -Inf -Inf -Inf -Inf
511s  num [1:4] -Inf -Inf -Inf -Inf
511s   range:
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
511s > 
511s 
511s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
511s Copyright (C) 2024 The R Foundation for Statistical Computing
511s Platform: arm-unknown-linux-gnueabihf (32-bit)
511s 
511s R is free software and comes with ABSOLUTELY NO WARRANTY.
511s You are welcome to redistribute it under certain conditions.
511s Type 'license()' or 'licence()' for distribution details.
511s 
511s R is a collaborative project with many contributors.
511s Type 'contributors()' for more information and
511s 'citation()' on how to cite R or R packages in publications.
511s 
511s Type 'demo()' for some demos, 'help()' for on-line help, or
511s 'help.start()' for an HTML browser interface to help.
511s Type 'q()' to quit R.
511s 
512s > library("matrixStats")
512s > 
512s > rowMins_R <- function(x, ..., useNames = NA) {
512s +   suppressWarnings({
512s +     res <- apply(x, MARGIN = 1L, FUN = min, ...)
512s +   })
512s +   if (is.na(useNames) || !useNames) names(res) <- NULL
512s +   res
512s + } # rowMins_R()
512s > 
512s > rowMaxs_R <- function(x, ..., useNames = NA) {
512s +   suppressWarnings({
512s +     res <- apply(x, MARGIN = 1L, FUN = max, ...)
512s +   })
512s +   if (is.na(useNames) || !useNames) names(res) <- NULL
512s +   res
512s + } # rowMaxs_R()
512s > 
512s > rowRanges_R <- function(x, ..., useNames = NA) {
512s +   suppressWarnings({
512s +     ans <- t(apply(x, MARGIN = 1L, FUN = range, ...))
512s +   })
512s + 
512s +   # Preserve rownames attribute
512s +   dim <- c(dim(x)[1], 2L)
512s +   if (!isTRUE(all.equal(dim(ans), dim))) {
512s +     dim(ans) <- dim
512s +     rownames <- rownames(x)
512s +     if (!is.null(dimnames)) rownames(ans) <- rownames
512s +   }
512s +   if (is.na(useNames) || !useNames) dimnames(ans) <- NULL
512s +   ans
512s + } # rowRanges_R()
512s > 
512s > 
512s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
512s > # Subsetted tests
512s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
512s > source("utils/validateIndicesFramework.R")
512s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
512s > storage.mode(x) <- "integer"
512s > 
512s > # To check rownames/names attributes
512s > dimnames <- list(letters[1:6], LETTERS[1:6])
512s > 
512s > # Test with and without dimnames on x
512s > for (setDimnames in c(TRUE, FALSE)) {
512s +   if (setDimnames) dimnames(x) <- dimnames
512s +   else dimnames(x) <- NULL
512s +   
512s +   count <- 0L
512s +   for (rows in index_cases) {
512s +     for (cols in index_cases) {
512s +       count <- count + 1L
512s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
512s +       useNames <- c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)
512s +       useNames <- useNames[count %% length(useNames) + 1]
512s + 
512s +       validateIndicesTestMatrix(x, rows, cols,
512s +                                 ftest = rowRanges, fsure = rowRanges_R,
512s +                                 na.rm = na.rm, useNames = useNames)
512s +       validateIndicesTestMatrix(x, rows, cols,
512s +                                 ftest = rowMins, fsure = rowMins_R,
512s +                                 na.rm = na.rm, useNames = useNames)
512s +       validateIndicesTestMatrix(x, rows, cols,
512s +                                 ftest = rowMaxs, fsure = rowMaxs_R,
512s +                                 na.rm = na.rm, useNames = useNames)
512s + 
512s +       validateIndicesTestMatrix(x, rows, cols,
512s +                                 fcoltest = colRanges, fsure = rowRanges_R,
512s +                                 na.rm = na.rm, useNames = useNames)
512s +       validateIndicesTestMatrix(x, rows, cols,
512s +                                 fcoltest = colMins, fsure = rowMins_R,
512s +                                 na.rm = na.rm, useNames = useNames)
512s +       validateIndicesTestMatrix(x, rows, cols,
512s +                                 fcoltest = colMaxs, fsure = rowMaxs_R,
512s +                                 na.rm = na.rm, useNames = useNames)
512s +     }
512s +   }
512s + }
516s > 
516s 
516s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
516s Copyright (C) 2024 The R Foundation for Statistical Computing
516s Platform: arm-unknown-linux-gnueabihf (32-bit)
516s 
516s R is free software and comes with ABSOLUTELY NO WARRANTY.
516s You are welcome to redistribute it under certain conditions.
516s Type 'license()' or 'licence()' for distribution details.
516s 
516s R is a collaborative project with many contributors.
516s Type 'contributors()' for more information and
516s 'citation()' on how to cite R or R packages in publications.
516s 
516s Type 'demo()' for some demos, 'help()' for on-line help, or
516s 'help.start()' for an HTML browser interface to help.
516s Type 'q()' to quit R.
516s 
516s > library("matrixStats")
516s > 
516s > dense_rank <- function(x) match(x, table = sort(unique(x)))
516s > 
516s > rowRanks_R <- function(x, ties.method, ..., useNames = NA) {
516s +   if (ties.method == "dense") {
516s +     res <- t(apply(x, MARGIN = 1L, FUN = dense_rank))
516s +   } else {
516s +     res <- t(apply(x, MARGIN = 1L, FUN = rank, na.last = "keep", ties.method = ties.method))
516s +   }
516s +   
516s +   # Preserve dimnames attribute?
516s +   dim(res) <- dim(x)
516s +   dimnames(res) <- if (isTRUE(useNames)) dimnames(x) else NULL
516s +   
516s +   res
516s + }
516s > 
516s > colRanks_R <- function(x, ties.method, preserveShape = FALSE, ..., useNames = NA) {
516s +   if (ties.method == "dense") {
516s +     res <- t(apply(x, MARGIN = 2L, FUN = dense_rank))
516s +   } else {
516s +     res <- t(apply(x, MARGIN = 2L, FUN = rank, na.last = "keep", ties.method = ties.method))
516s +   }
516s +   
516s +   # Preserve dimnames attribute?
516s +   tx <- t(x)
516s +   dim(res) <- dim(tx)
516s +   dimnames(res) <- if (isTRUE(useNames)) dimnames(tx) else NULL
516s +   
516s +   if (preserveShape) res <- t(res)
516s +   res
516s + }
516s > 
516s > set.seed(1)
516s > 
516s > cat("Consistency checks:\n")
516s Consistency checks:
516s > xs <- vector("list", length = 4L)
516s > for (kk in 1:4) {
516s +   
516s +   # Simulate data in a matrix of any shape
516s +   dim <- sample(40:80, size = 2L)
516s +   n <- prod(dim)
516s +   x <- rnorm(n, sd = 10)
516s +   dim(x) <- dim
516s +   
516s +   # Add NAs?
516s +   if ((kk %% 4) %in% c(3, 0)) {
516s +     cat("Adding NAs\n")
516s +     nna <- sample(n, size = 1L)
516s +     x[sample(length(x), size = nna)] <- NA_real_
516s +   }
516s +   
516s +   # Integer or double?
516s +   if ((kk %% 4) %in% c(2, 0)) {
516s +     cat("Coercing to integers\n")
516s +     storage.mode(x) <- "integer"
516s +   }
516s + 
516s +   xs[[kk]] <- x
516s + } # for (kk ...)
517s Coercing to integers
517s Adding NAs
517s Adding NAs
517s Coercing to integers
517s > str(xs)
517s List of 4
517s  $ : num [1:43, 1:78] 13.3 12.72 4.15 -15.4 -9.29 ...
517s  $ : int [1:46, 1:61] 2 11 -16 -5 19 5 26 -13 1 -9 ...
517s  $ : num [1:42, 1:47] NA -22.3 NA NA NA ...
517s  $ : int [1:42, 1:78] NA NA NA NA NA NA NA NA NA NA ...
517s > 
517s > for (kk in 1:4) {
517s +   cat("Random test #", kk, "\n", sep = "")
517s +   x <- xs[[kk]]
517s +   tx <- t(x)
517s +   
517s +   for (ties in c("max", "min", "average", "first", "last", "dense")) {
517s +     cat(sprintf("ties.method = %s\n", ties))
517s +     # rowRanks():
517s +     y1 <- matrixStats::rowRanks(x, ties.method = ties)
517s +     if (ties != "last" || getRversion() >= "3.3.0") {
517s +       y2 <- rowRanks_R(x, ties.method = ties)
517s +       stopifnot(identical(y1, y2))
517s +     }
517s +     
517s +     y3 <- matrixStats::colRanks(tx, ties.method = ties)
517s +     stopifnot(identical(y1, y3))
517s +     
517s +     # colRanks():
517s +     y1 <- matrixStats::colRanks(x, ties.method = ties)
517s +     if (ties != "last" || getRversion() >= "3.3.0") {
517s +       y2 <- colRanks_R(x, ties.method = ties)
517s +       stopifnot(identical(y1, y2))
517s +     }
517s +     
517s +     y3 <- matrixStats::rowRanks(tx, ties.method = ties)
517s +     stopifnot(identical(y1, y3))
517s +   }
517s + } # for (kk ...)
517s Random test #1
517s ties.method = max
517s ties.method = min
517s ties.method = average
517s ties.method = first
517s ties.method = last
517s ties.method = dense
517s Random test #2
517s ties.method = max
517s ties.method = min
517s ties.method = average
517s ties.method = first
517s ties.method = last
517s ties.method = dense
517s Random test #3
517s ties.method = max
517s ties.method = min
517s ties.method = average
517s ties.method = first
517s ties.method = last
517s ties.method = dense
517s Random test #4
517s ties.method = max
517s ties.method = min
517s ties.method = average
517s ties.method = first
517s ties.method = last
517s ties.method = dense
517s > 
517s > # Note, below we know ties.method %in% c("min", "max", "average") is correct
517s > 
517s > cat("Consistency checks for random:\n")
517s Consistency checks for random:
517s > tolerance <- 0.1
517s > nsamples <- 10000
517s > for (kk in 1:4) {
517s +   cat("Random test #", kk, "\n", sep = "")
517s +   x <- xs[[kk]]
517s +   tx <- t(x)
517s + 
517s +   for (ties in c("random")) {
517s +     cat(sprintf("ties.method = %s\n", ties))
517s +     
517s +     ## rowRanks():
517s +     y0 <- rowRanks_R(x, ties.method = ties)
517s +     y1 <- matrixStats::rowRanks(x, ties.method = ties)
517s +     
517s +     ## Assert symmetric rank differences
517s +     d <- y1 - y0
517s +     stopifnot(all(rowSums(d) == 0, na.rm = TRUE))
517s +     
517s +     ## Assert within [min, max]
517s +     y2min <- matrixStats::rowRanks(x, ties.method = "min")
517s +     y2max <- matrixStats::rowRanks(x, ties.method = "max")
517s +     stopifnot(all(y1 >= y2min, na.rm = TRUE) && all(y1 <= y2max, na.rm = TRUE))
517s +     ## Assert near average
517s +     y1list <- replicate(nsamples, matrixStats::rowRanks(x, ties.method = ties), simplify = FALSE)
517s +     y1mean <- Reduce(`+`, y1list) / nsamples
517s +     y2avg <- matrixStats::rowRanks(x, ties.method = "average")
517s +     stopifnot(all(abs(y1mean - y2avg) < tolerance, na.rm = TRUE))
517s + 
517s +     ## colRanks():
517s +     y0 <- colRanks_R(x, ties.method = ties)
517s +     y1 <- matrixStats::colRanks(x, ties.method = ties)
517s + 
517s +     ## Assert symmetric rank differences
517s +     d <- y1 - y0
517s +     stopifnot(all(rowSums(d) == 0, na.rm = TRUE))
517s + 
517s +     ## Assert within [min, max]
517s +     y2min <- matrixStats::colRanks(x, ties.method = "min")
517s +     y2max <- matrixStats::colRanks(x, ties.method = "max")
517s +     stopifnot(all(y1 >= y2min, na.rm = TRUE) && all(y1 <= y2max, na.rm = TRUE))
517s +     y1list <- replicate(nsamples, matrixStats::colRanks(x, ties.method = ties), simplify = FALSE)
517s +     y1mean <- Reduce(`+`, y1list) / nsamples
517s +     ## Assert near average
517s +     y2avg <- matrixStats::colRanks(x, ties.method = "average")
517s +     stopifnot(all(abs(y1mean - y2avg) < tolerance, na.rm = TRUE))
517s +   }
517s + } # for (kk ...)
517s Random test #1
517s ties.method = random
525s Random test #2
525s ties.method = random
530s Random test #3
530s ties.method = random
533s Random test #4
533s ties.method = random
535s > 
535s > 
535s > ## Exception handling
535s > x <- matrix(1:12, nrow = 3L, ncol = 4L)
535s > y <- try(rowRanks(x, ties.method = "unknown"), silent = TRUE)
535s > stopifnot(inherits(y, "try-error"))
535s > 
535s > y <- try(colRanks(x, ties.method = "unknown"), silent = TRUE)
535s > stopifnot(inherits(y, "try-error"))
535s > 
535s > dimnames <- list(letters[1:3], LETTERS[1:4])
535s > for (mode in c("integer", "double")){
535s +   storage.mode(x) <- mode
535s +   # Test with and without dimnames on x
535s +   for (setDimnames in c(TRUE, FALSE)) {
535s +     if (setDimnames) dimnames(x) <- dimnames
535s +     else dimnames(x) <- NULL
535s +     # Check names attribute
535s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
535s +       for (ties in c("max", "min", "average", "first", "last", "dense", "random")) {
535s +         cat(sprintf("ties.method = %s\n", ties))
535s +         # rowRanks():
535s +         y1 <- matrixStats::rowRanks(x, ties.method = ties, useNames = useNames)
535s +         if (ties != "last" || getRversion() >= "3.3.0") {
535s +           y2 <- rowRanks_R(x, ties.method = ties, useNames = useNames)
535s +           stopifnot(identical(y1, y2))
535s +         }
535s +         
535s +         y3 <- matrixStats::colRanks(t(x), ties.method = ties, useNames = useNames)
535s +         stopifnot(identical(y1, y3))
535s +         
535s +         # colRanks():
535s +         y1 <- matrixStats::colRanks(x, ties.method = ties, useNames = useNames)
535s +         if (ties != "last" || getRversion() >= "3.3.0") {
535s +           y2 <- colRanks_R(x, ties.method = ties, useNames = useNames)
535s +           stopifnot(identical(y1, y2))
535s +         }
535s +         
535s +         y3 <- matrixStats::rowRanks(t(x), ties.method = ties, useNames = useNames)
535s +         stopifnot(identical(y1, y3))
535s +         
535s +         # Check preserveShape
535s +         y1 <- matrixStats::colRanks(x, ties.method = ties, preserveShape = TRUE, useNames = useNames)
535s +         if (ties != "last" || getRversion() >= "3.3.0") {
535s +           y2 <- colRanks_R(x, ties.method = ties, preserveShape = TRUE, useNames = useNames)
535s +           stopifnot(identical(y1, y2))
535s +         }
535s +       }
535s +     }
535s +   }
535s + }
535s ties.method = max
535s ties.method = min
535s ties.method = average
535s ties.method = first
535s ties.method = last
535s ties.method = dense
535s ties.method = random
535s ties.method = max
535s ties.method = min
535s ties.method = average
535s ties.method = first
535s ties.method = last
535s ties.method = dense
535s ties.method = random
535s ties.method = max
535s ties.method = min
535s ties.method = average
535s ties.method = first
535s ties.method = last
535s ties.method = dense
535s ties.method = random
536s ties.method = max
536s ties.method = min
536s ties.method = average
536s ties.method = first
536s ties.method = last
536s ties.method = dense
536s ties.method = random
536s ties.method = max
536s ties.method = min
536s ties.method = average
536s ties.method = first
536s ties.method = last
536s ties.method = dense
536s ties.method = random
536s ties.method = max
536s ties.method = min
536s ties.method = average
536s ties.method = first
536s ties.method = last
536s ties.method = dense
536s ties.method = random
536s ties.method = max
536s ties.method = min
536s ties.method = average
536s ties.method = first
536s ties.method = last
536s ties.method = dense
536s ties.method = random
536s ties.method = max
536s ties.method = min
536s ties.method = average
536s ties.method = first
536s ties.method = last
536s ties.method = dense
536s ties.method = random
536s > 
536s 
536s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
536s Copyright (C) 2024 The R Foundation for Statistical Computing
536s Platform: arm-unknown-linux-gnueabihf (32-bit)
536s 
536s R is free software and comes with ABSOLUTELY NO WARRANTY.
536s You are welcome to redistribute it under certain conditions.
536s Type 'license()' or 'licence()' for distribution details.
536s 
536s R is a collaborative project with many contributors.
536s Type 'contributors()' for more information and
536s 'citation()' on how to cite R or R packages in publications.
536s 
536s Type 'demo()' for some demos, 'help()' for on-line help, or
536s 'help.start()' for an HTML browser interface to help.
536s Type 'q()' to quit R.
536s 
536s > library("matrixStats")
536s > 
536s > rowRanks_R <- function(x, ties.method = "average", ..., useNames = NA) {
536s +   ans <- t(apply(x, MARGIN = 1L, FUN = rank, na.last = "keep",
536s +                  ties.method = ties.method))
536s +   
536s +   # Preserve dimnames attribute?
536s +   dim(ans) <- dim(x)
536s +   dimnames(ans) <- if (isTRUE(useNames)) dimnames(x) else NULL
536s + 
536s +   ans
536s + }
536s > 
536s > colRanks_R <- function(x, ties.method, preserveShape = FALSE, ..., useNames = NA) {
536s +   ans <- t(apply(x, MARGIN = 2L, FUN = rank, na.last = "keep", ties.method = ties.method))
536s +   
536s +   # Preserve dimnames attribute?
536s +   tx <- t(x)
536s +   dim(ans) <- dim(tx)
536s +   dimnames(ans) <- if (isTRUE(useNames)) dimnames(tx) else NULL
536s +   
536s +   if (preserveShape) ans <- t(ans)
536s +   ans
536s + }
536s > 
536s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
536s > # Subsetted tests
536s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
536s > source("utils/validateIndicesFramework.R")
536s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
536s > storage.mode(x) <- "integer"
536s > 
536s > # To check dimnames attribute
536s > dimnames <- list(letters[1:6], LETTERS[1:6])
536s > 
536s > colRanks_R_t <- function(x, rows, cols, ..., useNames = NA) {
536s +   t(colRanks(t(x), rows = cols, cols = rows, preserveShape = TRUE, ..., useNames = useNames))
536s + }
536s > 
536s > # Test with and without dimnames on x
536s > for (setDimnames in c(TRUE, FALSE)) {
536s +   if (setDimnames) dimnames(x) <- dimnames
536s +   else dimnames(x) <- NULL
536s + 
536s +   count <- 0L
536s +   for (rows in index_cases) {
536s +     for (cols in index_cases) {
536s +       count <- count + 1L
536s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
536s +       useNames <- c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)
536s +       useNames <- useNames[count %% length(useNames) + 1]
536s + 
536s +       validateIndicesTestMatrix(x, rows, cols,
536s +                                 ftest = rowRanks, fsure = rowRanks_R,
536s +                                 ties.method = "average", useNames = useNames)
536s +       
536s +       validateIndicesTestMatrix(x, rows, cols,
536s +                                 ftest = colRanks_R_t, fsure = rowRanks_R,
536s +                                 ties.method = "average", useNames = useNames)
536s +       
536s +       for (perserveShape in c(TRUE, FALSE)) {
536s +         validateIndicesTestMatrix(x, rows, cols,
536s +                                   ftest = colRanks, fsure = colRanks_R,
536s +                                   ties.method = "average", perserveShape = perserveShape,
536s +                                   useNames = useNames)          
536s +       }
536s +     }
536s +   }
536s + }
540s > 
540s 
540s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
540s Copyright (C) 2024 The R Foundation for Statistical Computing
540s Platform: arm-unknown-linux-gnueabihf (32-bit)
540s 
540s R is free software and comes with ABSOLUTELY NO WARRANTY.
540s You are welcome to redistribute it under certain conditions.
540s Type 'license()' or 'licence()' for distribution details.
540s 
540s R is a collaborative project with many contributors.
540s Type 'contributors()' for more information and
540s 'citation()' on how to cite R or R packages in publications.
540s 
540s Type 'demo()' for some demos, 'help()' for on-line help, or
540s 'help.start()' for an HTML browser interface to help.
540s Type 'q()' to quit R.
540s 
541s > library("matrixStats")
541s > 
541s > ## Always allow testing of the 'center' argument (as long as it's not defunct)
541s > options(matrixStats.center.onUse = "ignore")
541s > 
541s > ## Create isFALSE() if running on an old version of R
541s > if (!exists("isFALSE", mode="function")) {
541s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
541s + }
541s > 
541s > rowSds_R <- function(x, na.rm = FALSE, center = NULL, ..., useNames = NA) {
541s +   suppressWarnings({
541s +     sigma <- apply(x, MARGIN = 1L, FUN = sd, na.rm = na.rm)
541s +   })
541s +   stopifnot(!any(is.infinite(sigma)))
541s +   
541s +   # Keep naming support consistency same as rowSds()
541s +   if (is.null(center) || ncol(x) <= 1L) {
541s +     if (is.na(useNames) || isFALSE(useNames)) names(sigma) <- NULL
541s +   }
541s +   else if (isFALSE(useNames)) names(sigma) <- NULL
541s +   sigma
541s + }
541s > 
541s > colSds_R <- function(x, na.rm = FALSE, center = NULL, ..., useNames = NA) {
541s +   suppressWarnings({
541s +     sigma <- apply(x, MARGIN = 2L, FUN = sd, na.rm = na.rm)
541s +   })
541s +   stopifnot(!any(is.infinite(sigma)))
541s +   
541s +   # Keep naming support consistency same as colSds()
541s +   if (is.null(center) || nrow(x) <= 1L) {
541s +     if (is.na(useNames) || isFALSE(useNames)) names(sigma) <- NULL
541s +   }
541s +   if (isFALSE(useNames)) names(sigma) <- NULL
541s +   sigma
541s + }
541s > 
541s > 
541s > rowSds_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = NA) {
541s +   center <- rowWeightedMeans(x, cols = cols, na.rm = na.rm, useNames = FALSE)
541s +   sigma <- rowSds(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
541s +   stopifnot(!any(is.infinite(sigma)))
541s +   sigma
541s + }
541s > 
541s > colSds_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = NA) {
541s +   center <- colWeightedMeans(x, rows = rows, na.rm = na.rm, useNames = FALSE)
541s +   sigma <- colSds(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
541s +   stopifnot(!any(is.infinite(sigma)))
541s +   sigma
541s + }
541s > 
541s > 
541s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
541s > # With and without some NAs
541s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
541s > for (mode in c("integer", "double")) {
541s +   for (add_na in c(FALSE, TRUE)) {
541s +     cat("add_na = ", add_na, "\n", sep = "")
541s + 
541s +     x <- matrix(1:50 + 0.1, nrow = 10L, ncol = 5L)
541s +     if (add_na) {
541s +       x[3:7, c(2, 4)] <- NA_real_
541s +     }
541s +     cat("mode: ", mode, "\n", sep = "")
541s +     storage.mode(x) <- mode
541s +     str(x)
541s +     
541s +     # To check names attribute
541s +     dimnames <- list(letters[1:10], LETTERS[1:5])
541s +     
541s +     # Test with and without dimnames on x
541s +     for (setDimnames in c(TRUE, FALSE)) {
541s +       if (setDimnames) dimnames(x) <- dimnames
541s +       else dimnames(x) <- NULL
541s +       # Row/column ranges
541s +       for (na.rm in c(FALSE, TRUE)) {
541s +         # Check names attribute
541s +         for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
541s +           r0 <- rowSds_R(x, na.rm = na.rm, useNames = useNames)
541s +           r1 <- rowSds(x, na.rm = na.rm, useNames = useNames)
541s +           r1b <- rowSds_center(x, na.rm = na.rm, useNames = useNames)
541s +           r2 <- colSds(t(x), na.rm = na.rm, useNames = useNames)
541s +           r2b <- colSds_center(t(x), na.rm = na.rm, useNames = useNames)
541s +           stopifnot(all.equal(r1, r2))
541s +           stopifnot(all.equal(r1, r0))
541s +           stopifnot(all.equal(r2, r0))
541s +           stopifnot(all.equal(r1b, r2b))
541s +           stopifnot(
541s +             !any(is.infinite(r1)),
541s +             !any(is.infinite(r2)),
541s +             !any(is.infinite(r1b)),
541s +             !any(is.infinite(r2b))
541s +           )
541s +         }
541s +       }
541s +     }
541s +   } # for (add_na ...)
541s + }
541s add_na = FALSE
541s mode: integer
541s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
541s add_na = TRUE
541s mode: integer
541s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
541s add_na = FALSE
541s mode: double
541s  num [1:10, 1:5] 1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1 10.1 ...
541s add_na = TRUE
541s mode: double
541s  num [1:10, 1:5] 1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1 10.1 ...
541s > 
541s > 
541s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
541s > # All NAs
541s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
541s > for (mode in c("integer", "double")) {
541s +   x <- matrix(NA_real_, nrow = 10L, ncol = 5L)
541s +   cat("mode: ", mode, "\n", sep = "")
541s +   storage.mode(x) <- mode
541s +   str(x)
541s +   
541s +   # Test with and without dimnames on x
541s +   for (setDimnames in c(TRUE, FALSE)) {
541s +     if (setDimnames) dimnames(x) <- dimnames
541s +     else dimnames(x) <- NULL
541s +     # Row/column ranges
541s +     for (na.rm in c(FALSE, TRUE)) {
541s +       # Check names attribute
541s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
541s +         r0 <- rowSds_R(x, na.rm = na.rm, useNames = useNames)
541s +         r1 <- rowSds(x, na.rm = na.rm, useNames = useNames)
541s +         r1b <- rowSds_center(x, na.rm = na.rm, useNames = useNames)
541s +         r2 <- colSds(t(x), na.rm = na.rm, useNames = useNames)
541s +         r2b <- colSds_center(t(x), na.rm = na.rm, useNames = useNames)
541s +         stopifnot(all.equal(r1, r2))
541s +         stopifnot(all.equal(r1, r0))
541s +         stopifnot(all.equal(r2, r0))
541s +         stopifnot(all.equal(r1b, r2b))
541s +         stopifnot(
541s +           !any(is.infinite(r1)),
541s +           !any(is.infinite(r2)),
541s +           !any(is.infinite(r1b)),
541s +           !any(is.infinite(r2b))
541s +         )
541s +       }
541s +     }
541s +   }
541s + }
541s mode: integer
541s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
541s mode: double
541s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
541s > 
541s > 
541s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
541s > # A 1x1 matrix
541s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
541s > x <- matrix(0, nrow = 1L, ncol = 1L)
541s > dimnames <- list("a", "A")
541s > for (na.rm in c(FALSE, TRUE)) {
541s +   cat("na.rm = ", na.rm, "\n", sep = "")
541s +   
541s +   # Test with and without dimnames on x
541s +   for (setDimnames in c(TRUE, FALSE)) {
541s +     if (setDimnames) dimnames(x) <- dimnames
541s +     else dimnames(x) <- NULL
541s +     # Row/column ranges
541s +     for (na.rm in c(FALSE, TRUE)) {
541s +       # Check names attribute
541s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
541s +         r0 <- rowSds_R(x, na.rm = na.rm, useNames = useNames)
541s +         r1 <- rowSds(x, na.rm = na.rm, useNames = useNames)
541s +         r1b <- rowSds_center(x, na.rm = na.rm, useNames = useNames)
541s +         r2 <- colSds(t(x), na.rm = na.rm, useNames = useNames)
541s +         r2b <- colSds_center(t(x), na.rm = na.rm, useNames = useNames)
541s +         stopifnot(all.equal(r1, r2))
541s +         stopifnot(all.equal(r1, r0))
541s +         stopifnot(all.equal(r2, r0))
541s +         stopifnot(all.equal(r1b, r2b))
541s +         stopifnot(
541s +           !any(is.infinite(r1)),
541s +           !any(is.infinite(r2)),
541s +           !any(is.infinite(r1b)),
541s +           !any(is.infinite(r2b))
541s +         )
541s +       }
541s +     }
541s +   }
541s + }
541s na.rm = FALSE
541s na.rm = TRUE
541s > 
541s 
541s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
541s Copyright (C) 2024 The R Foundation for Statistical Computing
541s Platform: arm-unknown-linux-gnueabihf (32-bit)
541s 
541s R is free software and comes with ABSOLUTELY NO WARRANTY.
541s You are welcome to redistribute it under certain conditions.
541s Type 'license()' or 'licence()' for distribution details.
541s 
541s R is a collaborative project with many contributors.
541s Type 'contributors()' for more information and
541s 'citation()' on how to cite R or R packages in publications.
541s 
541s Type 'demo()' for some demos, 'help()' for on-line help, or
541s 'help.start()' for an HTML browser interface to help.
541s Type 'q()' to quit R.
541s 
541s > library("matrixStats")
542s > 
542s > ## Always allow testing of the 'center' argument (as long as it's not defunct)
542s > options(matrixStats.center.onUse = "ignore")
542s > 
542s > ## Create isFALSE() if running on an old version of R
542s > if (!exists("isFALSE", mode="function")) {
542s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
542s + }
542s > 
542s > rowSds_R <- function(x, na.rm = FALSE, center = NULL, ..., useNames = NA) {
542s +   suppressWarnings({
542s +     sigma <- apply(x, MARGIN = 1L, FUN = sd, na.rm = na.rm)
542s +   })
542s +   stopifnot(!any(is.infinite(sigma)))
542s +   
542s +   # Keep naming support consistency same as rowSds()
542s +   if (is.null(center) || ncol(x) <= 1L) {
542s +     if (is.na(useNames) || isFALSE(useNames)) names(sigma) <- NULL
542s +   }
542s +   else if (isFALSE(useNames)) names(sigma) <- NULL
542s +   sigma
542s + }
542s > 
542s > colSds_R <- function(x, na.rm = FALSE, center = NULL, ..., useNames = NA) {
542s +   suppressWarnings({
542s +     sigma <- apply(x, MARGIN = 2L, FUN = sd, na.rm = na.rm)
542s +   })
542s +   stopifnot(!any(is.infinite(sigma)))
542s +   
542s +   # Keep naming support consistency same as colSds()
542s +   if (is.null(center) || nrow(x) <= 1L) {
542s +     if (is.na(useNames) || isFALSE(useNames)) names(sigma) <- NULL
542s +   }
542s +   else if (isFALSE(useNames)) names(sigma) <- NULL
542s +   sigma
542s + }
542s > 
542s > 
542s > rowSds_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = NA) {
542s +   center <- rowWeightedMeans(x, cols = cols, na.rm = na.rm, useNames = FALSE)
542s +   sigma <- rowSds(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
542s +   stopifnot(!any(is.infinite(sigma)))
542s +   sigma
542s + }
542s > 
542s > colSds_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = NA) {
542s +   center <- colWeightedMeans(x, rows = rows, na.rm = na.rm, useNames = FALSE)
542s +   sigma <- colSds(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
542s +   stopifnot(!any(is.infinite(sigma)))
542s +   sigma
542s + }
542s > 
542s > 
542s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
542s > # Subsetted tests
542s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
542s > source("utils/validateIndicesFramework.R")
542s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
542s > storage.mode(x) <- "integer"
542s > 
542s > # To check names attribute
542s > dimnames <- list(letters[1:6], LETTERS[1:6])
542s > 
542s > # Test with and without dimnames on x
542s > for (setDimnames in c(TRUE, FALSE)) {
542s +   if (setDimnames) dimnames(x) <- dimnames
542s +   else dimnames(x) <- NULL
542s + 
542s +   count <- 0L
542s +   for (rows in index_cases) {
542s +     for (cols in index_cases) {
542s +       count <- count + 1L
542s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
542s +       useNames <- c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)
542s +       useNames <- useNames[count %% length(useNames) + 1]
542s +       
542s +       validateIndicesTestMatrix(x, rows, cols,
542s +                                 ftest = rowSds, fsure = rowSds_R,
542s +                                 na.rm = na.rm, useNames = useNames)
542s +       validateIndicesTestMatrix(x, rows, cols,
542s +                                 ftest = rowSds_center, fsure = rowSds_R,
542s +                                 na.rm = na.rm, center = TRUE, useNames = useNames)
542s + 
542s +       validateIndicesTestMatrix(x, rows, cols,
542s +                                 fcoltest = colSds, fsure = rowSds_R,
542s +                                 na.rm = na.rm, useNames = useNames)
542s +       validateIndicesTestMatrix(x, rows, cols,
542s +                                 fcoltest = colSds_center, fsure = rowSds_R,
542s +                                 na.rm = na.rm, center = TRUE, useNames = useNames)
542s +     }
542s +   }
542s + }
544s > 
544s 
544s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
544s Copyright (C) 2024 The R Foundation for Statistical Computing
544s Platform: arm-unknown-linux-gnueabihf (32-bit)
544s 
544s R is free software and comes with ABSOLUTELY NO WARRANTY.
544s You are welcome to redistribute it under certain conditions.
544s Type 'license()' or 'licence()' for distribution details.
544s 
544s R is a collaborative project with many contributors.
544s Type 'contributors()' for more information and
544s 'citation()' on how to cite R or R packages in publications.
544s 
544s Type 'demo()' for some demos, 'help()' for on-line help, or
544s 'help.start()' for an HTML browser interface to help.
544s Type 'q()' to quit R.
544s 
545s > library("matrixStats")
545s > 
545s > rowSums2_R <- function(x, na.rm = FALSE, ..., useNames = NA) {
545s +   ## FIXME: sum() may overflow for integers, whereas
545s +   ## base::rowSums() doesn't.  What should rowSums2() do?
545s +   ## apply(x, MARGIN = 1L, FUN = sum, na.rm = na.rm)
545s +   res <- rowSums(x, na.rm = na.rm)
545s +   if (is.na(useNames) || !useNames) names(res) <- NULL
545s +   res
545s + }
545s > 
545s > colSums2_R <- function(x, na.rm = FALSE, ..., useNames = NA) {
545s +   ## FIXME: sum() may overflow for integers, whereas
545s +   ## base::colSums() doesn't.  What should colSums2() do?
545s +   ## apply(x, MARGIN = 2L, FUN = sum, na.rm = na.rm)
545s +   res <- colSums(x, na.rm = na.rm)
545s +   if (is.na(useNames) || !useNames) names(res) <- NULL
545s +   res
545s + }
545s > 
545s > for (mode in c("integer", "logical", "double")) {
545s +   x <- matrix(-4:4, nrow = 3, ncol = 3)
545s +   storage.mode(x) <- mode
545s +   if (mode == "double") x <- x + 0.1
545s +   
545s +   # To check names attribute
545s +   dimnames <- list(letters[1:3], LETTERS[1:3])
545s +   
545s +   # Test with and without dimnames on x
545s +   for (setDimnames in c(TRUE, FALSE)) {
545s +     if (setDimnames) dimnames(x) <- dimnames
545s +     else dimnames(x) <- NULL
545s +     # Check names attribute
545s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
545s +       y0 <- rowSums2_R(x, na.rm = FALSE, useNames = useNames)
545s +       y1 <- rowSums2(x, na.rm = FALSE, useNames = useNames)
545s +       stopifnot(all.equal(y1, y0))
545s +       
545s +       y0 <- colSums2_R(x, na.rm = FALSE, useNames = useNames)
545s +       y1 <- colSums2(x, na.rm = FALSE, useNames = useNames)
545s +       stopifnot(all.equal(y1, y0))
545s +     }
545s +   }
545s + }
545s > 
545s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
545s > # Special case: Single-element matrix
545s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
545s > cat("Special case: Single-element matrix:\n")
545s Special case: Single-element matrix:
545s > for (mode in c("integer", "logical", "double")) {
545s +   x <- matrix(1, nrow = 1, ncol = 1)
545s +   storage.mode(x) <- mode
545s +   
545s +   # To check names attribute
545s +   dimnames <- list("a", "A")
545s +   
545s +   # Test with and without dimnames on x
545s +   for (setDimnames in c(TRUE, FALSE)) {
545s +     if (setDimnames) dimnames(x) <- dimnames
545s +     else dimnames(x) <- NULL
545s +     # Check names attribute
545s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
545s +       y0 <- rowSums2_R(x, na.rm = FALSE, useNames = useNames)
545s +       y1 <- rowSums2(x, na.rm = FALSE, useNames = useNames)
545s +       stopifnot(all.equal(y1, y0))
545s +       
545s +       y0 <- colSums2_R(x, na.rm = FALSE, useNames = useNames)
545s +       y1 <- colSums2(x, na.rm = FALSE, useNames = useNames)
545s +       stopifnot(all.equal(y1, y0))
545s +     }
545s +   }
545s + }
545s > 
545s > 
545s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
545s > # Special case: Empty matrix
545s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
545s > cat("Special case: Empty matrix:\n")
545s Special case: Empty matrix:
545s > for (mode in c("integer", "logical", "double")) {
545s +   x <- matrix(integer(0), nrow = 0, ncol = 0)
545s +   storage.mode(x) <- mode
545s + 
545s +   y0 <- rowSums2_R(x, na.rm = FALSE)
545s +   y1 <- rowSums2(x, na.rm = FALSE)
545s +   stopifnot(all.equal(y1, y0))
545s + 
545s +   y0 <- colSums2_R(x, na.rm = FALSE)
545s +   y1 <- colSums2(x, na.rm = FALSE)
545s +   stopifnot(all.equal(y1, y0))
545s + }
545s > 
545s > 
545s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
545s > # Special case: All NAs
545s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
545s > cat("Special case: All NAs:\n")
545s Special case: All NAs:
545s > for (mode in c("integer", "logical", "double")) {
545s +   x <- matrix(NA_integer_, nrow = 3, ncol = 3)
545s +   storage.mode(x) <- mode
545s +   
545s +   # To check names attribute
545s +   dimnames <- list(letters[1:3], LETTERS[1:3])
545s +   
545s +   # Test with and without dimnames on x
545s +   for (setDimnames in c(TRUE, FALSE)) {
545s +     if (setDimnames) dimnames(x) <- dimnames
545s +     else dimnames(x) <- NULL
545s +     # Check names attribute
545s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
545s +       y0 <- rowSums2_R(x, na.rm = TRUE, useNames = useNames)
545s +       y1 <- rowSums2(x, na.rm = TRUE, useNames = useNames)
545s +       stopifnot(all.equal(y1, y0))
545s +       
545s +       y0 <- colSums2_R(x, na.rm = TRUE, useNames = useNames)
545s +       y1 <- colSums2(x, na.rm = TRUE, useNames = useNames)
545s +       stopifnot(all.equal(y1, y0))
545s +     }
545s +   }
545s + }
545s > 
545s > 
545s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
545s > # Special case: All NaNs
545s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
545s > cat("Special case: All NaNs:\n")
545s Special case: All NaNs:
545s > x <- matrix(NA_real_, nrow = 3, ncol = 3)
545s > 
545s > # Test with and without dimnames on x
545s > for (setDimnames in c(TRUE, FALSE)) {
545s +   if (setDimnames) dimnames(x) <- dimnames
545s +   else dimnames(x) <- NULL
545s +   # Check names attribute
545s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
545s +     y0 <- rowSums2_R(x, na.rm = TRUE, useNames = useNames)
545s +     y1 <- rowSums2(x, na.rm = TRUE, useNames = useNames)
545s +     stopifnot(all.equal(y1, y0))
545s +     
545s +     y0 <- colSums2_R(x, na.rm = TRUE, useNames = useNames)
545s +     y1 <- colSums2(x, na.rm = TRUE, useNames = useNames)
545s +     stopifnot(all.equal(y1, y0))
545s +   }
545s + }
545s > 
545s > 
545s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
545s > # Special case: All Infs
545s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
545s > cat("Special case: All Infs:\n")
545s Special case: All Infs:
545s > x <- matrix(Inf, nrow = 3, ncol = 3)
545s > 
545s > # Test with and without dimnames on x
545s > for (setDimnames in c(TRUE, FALSE)) {
545s +   if (setDimnames) dimnames(x) <- dimnames
545s +   else dimnames(x) <- NULL
545s +   # Check names attribute
545s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
545s +     y0 <- rowSums2_R(x, na.rm = FALSE, useNames = useNames)
545s +     y1 <- rowSums2(x, na.rm = FALSE, useNames = useNames)
545s +     stopifnot(all.equal(y1, y0))
545s +     
545s +     y0 <- colSums2_R(x, na.rm = FALSE, useNames = useNames)
545s +     y1 <- colSums2(x, na.rm = FALSE, useNames = useNames)
545s +     stopifnot(all.equal(y1, y0))
545s +   }
545s + }
545s > 
545s > 
545s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
545s > # Special case: All -Infs
545s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
545s > cat("Special case: All -Infs:\n")
545s Special case: All -Infs:
545s > x <- matrix(-Inf, nrow = 3, ncol = 3)
545s > 
545s > # Test with and without dimnames on x
545s > for (setDimnames in c(TRUE, FALSE)) {
545s +   if (setDimnames) dimnames(x) <- dimnames
545s +   else dimnames(x) <- NULL
545s +   # Check names attribute
545s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
545s +     y0 <- rowSums2_R(x, na.rm = FALSE, useNames = useNames)
545s +     y1 <- rowSums2(x, na.rm = FALSE, useNames = useNames)
545s +     stopifnot(all.equal(y1, y0))
545s +     
545s +     y0 <- colSums2_R(x, na.rm = FALSE, useNames = useNames)
545s +     y1 <- colSums2(x, na.rm = FALSE, useNames = useNames)
545s +     stopifnot(all.equal(y1, y0))
545s +   }
545s + }
545s > 
545s > 
545s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
545s > # Special case: Infs and -Infs
545s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
545s > cat("Special case: Infs and -Infs:\n")
545s Special case: Infs and -Infs:
545s > x <- matrix(c(-Inf, +Inf), nrow = 4, ncol = 4)
545s > 
545s > # To check names attribute
545s > dimnames <- list(letters[1:4], LETTERS[1:4])
545s > 
545s > # Test with and without dimnames on x
545s > for (setDimnames in c(TRUE, FALSE)) {
545s +   if (setDimnames) dimnames(x) <- dimnames
545s +   else dimnames(x) <- NULL
545s +   # Check names attribute
545s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
545s +     y0 <- rowSums2_R(x, na.rm = FALSE, useNames = useNames)
545s +     y1 <- rowSums2(x, na.rm = FALSE, useNames = useNames)
545s +     stopifnot(all.equal(y1, y0))
545s +     
545s +     y0 <- colSums2_R(x, na.rm = FALSE, useNames = useNames)
545s +     y1 <- colSums2(x, na.rm = FALSE, useNames = useNames)
545s +     stopifnot(all.equal(y1, y0))
545s +   }
545s + }
545s > 
545s > 
545s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
545s > # Special case: NaNs and NAs
545s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
545s > cat("Special case: Infs and -Infs:\n")
545s Special case: Infs and -Infs:
545s > x <- matrix(c(NaN, NA_real_), nrow = 4, ncol = 4)
545s > 
545s > y0 <- rowSums(x, na.rm = FALSE)
545s > str(y0)
545s  num [1:4] NaN NA NaN NA
545s > stopifnot(all(is.na(y0)), length(unique(y0)) >= 1L)
545s > y1 <- rowSums2(x, na.rm = FALSE)
545s > str(y0)
545s  num [1:4] NaN NA NaN NA
545s > stopifnot(all(is.na(y1)), length(unique(y1)) >= 1L)
545s > stopifnot(all.equal(y1, y0))
545s > 
545s > y0 <- colSums(x, na.rm = FALSE)
545s > stopifnot(all(is.na(y0)), length(unique(y0)) == 1L)
545s > y1 <- colSums2(x, na.rm = FALSE)
545s > stopifnot(all(is.na(y1)), length(unique(y1)) == 1L)
545s > ## NOTE, due to compiler optimization, it is not guaranteed that NA is
545s > ## returned here (as one would expect). NaN might very well be returned,
545s > ## when both NA and NaN are involved.  This is an accepted feature in R,
545s > ## which is documented in help("is.nan").  See also
545s > ## https://stat.ethz.ch/pipermail/r-devel/2017-April/074009.html.
545s > ## Thus, we cannot guarantee that y1 is identical to y0.
545s > 
545s > 
545s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
545s > # Special case: Integer overflow with ties
545s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
545s > cat("Special case: Integer overflow with ties:\n")
545s Special case: Integer overflow with ties:
545s > x <- matrix(.Machine$integer.max, nrow = 4, ncol = 4)
545s > 
545s > # Test with and without dimnames on x
545s > for (setDimnames in c(TRUE, FALSE)) {
545s +   if (setDimnames) dimnames(x) <- dimnames
545s +   else dimnames(x) <- NULL
545s +   # Check names attribute
545s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
545s +     y0 <- rowSums2_R(x, na.rm = FALSE, useNames = useNames)
545s +     y1 <- rowSums2(x, na.rm = FALSE, useNames = useNames)
545s +     stopifnot(all.equal(y1, y0))
545s +     
545s +     y0 <- colSums2_R(x, na.rm = FALSE, useNames = useNames)
545s +     y1 <- colSums2(x, na.rm = FALSE, useNames = useNames)
545s +     stopifnot(all.equal(y1, y0))
545s +   }
545s + }
545s > 
545s > 
545s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
545s > # Consistency checks
545s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
545s > set.seed(1)
545s > 
545s > cat("Consistency checks:\n")
545s Consistency checks:
545s > n_sims <- if (Sys.getenv("_R_CHECK_USE_VALGRIND_") != "") 4L else 20L
545s > for (kk in seq_len(n_sims)) {
545s +   cat("Random test #", kk, "\n", sep = "")
545s + 
545s +   # Simulate data in a matrix of any shape
545s +   dim <- sample(50:200, size = 2)
545s +   n <- prod(dim)
545s +   x <- rnorm(n, sd = 100)
545s +   dim(x) <- dim
545s + 
545s +   # Add NAs?
545s +   if ((kk %% 4) %in% c(3, 0)) {
545s +     cat("Adding NAs\n")
545s +     nna <- sample(n, size = 1)
545s +     na_values <- c(NA_real_, NaN)
545s +     t <- sample(na_values, size = nna, replace = TRUE)
545s +     x[sample(length(x), size = nna)] <- t
545s +   }
545s + 
545s +   # Mode?
545s +   modes <- "double"
545s +   if ((kk %% 4) %in% c(2, 0)) {
545s +     modes <- c("integer", "logical")
545s +   }
545s + 
545s +   for (mode in modes) {
545s +     if (mode != "double") {
545s +       cat(sprintf("Coercing from %s to %s\n", storage.mode(x), mode))
545s +       storage.mode(x) <- mode
545s +     }
545s + 
545s +     na.rm <- sample(c(TRUE, FALSE), size = 1)
545s +   
545s +     # rowSums2():
545s +     y0 <- rowSums2_R(x, na.rm = na.rm)
545s +     y1 <- rowSums2(x, na.rm = na.rm)
545s +     stopifnot(all.equal(y1, y0))
545s +     y2 <- colSums2(t(x), na.rm = na.rm)
545s +     stopifnot(all.equal(y2, y0))
545s +   
545s +     # colSums2():
545s +     y0 <- colSums2_R(x, na.rm = na.rm)
545s +     y1 <- colSums2(x, na.rm = na.rm)
545s +     stopifnot(all.equal(y1, y0))
545s +     y2 <- rowSums2(t(x), na.rm = na.rm)
545s +     stopifnot(all.equal(y2, y0))
545s +   }
545s + } # for (kk ...)
545s Random test #1
545s Random test #2
545s Coercing from double to integer
545s Coercing from integer to logical
545s Random test #3
545s Adding NAs
545s Random test #4
545s Adding NAs
545s Coercing from double to integer
545s Coercing from integer to logical
545s Random test #5
545s Random test #6
545s Coercing from double to integer
545s Coercing from integer to logical
545s Random test #7
545s Adding NAs
545s Random test #8
545s Adding NAs
545s Coercing from double to integer
545s Coercing from integer to logical
545s Random test #9
545s Random test #10
545s Coercing from double to integer
545s Coercing from integer to logical
545s Random test #11
545s Adding NAs
545s Random test #12
545s Adding NAs
545s Coercing from double to integer
545s Coercing from integer to logical
545s Random test #13
545s Random test #14
545s Coercing from double to integer
545s Coercing from integer to logical
545s Random test #15
545s Adding NAs
545s Random test #16
545s Adding NAs
545s Coercing from double to integer
545s Coercing from integer to logical
545s Random test #17
545s Random test #18
545s Coercing from double to integer
545s Coercing from integer to logical
545s Random test #19
545s Adding NAs
545s Random test #20
545s Adding NAs
545s Coercing from double to integer
545s Coercing from integer to logical
545s > 
546s 
546s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
546s Copyright (C) 2024 The R Foundation for Statistical Computing
546s Platform: arm-unknown-linux-gnueabihf (32-bit)
546s 
546s R is free software and comes with ABSOLUTELY NO WARRANTY.
546s You are welcome to redistribute it under certain conditions.
546s Type 'license()' or 'licence()' for distribution details.
546s 
546s R is a collaborative project with many contributors.
546s Type 'contributors()' for more information and
546s 'citation()' on how to cite R or R packages in publications.
546s 
546s Type 'demo()' for some demos, 'help()' for on-line help, or
546s 'help.start()' for an HTML browser interface to help.
546s Type 'q()' to quit R.
546s 
546s > library("matrixStats")
546s > 
546s > rowSums2_R <- function(x, na.rm = FALSE, ..., useNames = NA) {
546s +   ## FIXME: sum() may overflow for integers, whereas
546s +   ## base::rowSums() doesn't.  What should rowSums2() do?
546s +   ## apply(x, MARGIN = 1L, FUN = sum, na.rm = na.rm)
546s +   res <- rowSums(x, na.rm = na.rm)
546s +   if (is.na(useNames) || !useNames) names(res) <- NULL
546s +   res
546s + }
546s > 
546s > colSums2_R <- function(x, na.rm = FALSE, ..., useNames = NA) {
546s +   ## FIXME: sum() may overflow for integers, whereas
546s +   ## base::colSums() doesn't.  What should colSums2() do?
546s +   ## apply(x, MARGIN = 2L, FUN = sum, na.rm = na.rm)
546s +   res <- colSums(x, na.rm = na.rm)
546s +   if (is.na(useNames) || !useNames) names(res) <- NULL
546s +   res
546s + }
546s > 
546s > 
546s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
546s > # Subsetted tests
546s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
546s > source("utils/validateIndicesFramework.R")
546s > x <- matrix(runif(6 * 6, min = -3, max = 3), nrow = 6, ncol = 6)
546s > storage.mode(x) <- "integer"
546s > 
546s > # To check names attribute
546s > dimnames <- list(letters[1:6], LETTERS[1:6])
546s > 
546s > # Test with and without dimnames on x
546s > for (setDimnames in c(TRUE, FALSE)) {
546s +   if (setDimnames) dimnames(x) <- dimnames
546s +   else dimnames(x) <- NULL
546s +   for (rows in index_cases) {
546s +     for (cols in index_cases) {
546s +       for (na.rm in c(TRUE, FALSE)) {
546s +         for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
546s +           validateIndicesTestMatrix(x, rows, cols,
546s +                                     ftest = rowSums2, fsure = rowSums2_R,
546s +                                     na.rm = na.rm, useNames = useNames)
546s +           validateIndicesTestMatrix(x, rows, cols,
546s +                                     fcoltest = colSums2, fsure = rowSums2_R,
546s +                                     na.rm = na.rm, useNames = useNames)
546s +         }
546s +       }
546s +     }
546s +   }
546s + }
548s > 
548s 
548s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
548s Copyright (C) 2024 The R Foundation for Statistical Computing
548s Platform: arm-unknown-linux-gnueabihf (32-bit)
548s 
548s R is free software and comes with ABSOLUTELY NO WARRANTY.
548s You are welcome to redistribute it under certain conditions.
548s Type 'license()' or 'licence()' for distribution details.
548s 
548s R is a collaborative project with many contributors.
548s Type 'contributors()' for more information and
548s 'citation()' on how to cite R or R packages in publications.
548s 
548s Type 'demo()' for some demos, 'help()' for on-line help, or
548s 'help.start()' for an HTML browser interface to help.
548s Type 'q()' to quit R.
548s 
549s > library("matrixStats")
549s > 
549s > nrow <- 6L
549s > ncol <- 5L
549s > data <- matrix(0:4, nrow = nrow, ncol = ncol)
549s > 
549s > # To check names attribute
549s > dimnames <- list(letters[1:6], LETTERS[1:5])
549s > 
549s > modes <- c("integer", "logical", "raw")
549s > for (mode in modes) {
549s +   cat(sprintf("Mode: %s...\n", mode))
549s + 
549s +   x <- data
549s +   if (mode == "logical") x <- x - 2L
549s +   if (mode != "raw") x[c(2,5,7)] <- NA_integer_
549s +   storage.mode(x) <- mode
549s +   print(x)
549s + 
549s +   unique_values <- unique(as.vector(x))
549s +   nbr_of_unique_values <- length(unique_values)
549s + 
549s +   y <- rowTabulates(x)
549s +   print(y)
549s +   stopifnot(
549s +     identical(dim(y), c(nrow, nbr_of_unique_values)),
549s +     all(y >= 0)
549s +   )
549s +   if (mode != "raw") {
549s +     y0 <- t(table(x, row(x), useNA = "always")[, seq_len(nrow(x))])
549s +     stopifnot(all(y == y0))
549s +   }
549s +   # Check names attribute
549s +   dimnames(x) <- dimnames
549s +   y1 <- rowTabulates(x, useNames = FALSE)
549s +   stopifnot(all.equal(y1, y))
549s +   if (!matrixStats:::isUseNamesNADefunct()) {
549s +     y2 <- rowTabulates(x, useNames = NA)
549s +     stopifnot(all.equal(y2, y))
549s +   }
549s +   y <- rowTabulates(x, useNames = TRUE)
549s +   stopifnot(identical(rownames(y), rownames(x)))
549s +   dimnames(x) <- NULL
549s + 
549s +   y <- colTabulates(x)
549s +   print(y)
549s +   stopifnot(
549s +     identical(dim(y), c(ncol, nbr_of_unique_values)),
549s +     all(y >= 0)
549s +   )
549s +   if (mode != "raw") {
549s +     y0 <- t(table(x, col(x), useNA = "always")[, seq_len(ncol(x))])
549s +     stopifnot(all(y == y0))
549s +   }
549s +   # Check names attribute
549s +   dimnames(x) <- dimnames
549s +   y1 <- colTabulates(x, useNames = FALSE)
549s +   stopifnot(all.equal(y1, y))
549s +   if (!matrixStats:::isUseNamesNADefunct()) {
549s +     y2 <- colTabulates(x, useNames = NA)
549s +     stopifnot(all.equal(y2, y))
549s +   }
549s +   y <- colTabulates(x, useNames = TRUE)
549s +   stopifnot(identical(rownames(y), colnames(x)))
549s +   dimnames(x) <- NULL
549s + 
549s +   # Count only certain values
549s +   if (mode == "integer") {
549s +     subset <- c(0:2, NA_integer_)
549s +   } else if (mode == "logical") {
549s +     subset <- c(TRUE, FALSE, NA)
549s +   } else {
549s +     subset <- c(0:2)
549s +   }
549s +   y <- rowTabulates(x, values = subset)
549s +   print(y)
549s +   stopifnot(identical(dim(y), c(nrow, length(subset))))
549s +   # Check names attribute
549s +   dimnames(x) <- dimnames
549s +   y1 <- rowTabulates(x, values = subset, useNames = FALSE)
549s +   stopifnot(all.equal(y1, y))
549s +   if (!matrixStats:::isUseNamesNADefunct()) {
549s +     y2 <- rowTabulates(x, values = subset, useNames = NA)
549s +     stopifnot(all.equal(y2, y))
549s +   }  
549s +   y <- rowTabulates(x, values = subset, useNames = TRUE)
549s +   stopifnot(identical(rownames(y), rownames(x)))
549s +   dimnames(x) <- NULL
549s + 
549s +   y <- colTabulates(x, values = subset)
549s +   print(y)
549s +   stopifnot(identical(dim(y), c(ncol, length(subset))))
549s +   # Check names attribute
549s +   dimnames(x) <- dimnames
549s +   y1 <- colTabulates(x, values = subset, useNames = FALSE)
549s +   stopifnot(all.equal(y1, y))
549s +   if (!matrixStats:::isUseNamesNADefunct()) {
549s +     y2 <- colTabulates(x, values = subset, useNames = NA)
549s +     stopifnot(all.equal(y2, y))
549s +   }
549s +   y <- colTabulates(x, values = subset, useNames = TRUE)
549s +   stopifnot(identical(rownames(y), colnames(x)))
549s +   dimnames(x) <- NULL
549s + 
549s +   # Raw
549s +   if (mode %in% c("integer", "raw")) {
549s +     subset <- c(0:2)
549s +     
549s +     y <- rowTabulates(x, values = as.raw(subset))
549s +     print(y)
549s +     stopifnot(identical(dim(y), c(nrow, length(subset))))
549s +     # Check names attribute
549s +     dimnames(x) <- dimnames
549s +     y1 <- rowTabulates(x, values = as.raw(subset), useNames = FALSE)
549s +     stopifnot(all.equal(y1, y))
549s +     if (!matrixStats:::isUseNamesNADefunct()) {
549s +       y2 <- rowTabulates(x, values = as.raw(subset), useNames = NA)
549s +       stopifnot(all.equal(y2, y))
549s +     }
549s +     y3 <- rowTabulates(x, values = as.raw(subset), useNames = TRUE)
549s +     stopifnot(identical(rownames(y3), rownames(x)))
549s +     dimnames(x) <- NULL
549s +     
549s +     y2 <- colTabulates(t(x), values = as.raw(subset))
549s +     print(y2)
549s +     stopifnot(
549s +       identical(dim(y2), c(nrow, length(subset))),
549s +       identical(y2, y)
549s +     )
549s +     # Check names attribute
549s +     dimnames(x) <- dimnames
549s +     y1 <- colTabulates(t(x), values = as.raw(subset), useNames = FALSE)
549s +     stopifnot(all.equal(y1, y))
549s +     if (!matrixStats:::isUseNamesNADefunct()) {
549s +       y2 <- colTabulates(t(x), values = as.raw(subset), useNames = NA)
549s +       stopifnot(all.equal(y2, y))
549s +     }
549s +     y <- colTabulates(t(x), values = as.raw(subset), useNames = TRUE)
549s +     stopifnot(identical(rownames(y), colnames(t(x))))
549s +     dimnames(x) <- NULL
549s +   }
549s + 
549s +   cat(sprintf("Mode: %s...done\n", mode))
549s + } # for (mode ...)
549s Mode: integer...
549s      [,1] [,2] [,3] [,4] [,5]
549s [1,]    0   NA    2    3    4
549s [2,]   NA    2    3    4    0
549s [3,]    2    3    4    0    1
549s [4,]    3    4    0    1    2
549s [5,]   NA    0    1    2    3
549s [6,]    0    1    2    3    4
549s      0 1 2 3 4 <NA>
549s [1,] 1 0 1 1 1    1
549s [2,] 1 0 1 1 1    1
549s [3,] 1 1 1 1 1    0
549s [4,] 1 1 1 1 1    0
549s [5,] 1 1 1 1 0    1
549s [6,] 1 1 1 1 1    0
549s      0 1 2 3 4 <NA>
549s [1,] 2 0 1 1 0    2
549s [2,] 1 1 1 1 1    1
549s [3,] 1 1 2 1 1    0
549s [4,] 1 1 1 2 1    0
549s [5,] 1 1 1 1 2    0
549s      0 1 2 <NA>
549s [1,] 1 0 1    1
549s [2,] 1 0 1    1
549s [3,] 1 1 1    0
549s [4,] 1 1 1    0
549s [5,] 1 1 1    1
549s [6,] 1 1 1    0
549s      0 1 2 <NA>
549s [1,] 2 0 1    2
549s [2,] 1 1 1    1
549s [3,] 1 1 2    0
549s [4,] 1 1 1    0
549s [5,] 1 1 1    0
549s      0x0 0x1 0x2
549s [1,]   1   0   1
549s [2,]   1   0   1
549s [3,]   1   1   1
549s [4,]   1   1   1
549s [5,]   1   1   1
549s [6,]   1   1   1
549s      0x0 0x1 0x2
549s [1,]   1   0   1
549s [2,]   1   0   1
549s [3,]   1   1   1
549s [4,]   1   1   1
549s [5,]   1   1   1
549s [6,]   1   1   1
549s Mode: integer...done
549s Mode: logical...
549s       [,1]  [,2]  [,3]  [,4]  [,5]
549s [1,]  TRUE    NA FALSE  TRUE  TRUE
549s [2,]    NA FALSE  TRUE  TRUE  TRUE
549s [3,] FALSE  TRUE  TRUE  TRUE  TRUE
549s [4,]  TRUE  TRUE  TRUE  TRUE FALSE
549s [5,]    NA  TRUE  TRUE FALSE  TRUE
549s [6,]  TRUE  TRUE FALSE  TRUE  TRUE
549s      FALSE TRUE <NA>
549s [1,]     1    3    1
549s [2,]     1    3    1
549s [3,]     1    4    0
549s [4,]     1    4    0
549s [5,]     1    3    1
549s [6,]     1    4    0
549s      FALSE TRUE <NA>
549s [1,]     1    3    2
549s [2,]     1    4    1
549s [3,]     2    4    0
549s [4,]     1    5    0
549s [5,]     1    5    0
549s      TRUE FALSE <NA>
549s [1,]    3     1    1
549s [2,]    3     1    1
549s [3,]    4     1    0
549s [4,]    4     1    0
549s [5,]    3     1    1
549s [6,]    4     1    0
549s      TRUE FALSE <NA>
549s [1,]    3     1    2
549s [2,]    4     1    1
549s [3,]    4     2    0
549s [4,]    5     1    0
549s [5,]    5     1    0
549s Mode: logical...done
549s Mode: raw...
549s      [,1] [,2] [,3] [,4] [,5]
549s [1,]   00   01   02   03   04
549s [2,]   01   02   03   04   00
549s [3,]   02   03   04   00   01
549s [4,]   03   04   00   01   02
549s [5,]   04   00   01   02   03
549s [6,]   00   01   02   03   04
549s      0x0 0x1 0x2 0x3 0x4
549s [1,]   1   1   1   1   1
549s [2,]   1   1   1   1   1
549s [3,]   1   1   1   1   1
549s [4,]   1   1   1   1   1
549s [5,]   1   1   1   1   1
549s [6,]   1   1   1   1   1
549s      0x0 0x1 0x2 0x3 0x4
549s [1,]   2   1   1   1   1
549s [2,]   1   2   1   1   1
549s [3,]   1   1   2   1   1
549s [4,]   1   1   1   2   1
549s [5,]   1   1   1   1   2
549s      0 1 2
549s [1,] 1 1 1
549s [2,] 1 1 1
549s [3,] 1 1 1
549s [4,] 1 1 1
549s [5,] 1 1 1
549s [6,] 1 1 1
549s      0 1 2
549s [1,] 2 1 1
549s [2,] 1 2 1
549s [3,] 1 1 2
549s [4,] 1 1 1
549s [5,] 1 1 1
549s      0x0 0x1 0x2
549s [1,]   1   1   1
549s [2,]   1   1   1
549s [3,]   1   1   1
549s [4,]   1   1   1
549s [5,]   1   1   1
549s [6,]   1   1   1
549s      0x0 0x1 0x2
549s [1,]   1   1   1
549s [2,]   1   1   1
549s [3,]   1   1   1
549s [4,]   1   1   1
549s [5,]   1   1   1
549s [6,]   1   1   1
549s Mode: raw...done
549s > 
549s 
549s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
549s Copyright (C) 2024 The R Foundation for Statistical Computing
549s Platform: arm-unknown-linux-gnueabihf (32-bit)
549s 
549s R is free software and comes with ABSOLUTELY NO WARRANTY.
549s You are welcome to redistribute it under certain conditions.
549s Type 'license()' or 'licence()' for distribution details.
549s 
549s R is a collaborative project with many contributors.
549s Type 'contributors()' for more information and
549s 'citation()' on how to cite R or R packages in publications.
549s 
549s Type 'demo()' for some demos, 'help()' for on-line help, or
549s 'help.start()' for an HTML browser interface to help.
549s Type 'q()' to quit R.
549s 
550s > library("matrixStats")
550s > 
550s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
550s > # Subsetted tests
550s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
550s > source("utils/validateIndicesFramework.R")
550s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
550s > storage.mode(x) <- "integer"
550s > 
550s > # To check names attribute
550s > dimnames <- list(letters[1:6], LETTERS[1:6])
550s > 
550s > # Test with and without dimnames on x
550s > for (setDimnames in c(TRUE, FALSE)) {
550s +   if (setDimnames) dimnames(x) <- dimnames
550s +   else dimnames(x) <- NULL
550s +   
550s +   count <- 0L
550s +   for (rows in index_cases) {
550s +     for (cols in index_cases) {
550s +       count <- count + 1L
550s +       useNames <- c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)
550s +       useNames <- useNames[count %% length(useNames) + 1]
550s +       
550s +       validateIndicesTestMatrix(x, rows, cols,
550s +                                 ftest = rowTabulates, fsure = rowTabulates, useNames = useNames)
550s +       validateIndicesTestMatrix(x, rows, cols,
550s +                                 ftest = rowTabulates, fsure = rowTabulates,
550s +                                 values = 1:3, useNames = useNames)
550s +   
550s +       validateIndicesTestMatrix(x, rows, cols,
550s +                                 ftest = colTabulates, fsure = colTabulates, useNames = useNames)
550s +       validateIndicesTestMatrix(x, rows, cols,
550s +                                 ftest = colTabulates, fsure = colTabulates,
550s +                                 values = 1:3, useNames = useNames)
550s +     }
550s +   }
550s + }
554s > 
554s 
554s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
554s Copyright (C) 2024 The R Foundation for Statistical Computing
554s Platform: arm-unknown-linux-gnueabihf (32-bit)
554s 
554s R is free software and comes with ABSOLUTELY NO WARRANTY.
554s You are welcome to redistribute it under certain conditions.
554s Type 'license()' or 'licence()' for distribution details.
554s 
554s R is a collaborative project with many contributors.
554s Type 'contributors()' for more information and
554s 'citation()' on how to cite R or R packages in publications.
554s 
554s Type 'demo()' for some demos, 'help()' for on-line help, or
554s 'help.start()' for an HTML browser interface to help.
554s Type 'q()' to quit R.
554s 
554s > library("matrixStats")
554s > 
554s > fcns <- list(
554s +   rowVarDiffs = list(rowVarDiffs, colVarDiffs),
554s +   rowSdDiffs  = list(rowSdDiffs, colSdDiffs),
554s +   rowMadDiffs = list(rowMadDiffs, colMadDiffs),
554s +   rowIQRDiffs = list(rowIQRDiffs, colIQRDiffs)
554s + )
554s > 
554s > for (fcn in names(fcns)) {
554s +   cat(sprintf("%s()...\n", fcn))
554s +   row_fcn <- fcns[[fcn]][[1L]]
554s +   col_fcn <- fcns[[fcn]][[2L]]
554s + 
554s +   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
554s +   # With and without some NAs
554s +   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
554s +   for (mode in c("integer", "double")) {
554s +     for (add_na in c(FALSE, TRUE)) {
554s +       cat("add_na = ", add_na, "\n", sep = "")
554s + 
554s +       x <- matrix(1:50 + 0.1, nrow = 10L, ncol = 5L)
554s +       if (add_na) {
554s +         x[3:7, c(2, 4)] <- NA_real_
554s +       }
554s +       cat("mode: ", mode, "\n", sep = "")
554s +       storage.mode(x) <- mode
554s +       str(x)
554s +       
554s +       # To check names attribute
554s +       dimnames <- list(letters[1:10], LETTERS[1:5])
554s + 
554s +       # Test with and without dimnames on x
554s +       for (setDimnames in c(TRUE, FALSE)) {
554s +         if (setDimnames) dimnames(x) <- dimnames
554s +         else dimnames(x) <- NULL
554s +         # Row/column ranges
554s +         for (na.rm in c(FALSE, TRUE)) {
554s +           # Check names attribute
554s +           for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
554s +             cat("na.rm = ", na.rm, "\n", sep = "")
554s +             r1 <- row_fcn(x, na.rm = na.rm, useNames = useNames)
554s +             r2 <- col_fcn(t(x), na.rm = na.rm, useNames = useNames)
554s +             stopifnot(all.equal(r1, r2))
554s +           }
554s +         }
554s +       }
554s +     } # for (add_na ...)
554s +   }
554s + 
554s + 
554s +   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
554s +   # All NAs
554s +   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
554s +   for (mode in c("integer", "double")) {
554s +     x <- matrix(NA_real_, nrow = 10L, ncol = 5L)
554s +     cat("mode: ", mode, "\n", sep = "")
554s +     storage.mode(x) <- mode
554s +     str(x)
554s + 
554s +     # Test with and without dimnames on x
554s +     for (setDimnames in c(TRUE, FALSE)) {
554s +       if (setDimnames) dimnames(x) <- dimnames
554s +       else dimnames(x) <- NULL
554s +       # Row/column ranges
554s +       for (na.rm in c(FALSE, TRUE)) {
554s +         # Check names attribute
554s +         for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
554s +           cat("na.rm = ", na.rm, "\n", sep = "")
554s +           r1 <- row_fcn(x, na.rm = na.rm, useNames = useNames)
554s +           r2 <- col_fcn(t(x), na.rm = na.rm, useNames = useNames)
554s +           stopifnot(all.equal(r1, r2))
554s +         }
554s +       }
554s +     }
554s +   }
554s + 
554s + 
554s +   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
554s +   # A 1x1 matrix
554s +   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
554s +   x <- matrix(0, nrow = 1L, ncol = 1L)
554s +   dimnames <- list("a", "A")
554s +   # Test with and without dimnames on x
554s +   for (setDimnames in c(TRUE, FALSE)) {
554s +     if (setDimnames) dimnames(x) <- dimnames
554s +     else dimnames(x) <- NULL
554s +     # Row/column ranges
554s +     for (na.rm in c(FALSE, TRUE)) {
554s +       # Check names attribute
554s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
554s +         cat("na.rm = ", na.rm, "\n", sep = "")
554s +         r1 <- row_fcn(x, na.rm = na.rm, useNames = useNames)
554s +         r2 <- col_fcn(t(x), na.rm = na.rm, useNames = useNames)
554s +         stopifnot(all.equal(r1, r2))
554s +       }
554s +     }
554s +   }
554s + 
554s +   cat(sprintf("%s()...DONE\n", fcn))
554s + } # for (fcn ...)
555s rowVarDiffs()...
555s add_na = FALSE
555s mode: integer
555s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s add_na = TRUE
555s mode: integer
555s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s add_na = FALSE
555s mode: double
555s  num [1:10, 1:5] 1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1 10.1 ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s add_na = TRUE
555s mode: double
555s  num [1:10, 1:5] 1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1 10.1 ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s mode: integer
555s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s mode: double
555s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s rowVarDiffs()...DONE
555s rowSdDiffs()...
555s add_na = FALSE
555s mode: integer
555s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s add_na = TRUE
555s mode: integer
555s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s add_na = FALSE
555s mode: double
555s  num [1:10, 1:5] 1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1 10.1 ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s add_na = TRUE
555s mode: double
555s  num [1:10, 1:5] 1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1 10.1 ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s mode: integer
555s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s mode: double
555s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s rowSdDiffs()...DONE
555s rowMadDiffs()...
555s add_na = FALSE
555s mode: integer
555s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s add_na = TRUE
555s mode: integer
555s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s add_na = FALSE
555s mode: double
555s  num [1:10, 1:5] 1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1 10.1 ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s add_na = TRUE
555s mode: double
555s  num [1:10, 1:5] 1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1 10.1 ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s mode: integer
555s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s mode: double
555s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s rowMadDiffs()...DONE
555s rowIQRDiffs()...
555s add_na = FALSE
555s mode: integer
555s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s add_na = TRUE
555s mode: integer
555s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s add_na = FALSE
555s mode: double
555s  num [1:10, 1:5] 1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1 10.1 ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s add_na = TRUE
555s mode: double
555s  num [1:10, 1:5] 1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1 10.1 ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s mode: integer
555s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s mode: double
555s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s na.rm = FALSE
555s na.rm = FALSE
555s na.rm = TRUE
555s na.rm = TRUE
555s rowIQRDiffs()...DONE
555s > 
555s 
555s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
555s Copyright (C) 2024 The R Foundation for Statistical Computing
555s Platform: arm-unknown-linux-gnueabihf (32-bit)
555s 
555s R is free software and comes with ABSOLUTELY NO WARRANTY.
555s You are welcome to redistribute it under certain conditions.
555s Type 'license()' or 'licence()' for distribution details.
555s 
555s R is a collaborative project with many contributors.
555s Type 'contributors()' for more information and
555s 'citation()' on how to cite R or R packages in publications.
555s 
555s Type 'demo()' for some demos, 'help()' for on-line help, or
555s 'help.start()' for an HTML browser interface to help.
555s Type 'q()' to quit R.
555s 
556s > library("matrixStats")
556s > 
556s > fcns <- list(
556s +   madDiff = c(rowMadDiffs, colMadDiffs),
556s +   iqrDiff = c(rowIQRDiffs, colIQRDiffs)
556s + )
556s > 
556s > 
556s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
556s > # Subsetted tests
556s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
556s > source("utils/validateIndicesFramework.R")
556s > # To check names attribute
556s > dimnames <- list(letters[1:6], LETTERS[1:6])
556s > trim <- runif(1, min = 0, max = 0.5)
556s > for (fcn in names(fcns)) {
556s +   cat(sprintf("subsetted tests on %s()...\n", fcn))
556s +   row_fcn <- fcns[[fcn]][[1L]]
556s +   col_fcn <- fcns[[fcn]][[2L]]
556s + 
556s +   for (mode in c("numeric", "integer")) {
556s +     x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6L, ncol = 6L)
556s +     storage.mode(x) <- mode
556s +     if (mode == "numeric") x[1:2, 3:4] <- Inf
556s + 
556s +     # Test with and without dimnames on x
556s +     for (setDimnames in c(TRUE, FALSE)) {
556s +       if (setDimnames) dimnames(x) <- dimnames
556s +       else dimnames(x) <- NULL
556s +       
556s +       count <- 0L
556s +       for (diff in 1:2) {
556s +         for (rows in index_cases) {
556s +           for (cols in index_cases) {
556s +             count <- count + 1L
556s +             na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
556s +             useNames <- c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)
556s +             useNames <- useNames[count %% length(useNames) + 1]
556s +             validateIndicesTestMatrix(x, rows, cols,
556s +                                       ftest = row_fcn, fsure = row_fcn,
556s +                                       na.rm = na.rm, diff = diff, trim = trim, useNames = useNames)
556s +             validateIndicesTestMatrix(x, rows, cols,
556s +                                       fcoltest = col_fcn, fsure = row_fcn,
556s +                                       na.rm = na.rm, diff = diff, trim = trim, useNames = useNames)
556s +           }
556s +         }
556s +       }
556s +     }
556s +   }
556s +   cat(sprintf("%s()...DONE\n", fcn))
556s + }
556s subsetted tests on madDiff()...
564s madDiff()...DONE
564s subsetted tests on iqrDiff()...
572s iqrDiff()...DONE
572s > 
572s 
572s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
572s Copyright (C) 2024 The R Foundation for Statistical Computing
572s Platform: arm-unknown-linux-gnueabihf (32-bit)
572s 
572s R is free software and comes with ABSOLUTELY NO WARRANTY.
572s You are welcome to redistribute it under certain conditions.
572s Type 'license()' or 'licence()' for distribution details.
572s 
572s R is a collaborative project with many contributors.
572s Type 'contributors()' for more information and
572s 'citation()' on how to cite R or R packages in publications.
572s 
572s Type 'demo()' for some demos, 'help()' for on-line help, or
572s 'help.start()' for an HTML browser interface to help.
572s Type 'q()' to quit R.
572s 
573s > library("matrixStats")
573s > 
573s > fcns <- list(
573s +   varDiff  = c(rowVarDiffs, colVarDiffs),
573s +   sdDiff   = c(rowSdDiffs, colSdDiffs)
573s + )
573s > 
573s > 
573s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
573s > # Subsetted tests
573s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
573s > source("utils/validateIndicesFramework.R")
573s > # To check names attribute
573s > dimnames <- list(letters[1:6], LETTERS[1:6])
573s > trim <- runif(1, min = 0, max = 0.5)
573s > for (fcn in names(fcns)) {
573s +   cat(sprintf("subsetted tests on %s()...\n", fcn))
573s +   row_fcn <- fcns[[fcn]][[1L]]
573s +   col_fcn <- fcns[[fcn]][[2L]]
573s + 
573s +   for (mode in c("numeric", "integer")) {
573s +     x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6L, ncol = 6L)
573s +     storage.mode(x) <- mode
573s +     if (mode == "numeric") x[1:2, 3:4] <- Inf
573s +   
573s +     # Test with and without dimnames on x
573s +     for (setDimnames in c(TRUE, FALSE)) {
573s +       if (setDimnames) dimnames(x) <- dimnames
573s +       else dimnames(x) <- NULL
573s + 
573s +       count <- 0L
573s +       for (diff in 1:2) {
573s +         for (rows in index_cases) {
573s +           for (cols in index_cases) {
573s +             count <- count + 1L
573s +             na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
573s +             useNames <- c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)
573s +             useNames <- useNames[count %% length(useNames) + 1]
573s +             
573s +             validateIndicesTestMatrix(x, rows, cols,
573s +                                       ftest = row_fcn, fsure = row_fcn,
573s +                                       na.rm = na.rm, diff = diff, trim = trim, useNames = useNames)
573s +             validateIndicesTestMatrix(x, rows, cols,
573s +                                       fcoltest = col_fcn, fsure = row_fcn,
573s +                                       na.rm = na.rm, diff = diff, trim = trim, useNames = useNames)
573s +           }
573s +         }
573s +       }
573s +     }
573s +   }
573s +   cat(sprintf("%s()...DONE\n", fcn))
573s + }
573s subsetted tests on varDiff()...
579s varDiff()...DONE
579s subsetted tests on sdDiff()...
585s sdDiff()...DONE
585s > 
585s 
585s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
585s Copyright (C) 2024 The R Foundation for Statistical Computing
585s Platform: arm-unknown-linux-gnueabihf (32-bit)
585s 
585s R is free software and comes with ABSOLUTELY NO WARRANTY.
585s You are welcome to redistribute it under certain conditions.
585s Type 'license()' or 'licence()' for distribution details.
585s 
585s R is a collaborative project with many contributors.
585s Type 'contributors()' for more information and
585s 'citation()' on how to cite R or R packages in publications.
585s 
585s Type 'demo()' for some demos, 'help()' for on-line help, or
585s 'help.start()' for an HTML browser interface to help.
585s Type 'q()' to quit R.
585s 
585s > library("matrixStats")
585s > 
585s > ## Always allow testing of the 'center' argument (as long as it's not defunct)
585s > options(matrixStats.center.onUse = "ignore")
585s > options(matrixStats.vars.formula.freq = Inf)
585s > 
585s > ## Create isFALSE() if running on an old version of R
585s > if (!exists("isFALSE", mode="function")) {
585s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
585s + }
585s > 
585s > rowVars_R <- function(x, na.rm = FALSE, center = NULL, ..., useNames = NA) {
585s +   suppressWarnings({
585s +     res <- apply(x, MARGIN = 1L, FUN = var, na.rm = na.rm)
585s +   })
585s +   stopifnot(!any(is.infinite(res)))
585s +   
585s +   # Keep naming support consistency same as rowVars()
585s +   if (is.null(center) || ncol(x) <= 1L) {
585s +     if (is.na(useNames) || isFALSE(useNames)) names(res) <- NULL
585s +   }
585s +   else if (isFALSE(useNames)) names(res) <- NULL
585s +   res
585s + }
585s > 
585s > colVars_R <- function(x, na.rm = FALSE, center = NULL, ..., useNames = NA) {
585s +   suppressWarnings({
585s +     res <- apply(x, MARGIN = 2L, FUN = var, na.rm = na.rm)
585s +   })
585s +   stopifnot(!any(is.infinite(res)))
585s +   
585s +   # Keep naming support consistency same as colVars()
585s +   if (is.null(center) || ncol(x) <= 1L) {
585s +     if (is.na(useNames) || isFALSE(useNames)) names(res) <- NULL
585s +   }
585s +   else if (isFALSE(useNames)) names(res) <- NULL
585s +   res
585s + }
585s > 
585s > 
585s > rowVars_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = NA) {
585s +   center <- rowWeightedMeans(x, cols = cols, na.rm = na.rm, useNames = FALSE)
585s +   res <- rowVars(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
585s +   stopifnot(!any(is.infinite(res)))
585s +   res
585s + }
585s > 
585s > colVars_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = NA) {
585s +   center <- colWeightedMeans(x, rows = rows, na.rm = na.rm, useNames = FALSE)
585s +   res <- colVars(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
585s +   stopifnot(!any(is.infinite(res)))
585s +   res
585s + }
585s > 
585s > rowVars_center_naive <- function(x, rows = NULL, cols = NULL, center = NULL, na.rm = FALSE, ..., useNames = NA) {
585s +   x <- sweep(x, MARGIN = 1, STATS = as.array(center), FUN = "-")
585s +   x[is.infinite(center), ] <- NaN
585s +   res <- rowVars(x, rows = rows, cols = cols, center = rep(0, times = nrow(x)), na.rm = na.rm, useNames = useNames)
585s +   stopifnot(!any(is.infinite(res)))
585s +   res
585s + }
585s > 
585s > colVars_center_naive <- function(x, rows = NULL, cols = NULL, center = NULL, na.rm = FALSE, ..., useNames = NA) {
585s +   x <- sweep(x, MARGIN = 2, STATS = as.array(center), FUN = "-")
585s +   x[, is.infinite(center)] <- NaN
585s +   res <- colVars(x, rows = rows, cols = cols, center = rep(0, times = ncol(x)), na.rm = na.rm, useNames = useNames)
585s +   stopifnot(!any(is.infinite(res)))
585s +   res
585s + }
585s > 
585s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
585s > # With and without some NAs or Infs
585s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
585s > for (mode in c("integer", "double")) {
585s +   if (mode == "integer") {
585s +     specials <- c(0L, NA_integer_)
585s +     delta <- 0L
585s +   } else {
585s +     specials <- c(0, NA_real_, Inf)
585s +     delta <- 0.1
585s +   }
585s +   
585s +   for (special in specials) {
585s +     cat("special = ", special, "\n", sep = "")
585s +     x <- matrix(1:50 + delta, nrow = 10L, ncol = 5L)
585s +     x[3:7, c(2, 4)] <- special
585s +     cat("mode: ", mode, "\n", sep = "")
585s +     str(x)
585s +     stopifnot(storage.mode(x) == mode)
585s +     
585s +     # To check names attribute
585s +     dimnames <- list(letters[1:10], LETTERS[1:5])
585s +     
585s +     # Test with and without dimnames on x
585s +     for (setDimnames in c(TRUE, FALSE)) {
585s +       if (setDimnames) dimnames(x) <- dimnames
585s +       else dimnames(x) <- NULL
585s +       # Row/column variance
585s +       for (na.rm in c(FALSE, TRUE)) {
585s +         # Check names attribute
585s +         for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
585s +           cat("na.rm = ", na.rm, "\n", sep = "")
585s +           center <- rowMeans(x, na.rm = na.rm)
585s +           
585s +           r0 <- rowVars_R(x, na.rm = na.rm, useNames = useNames)
586s +           r1 <- rowVars(x, na.rm = na.rm, useNames = useNames)
586s +           r1b <- rowVars_center(x, na.rm = na.rm, useNames = useNames)
586s +           r1c <- rowVars(x, center = center, na.rm = na.rm, useNames = useNames)
586s +           
586s +           tx <- t(x)
586s +           r2 <- colVars(tx, na.rm = na.rm, useNames = useNames)
586s +           r2b <- colVars_center(tx, na.rm = na.rm, useNames = useNames)
586s +           r2c <- colVars(tx, center = center, na.rm = na.rm, useNames = useNames)
586s +           tx <- NULL
586s +           
586s +           stopifnot(all.equal(r1, r2))
586s +           stopifnot(all.equal(r1, r0))
586s +           stopifnot(all.equal(r1b, r1c))
586s +           stopifnot(all.equal(r2, r0))
586s +           stopifnot(all.equal(r2b, r2c))
586s +           
586s +           center <- colMeans(x, na.rm = na.rm)
586s + 
586s +           r3 <- colVars(x, center = center, na.rm = na.rm, useNames = useNames)
586s +           r3b <- colVars_center_naive(x, center = center, na.rm = na.rm, useNames = useNames)
586s +           r3c <- rowVars(t(x), center = center, na.rm = na.rm, useNames = useNames)
586s +           r3d <- rowVars_center_naive(t(x), center = center, na.rm = na.rm, useNames = useNames)
586s +           stopifnot(all.equal(r3b, r3))
586s +           stopifnot(all.equal(r3c, r3))
586s +           stopifnot(all.equal(r3d, r3))
586s +           
586s +           stopifnot(
586s +             !any(is.infinite(r0)),
586s +             !any(is.infinite(r1)),
586s +             !any(is.infinite(r2)),
586s +             !any(is.infinite(r3)),
586s +             !any(is.infinite(r1b)),
586s +             !any(is.infinite(r1c)),
586s +             !any(is.infinite(r2b)),
586s +             !any(is.infinite(r2c)),
586s +             !any(is.infinite(r3b)),
586s +             !any(is.infinite(r3c)),
586s +             !any(is.infinite(r3d))
586s +           )
586s +         }
586s +       }
586s +     }
586s +   } # for (special ...)
586s + }
586s special = 0
586s mode: integer
586s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
586s na.rm = FALSE
586s na.rm = FALSE
586s na.rm = TRUE
586s na.rm = TRUE
586s na.rm = FALSE
586s na.rm = FALSE
586s na.rm = TRUE
586s na.rm = TRUE
586s special = NA
586s mode: integer
586s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
586s na.rm = FALSE
586s na.rm = FALSE
586s na.rm = TRUE
586s na.rm = TRUE
586s na.rm = FALSE
586s na.rm = FALSE
586s na.rm = TRUE
586s na.rm = TRUE
586s special = 0
586s mode: double
586s  num [1:10, 1:5] 1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1 10.1 ...
586s na.rm = FALSE
586s na.rm = FALSE
586s na.rm = TRUE
586s na.rm = TRUE
586s na.rm = FALSE
586s na.rm = FALSE
586s na.rm = TRUE
586s na.rm = TRUE
586s special = NA
586s mode: double
586s  num [1:10, 1:5] 1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1 10.1 ...
586s na.rm = FALSE
586s na.rm = FALSE
586s na.rm = TRUE
586s na.rm = TRUE
586s na.rm = FALSE
586s na.rm = FALSE
586s na.rm = TRUE
586s na.rm = TRUE
586s special = Inf
586s mode: double
586s  num [1:10, 1:5] 1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1 10.1 ...
586s na.rm = FALSE
586s na.rm = FALSE
586s na.rm = TRUE
586s na.rm = TRUE
586s na.rm = FALSE
586s na.rm = FALSE
586s na.rm = TRUE
586s na.rm = TRUE
586s > 
586s > 
586s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
586s > # All NAs
586s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
586s > for (mode in c("integer", "double")) {
586s +   x <- matrix(NA_real_, nrow = 10L, ncol = 5L)
586s +   cat("mode: ", mode, "\n", sep = "")
586s +   storage.mode(x) <- mode
586s +   str(x)
586s +   
586s +   # Test with and without dimnames on x
586s +   for (setDimnames in c(TRUE, FALSE)) {
586s +     if (setDimnames) dimnames(x) <- dimnames
586s +     else dimnames(x) <- NULL
586s +     # Row/column variance
586s +     for (na.rm in c(FALSE, TRUE)) {
586s +       # Check names attribute
586s +       for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
586s +         cat("na.rm = ", na.rm, "\n", sep = "")
586s +         
586s +         r0 <- rowVars_R(x, na.rm = na.rm, useNames = useNames)
586s +         r1 <- rowVars(x, na.rm = na.rm, useNames = useNames)
586s +         r1b <- rowVars_center(x, na.rm = na.rm, useNames = useNames)
586s +         r2 <- colVars(t(x), na.rm = na.rm, useNames = useNames)
586s +         r2b <- colVars_center(t(x), na.rm = na.rm, useNames = useNames)
586s +         stopifnot(all.equal(r1, r2))
586s +         stopifnot(all.equal(r1, r0))
586s +         stopifnot(all.equal(r2, r0))
586s +         stopifnot(all.equal(r1b, r2b))
586s +         stopifnot(
586s +           !any(is.infinite(r0)),
586s +           !any(is.infinite(r1)),
586s +           !any(is.infinite(r2)),
586s +           !any(is.infinite(r1b)),
586s +           !any(is.infinite(r2b))
586s +         )
586s +       }
586s +     }
586s +   }
586s + }
586s mode: integer
586s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
586s na.rm = FALSE
586s na.rm = FALSE
586s na.rm = TRUE
586s na.rm = TRUE
586s na.rm = FALSE
586s na.rm = FALSE
586s na.rm = TRUE
586s na.rm = TRUE
586s mode: double
586s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
586s na.rm = FALSE
586s na.rm = FALSE
586s na.rm = TRUE
586s na.rm = TRUE
586s na.rm = FALSE
586s na.rm = FALSE
586s na.rm = TRUE
586s na.rm = TRUE
586s > 
586s > 
586s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
586s > # A 1x1 matrix
586s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
586s > x <- matrix(0, nrow = 1L, ncol = 1L)
586s > dimnames <- list("a", "A")
586s > # Test with and without dimnames on x
586s > for (setDimnames in c(TRUE, FALSE)) {
586s +   if (setDimnames) dimnames(x) <- dimnames
586s +   else dimnames(x) <- NULL
586s +   # Row/column variance
586s +   for (na.rm in c(FALSE, TRUE)) {
586s +     # Check names attribute
586s +     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
586s +       cat("na.rm = ", na.rm, "\n", sep = "")
586s +       
586s +       r0 <- rowVars_R(x, na.rm = na.rm, useNames = useNames)
586s +       r1 <- rowVars(x, na.rm = na.rm, useNames = useNames)
586s +       r1b <- rowVars_center(x, na.rm = na.rm, useNames = useNames)
586s +       r2 <- colVars(t(x), na.rm = na.rm, useNames = useNames)
586s +       r2b <- colVars_center(t(x), na.rm = na.rm, useNames = useNames)
586s +       stopifnot(all.equal(r1, r2))
586s +       stopifnot(all.equal(r1, r0))
586s +       stopifnot(all.equal(r2, r0))
586s +       stopifnot(all.equal(r1b, r2b))
586s +       stopifnot(
586s +         !any(is.infinite(r0)),
586s +         !any(is.infinite(r1)),
586s +         !any(is.infinite(r2)),
586s +         !any(is.infinite(r1b)),
586s +         !any(is.infinite(r2b))
586s +       )
586s +     }
586s +   }
586s + }
586s na.rm = FALSE
586s na.rm = FALSE
586s na.rm = TRUE
586s na.rm = TRUE
586s na.rm = FALSE
586s na.rm = FALSE
586s na.rm = TRUE
586s na.rm = TRUE
586s > 
586s > 
586s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
586s > # center and .dim
586s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
586s > m <- matrix(1:12, nrow = 3L, ncol = 4L)
586s > a <- array(m, dim = c(3, 2, 2))
586s > stopifnot(prod(dim(a)) == prod(dim(m)))
586s > 
586s > y0 <- rowVars(m, dim. = dim(m))
586s > print(y0)
586s [1] 15 15 15
586s > y1 <- rowVars(a, dim. = dim(m))
586s > print(y1)
586s [1] 15 15 15
586s > stopifnot(identical(y1, y0))
586s > stopifnot(
586s +   !any(is.infinite(y0)),
586s +   !any(is.infinite(y1))
586s + )
586s > 
586s > mu <- rowMeans(m)
586s > y0 <- rowVars(m, center = mu, dim. = dim(m))
586s > print(y0)
586s [1] 15 15 15
586s > y1 <- rowVars(a, center = mu, dim. = dim(m))
586s > print(y1)
586s [1] 15 15 15
586s > stopifnot(identical(y1, y0))
586s > stopifnot(
586s +   !any(is.infinite(y0)),
586s +   !any(is.infinite(y1))
586s + )
586s > 
586s > 
586s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
586s > # Corner cases
586s > # https://github.com/HenrikBengtsson/matrixStats/issues/195
586s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
586s > x <- matrix(c(1,2,3,4), nrow = 2L, ncol = 2L)
586s > x[1,1] <- NA_real_
586s > x[1,2] <- Inf
586s > 
586s > center <- colMeans2(x, na.rm = TRUE)
586s > y <- colVars(x, center = center, na.rm = TRUE)
586s > stopifnot(!any(is.infinite(y)))
586s > 
586s > x <- t(x)
586s > center <- rowMeans2(x, na.rm = TRUE)
586s > y <- rowVars(x, center = center, na.rm = TRUE)
586s > stopifnot(!any(is.infinite(y)))
586s > 
586s 
586s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
586s Copyright (C) 2024 The R Foundation for Statistical Computing
586s Platform: arm-unknown-linux-gnueabihf (32-bit)
586s 
586s R is free software and comes with ABSOLUTELY NO WARRANTY.
586s You are welcome to redistribute it under certain conditions.
586s Type 'license()' or 'licence()' for distribution details.
586s 
586s R is a collaborative project with many contributors.
586s Type 'contributors()' for more information and
586s 'citation()' on how to cite R or R packages in publications.
586s 
586s Type 'demo()' for some demos, 'help()' for on-line help, or
586s 'help.start()' for an HTML browser interface to help.
586s Type 'q()' to quit R.
586s 
587s > library("matrixStats")
587s > 
587s > ## Always allow testing of the 'center' argument (as long as it's not defunct)
587s > options(matrixStats.center.onUse = "ignore")
587s > 
587s > ## Create isFALSE() if running on an old version of R
587s > if (!exists("isFALSE", mode="function")) {
587s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
587s + }
587s > 
587s > rowVars_R <- function(x, na.rm = FALSE, center = NULL, ..., useNames = NA) {
587s +   suppressWarnings({
587s +     res <- apply(x, MARGIN = 1L, FUN = var, na.rm = na.rm)
587s +   })
587s +   stopifnot(!any(is.infinite(res)))
587s +   
587s +   # Keep naming support consistency same as rowVars()
587s +   if (is.null(center) || ncol(x) <= 1L) {
587s +     if (is.na(useNames) || isFALSE(useNames)) names(res) <- NULL
587s +   }
587s +   else if (isFALSE(useNames)) names(res) <- NULL
587s +   res
587s + }
587s > 
587s > colVars_R <- function(x, na.rm = FALSE, center = NULL, ..., useNames = NA) {
587s +   suppressWarnings({
587s +     res <- apply(x, MARGIN = 2L, FUN = var, na.rm = na.rm)
587s +   })
587s +   stopifnot(!any(is.infinite(res)))
587s +   
587s +   # Keep naming support consistency same as colVars()
587s +   if (is.null(center) || nrow(x) <= 1L) {
587s +     if (is.na(useNames) || isFALSE(useNames)) names(res) <- NULL
587s +   }
587s +   else if (isFALSE(useNames)) names(res) <- NULL
587s +   res
587s + }
587s > 
587s > 
587s > rowVars_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = NA) {
587s +   center <- rowWeightedMeans(x, cols = cols, na.rm = na.rm, useNames = FALSE)
587s +   res <- rowVars(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
587s +   stopifnot(!any(is.infinite(res)))
587s +   res
587s + }
587s > 
587s > colVars_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = NA) {
587s +   center <- colWeightedMeans(x, rows = rows, na.rm = na.rm, useNames = FALSE)
587s +   res <- colVars(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
587s +   stopifnot(!any(is.infinite(res)))
587s +   res
587s + }
587s > 
587s > 
587s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
587s > # Subsetted tests
587s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
587s > source("utils/validateIndicesFramework.R")
587s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
587s > storage.mode(x) <- "integer"
587s > 
587s > # To check names attribute
587s > dimnames <- list(letters[1:6], LETTERS[1:6])
587s > 
587s > # Test with and without dimnames on x
587s > for (setDimnames in c(TRUE, FALSE)) {
587s +   if (setDimnames) dimnames(x) <- dimnames
587s +   else dimnames(x) <- NULL
587s + 
587s +   count <- 0L
587s +   for (rows in index_cases) {
587s +     for (cols in index_cases) {
587s +       count <- count + 1L
587s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
587s +       useNames <- c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)
587s +       useNames <- useNames[count %% length(useNames) + 1]
587s +       
587s +       validateIndicesTestMatrix(x, rows, cols,
587s +                                 ftest = rowVars, fsure = rowVars_R,
587s +                                 na.rm = na.rm, useNames = useNames)
587s +       validateIndicesTestMatrix(x, rows, cols,
587s +                                 ftest = rowVars_center, fsure = rowVars_R,
587s +                                 na.rm = na.rm, center = TRUE, useNames = useNames)
587s + 
587s +       validateIndicesTestMatrix(x, rows, cols,
587s +                                 fcoltest = colVars, fsure = rowVars_R,
587s +                                 na.rm = na.rm, useNames = useNames)
587s +       validateIndicesTestMatrix(x, rows, cols,
587s +                                 fcoltest = colVars_center, fsure = rowVars_R,
587s +                                 na.rm = na.rm, center = TRUE, useNames = useNames)
587s +     }
587s +   }
587s + }
589s > 
589s 
589s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
589s Copyright (C) 2024 The R Foundation for Statistical Computing
589s Platform: arm-unknown-linux-gnueabihf (32-bit)
589s 
589s R is free software and comes with ABSOLUTELY NO WARRANTY.
589s You are welcome to redistribute it under certain conditions.
589s Type 'license()' or 'licence()' for distribution details.
589s 
589s R is a collaborative project with many contributors.
589s Type 'contributors()' for more information and
589s 'citation()' on how to cite R or R packages in publications.
589s 
589s Type 'demo()' for some demos, 'help()' for on-line help, or
589s 'help.start()' for an HTML browser interface to help.
589s Type 'q()' to quit R.
589s 
590s > library("matrixStats")
590s > 
590s > ## Create isFALSE() if running on an old version of R
590s > if (!exists("isFALSE", mode="function")) {
590s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
590s + }
590s > 
590s > rowWeightedMeans_R <- function(x, w, na.rm = FALSE, ..., useNames = NA) {
590s +   res <- apply(x, MARGIN = 1L, FUN = weighted.mean, w = w, na.rm = na.rm, ...)
590s +   
590s +   # Keep naming support consistency same as rowWeightedMeans()
590s +   idxs <- which(is.na(w) | w != 0)
590s +   nw <- length(idxs)
590s +   if (na.rm) na.rm <- anyMissing(x)
590s +   if ((!is.null(w) && nw == 0L) || isFALSE(na.rm)) {
590s +     if (is.na(useNames) || !useNames) names(res) <- NULL
590s +   }
590s +   else if (isFALSE(useNames)) names(res) <- NULL
590s +   
590s +   res
590s + }
590s > 
590s > colWeightedMeans_R <- function(x, w, na.rm = FALSE, ..., useNames = NA) {
590s +   res <- apply(x, MARGIN = 2L, FUN = weighted.mean, w = w, na.rm = na.rm, ...)
590s +   
590s +   # Keep naming support consistency same as colWeightedMeans()
590s +   idxs <- which(is.na(w) | w != 0)
590s +   nw <- length(idxs)
590s +   if (!is.null(w) && nw == 0L) {
590s +     if (is.na(useNames) || !useNames) names(res) <- NULL
590s +   }
590s +   else if (isFALSE(useNames)) names(res) <- NULL
590s +   
590s +   res
590s + }
590s > 
590s > set.seed(1)
590s > 
590s > x <- matrix(rnorm(20), nrow = 5, ncol = 4)
590s > print(x)
590s            [,1]       [,2]       [,3]        [,4]
590s [1,] -0.6264538 -0.8204684  1.5117812 -0.04493361
590s [2,]  0.1836433  0.4874291  0.3898432 -0.01619026
590s [3,] -0.8356286  0.7383247 -0.6212406  0.94383621
590s [4,]  1.5952808  0.5757814 -2.2146999  0.82122120
590s [5,]  0.3295078 -0.3053884  1.1249309  0.59390132
590s > 
590s > # To check names attribute
590s > dimnames <- list(letters[1:5], LETTERS[1:4])
590s > 
590s > # Non-weighted row averages
590s > x_est0 <- rowMeans(x)
590s > x_est1 <- rowWeightedMeans(x)
590s > print(x_est1)
590s [1] 0.004981341 0.261181337 0.056322931 0.194395865 0.435737906
590s > stopifnot(all.equal(x_est1, x_est0))
590s > x_est2 <- colWeightedMeans(t(x))
590s > stopifnot(all.equal(x_est2, x_est0))
590s > # Check names attribute
590s > dimnames(x) <- dimnames
590s > x_est1 <- rowWeightedMeans(x, useNames = FALSE)
590s > x_est2 <- colWeightedMeans(t(x), useNames = FALSE)
590s > stopifnot(all.equal(x_est1, x_est0))
590s > stopifnot(all.equal(x_est2, x_est0))
590s > x_est0 <- rowMeans(x)
590s > x_est1 <- rowWeightedMeans(x, useNames = TRUE)
590s > x_est2 <- colWeightedMeans(t(x), useNames = TRUE)
590s > stopifnot(all.equal(x_est1, x_est0))
590s > stopifnot(all.equal(x_est2, x_est0))
590s > dimnames(x) <- NULL
590s > 
590s > 
590s > # Weighted row averages (uniform weights)
590s > w <- rep(2.5, times = ncol(x))
590s > x_est0 <- rowMeans(x)
590s > x_est1 <- rowWeightedMeans(x, w = w)
590s > print(x_est1)
590s [1] 0.004981341 0.261181337 0.056322931 0.194395865 0.435737906
590s > stopifnot(all.equal(x_est1, x_est0))
590s > x_est2 <- colWeightedMeans(t(x), w = w)
590s > stopifnot(all.equal(x_est2, x_est0))
590s > # Test with and without dimnames on x
590s > for (setDimnames in c(TRUE, FALSE)) {
590s +   if (setDimnames) dimnames(x) <- dimnames
590s +   else dimnames(x) <- NULL    
590s +   # Check names attribute
590s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
590s +     x_est0 <- rowWeightedMeans_R(x, w = w, useNames = useNames)
590s +     x_est1 <- rowWeightedMeans(x, w = w, useNames = useNames)
590s +     stopifnot(all.equal(x_est1, x_est0))
590s +     x_est0 <- colWeightedMeans_R(t(x), w = w, useNames = useNames)
590s +     x_est1 <- colWeightedMeans(t(x), w = w, useNames = useNames)
590s +     stopifnot(all.equal(x_est1, x_est0))
590s +   }
590s + }
590s > 
590s > 
590s > # Weighted row averages (excluding some columns)
590s > w <- c(1, 1, 0, 1)
590s > x_est0 <- rowMeans(x[, (w == 1), drop = FALSE])
590s > x_est1 <- rowWeightedMeans(x, w = w)
590s > print(x_est1)
590s [1] -0.4972853  0.2182940  0.2821774  0.9974278  0.2060069
590s > stopifnot(all.equal(x_est1, x_est0))
590s > x_est2 <- colWeightedMeans(t(x), w = w)
590s > stopifnot(all.equal(x_est2, x_est0))
590s > # Test with and without dimnames on x
590s > for (setDimnames in c(TRUE, FALSE)) {
590s +   if (setDimnames) dimnames(x) <- dimnames
590s +   else dimnames(x) <- NULL    
590s +   # Check names attribute
590s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
590s +     x_est0 <- rowWeightedMeans_R(x, w = w, useNames = useNames)
590s +     x_est1 <- rowWeightedMeans(x, w = w, useNames = useNames)
590s +     stopifnot(all.equal(x_est1, x_est0))
590s +     x_est0 <- colWeightedMeans_R(t(x), w = w, useNames = useNames)
590s +     x_est1 <- colWeightedMeans(t(x), w = w, useNames = useNames)
590s +     stopifnot(all.equal(x_est1, x_est0))
590s +   }
590s + }
590s > 
590s > 
590s > # Weighted row averages (excluding some columns)
590s > w <- c(0, 1, 0, 0)
590s > x_est0 <- rowMeans(x[, (w == 1), drop = FALSE])
590s > x_est1 <- rowWeightedMeans(x, w = w)
590s > stopifnot(all.equal(x_est1, x_est0))
590s > x_est2 <- colWeightedMeans(t(x), w = w)
590s > stopifnot(all.equal(x_est2, x_est0))
590s > # Test with and without dimnames on x
590s > for (setDimnames in c(TRUE, FALSE)) {
590s +   if (setDimnames) dimnames(x) <- dimnames
590s +   else dimnames(x) <- NULL    
590s +   # Check names attribute
590s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
590s +     x_est0 <- rowWeightedMeans_R(x, w = w, useNames = useNames)
590s +     x_est1 <- rowWeightedMeans(x, w = w, useNames = useNames)
590s +     stopifnot(all.equal(x_est1, x_est0))
590s +     x_est0 <- colWeightedMeans_R(t(x), w = w, useNames = useNames)
590s +     x_est1 <- colWeightedMeans(t(x), w = w, useNames = useNames)
590s +     stopifnot(all.equal(x_est1, x_est0))
590s +   }
590s + }
590s > 
590s > 
590s > # Weighted row averages (all zero weights)
590s > w <- c(0, 0, 0, 0)
590s > x_est0 <- rowMeans(x[, (w == 1), drop = FALSE])
590s > x_est1 <- rowWeightedMeans(x, w = w)
590s > stopifnot(all.equal(x_est1, x_est0))
590s > x_est2 <- colWeightedMeans(t(x), w = w)
590s > stopifnot(all.equal(x_est2, x_est0))
590s > # Test with and without dimnames on x
590s > for (setDimnames in c(TRUE, FALSE)) {
590s +   if (setDimnames) dimnames(x) <- dimnames
590s +   else dimnames(x) <- NULL    
590s +   # Check names attribute
590s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
590s +     x_est0 <- rowWeightedMeans_R(x, w = w, useNames = useNames)
590s +     x_est1 <- rowWeightedMeans(x, w = w, useNames = useNames)
590s +     stopifnot(all.equal(x_est1, x_est0))
590s +     x_est0 <- colWeightedMeans_R(t(x), w = w, useNames = useNames)
590s +     x_est1 <- colWeightedMeans(t(x), w = w, useNames = useNames)
590s +     stopifnot(all.equal(x_est1, x_est0))
590s +   }
590s + }
590s > 
590s > 
590s > # Weighted averages by rows and columns
590s > w <- 1:4
590s > x_est1 <- rowWeightedMeans(x, w = w)
590s > print(x_est1)
590s [1]  0.20882185  0.22632701  0.25526439 -0.06123714  0.54691290
590s > x_est2 <- colWeightedMeans(t(x), w = w)
590s > stopifnot(all.equal(x_est2, x_est1))
590s > # Test with and without dimnames on x
590s > for (setDimnames in c(TRUE, FALSE)) {
590s +   if (setDimnames) dimnames(x) <- dimnames
590s +   else dimnames(x) <- NULL    
590s +   # Check names attribute
590s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
590s +     x_est0 <- rowWeightedMeans_R(x, w = w, useNames = useNames)
590s +     x_est1 <- rowWeightedMeans(x, w = w, useNames = useNames)
590s +     stopifnot(all.equal(x_est1, x_est0))
590s +     x_est0 <- colWeightedMeans_R(t(x), w = w, useNames = useNames)
590s +     x_est1 <- colWeightedMeans(t(x), w = w, useNames = useNames)
590s +     stopifnot(all.equal(x_est1, x_est0))
590s +   }
590s + }
590s > 
590s > 
590s > x[sample(length(x), size = 0.3 * length(x))] <- NA
590s > print(x)
590s            [,1]      [,2]       [,3]        [,4]
590s [1,] -0.6264538        NA  1.5117812 -0.04493361
590s [2,]  0.1836433        NA         NA -0.01619026
590s [3,] -0.8356286 0.7383247 -0.6212406  0.94383621
590s [4,]  1.5952808        NA -2.2146999  0.82122120
590s [5,]  0.3295078        NA         NA  0.59390132
590s > 
590s > # Non-weighted row averages with missing values
590s > x_est0 <- rowMeans(x, na.rm = TRUE)
590s > x_est1 <- rowWeightedMeans(x, na.rm = TRUE)
590s > print(x_est1)
590s [1] 0.28013125 0.08372653 0.05632293 0.06726737 0.46170455
590s > stopifnot(all.equal(x_est1, x_est0))
590s > x_est2 <- colWeightedMeans(t(x), na.rm = TRUE)
590s > stopifnot(all.equal(x_est2, x_est0))
590s > # Check names attribute
590s > dimnames(x) <- dimnames
590s > x_est1 <- rowWeightedMeans(x, na.rm = TRUE, useNames = FALSE)
590s > x_est2 <- colWeightedMeans(t(x), na.rm = TRUE, useNames = FALSE)
590s > stopifnot(all.equal(x_est1, x_est0))
590s > stopifnot(all.equal(x_est2, x_est0))
590s > x_est0 <- rowMeans(x, na.rm = TRUE)
590s > x_est1 <- rowWeightedMeans(x, na.rm = TRUE, useNames = TRUE)
590s > x_est2 <- colWeightedMeans(t(x), na.rm = TRUE, useNames = TRUE)
590s > stopifnot(all.equal(x_est1, x_est0))
590s > stopifnot(all.equal(x_est2, x_est0))
590s > dimnames(x) <- NULL
590s > 
590s > 
590s > # Weighted row averages with missing values
590s > x_est0 <- apply(x, MARGIN = 1L, FUN = weighted.mean, w = w, na.rm = TRUE)
590s > print(x_est0)
590s [1]  0.46614441  0.02377645  0.25526439 -0.22049176  0.54102261
590s > x_est1 <- rowWeightedMeans(x, w = w, na.rm = TRUE)
590s > print(x_est1)
590s [1]  0.46614441  0.02377645  0.25526439 -0.22049176  0.54102261
590s > stopifnot(all.equal(x_est1, x_est0))
590s > x_est2 <- colWeightedMeans(t(x), w = w, na.rm = TRUE)
590s > stopifnot(all.equal(x_est2, x_est0))
590s > # Test with and without dimnames on x
590s > for (setDimnames in c(TRUE, FALSE)) {
590s +   if (setDimnames) dimnames(x) <- dimnames
590s +   else dimnames(x) <- NULL    
590s +   # Check names attribute
590s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
590s +     x_est0 <- rowWeightedMeans_R(x, w = w, na.rm = TRUE, useNames = useNames)
590s +     x_est1 <- rowWeightedMeans(x, w = w, na.rm = TRUE, useNames = useNames)
590s +     stopifnot(all.equal(x_est1, x_est0))
590s +     x_est0 <- colWeightedMeans_R(t(x), w = w, na.rm = TRUE, useNames = useNames)
590s +     x_est1 <- colWeightedMeans(t(x), w = w, na.rm = TRUE, useNames = useNames)
590s +     stopifnot(all.equal(x_est1, x_est0))
590s +   }
590s + }
590s > 
590s > 
590s > # Weighted averages by rows and columns
590s > w <- 1:4
590s > x_est1 <- rowWeightedMeans(x, w = w, na.rm = TRUE)
590s > x_est2 <- colWeightedMeans(t(x), w = w, na.rm = TRUE)
590s > stopifnot(all.equal(x_est2, x_est1))
590s > # Test with and without dimnames on x
590s > for (setDimnames in c(TRUE, FALSE)) {
590s +   if (setDimnames) dimnames(x) <- dimnames
590s +   else dimnames(x) <- NULL    
590s +   # Check names attribute
590s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
590s +     x_est0 <- rowWeightedMeans_R(x, w = w, na.rm = TRUE, useNames = useNames)
590s +     x_est1 <- rowWeightedMeans(x, w = w, na.rm = TRUE, useNames = useNames)
590s +     stopifnot(all.equal(x_est1, x_est0))
590s +     x_est0 <- colWeightedMeans_R(t(x), w = w, na.rm = TRUE, useNames = useNames)
590s +     x_est1 <- colWeightedMeans(t(x), w = w, na.rm = TRUE, useNames = useNames)
590s +     stopifnot(all.equal(x_est1, x_est0))
590s +   }
590s + }
590s > 
590s > 
590s > # w contains missing value
590s > w[1] <- NA_integer_
590s > x_est1 <- rowWeightedMeans(x, w = w, na.rm = TRUE)
590s > x_est2 <- colWeightedMeans(t(x), w = w, na.rm = TRUE)
590s > stopifnot(all.equal(x_est2, x_est1))
590s > # Test with and without dimnames on x
590s > for (setDimnames in c(TRUE, FALSE)) {
590s +   if (setDimnames) dimnames(x) <- dimnames
590s +   else dimnames(x) <- NULL    
590s +   # Check names attribute
590s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
590s +     x_est0 <- rowWeightedMeans_R(x, w = w, na.rm = TRUE, useNames = useNames)
590s +     x_est1 <- rowWeightedMeans(x, w = w, na.rm = TRUE, useNames = useNames)
590s +     stopifnot(all.equal(x_est1, x_est0))
590s +     x_est0 <- colWeightedMeans_R(t(x), w = w, na.rm = TRUE, useNames = useNames)
590s +     x_est1 <- colWeightedMeans(t(x), w = w, na.rm = TRUE, useNames = useNames)
590s +     stopifnot(all.equal(x_est1, x_est0))
590s +   }
590s + }
590s > 
590s > x_est1 <- rowWeightedMeans(x, w = w, na.rm = FALSE)
590s > x_est2 <- colWeightedMeans(t(x), w = w, na.rm = FALSE)
590s > stopifnot(all.equal(x_est2, x_est1))
590s > # Test with and without dimnames on x
590s > for (setDimnames in c(TRUE, FALSE)) {
590s +   if (setDimnames) dimnames(x) <- dimnames
590s +   else dimnames(x) <- NULL    
590s +   # Check names attribute
590s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
590s +     x_est0 <- rowWeightedMeans_R(x, w = w, na.rm = FALSE, useNames = useNames)
590s +     x_est1 <- rowWeightedMeans(x, w = w, na.rm = FALSE, useNames = useNames)
590s +     stopifnot(all.equal(x_est1, x_est0))
590s +     x_est0 <- colWeightedMeans_R(t(x), w = w, na.rm = FALSE, useNames = useNames)
590s +     x_est1 <- colWeightedMeans(t(x), w = w, na.rm = FALSE, useNames = useNames)
590s +     stopifnot(all.equal(x_est1, x_est0))
590s +   }
590s + }
590s > 
590s 
590s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
590s Copyright (C) 2024 The R Foundation for Statistical Computing
590s Platform: arm-unknown-linux-gnueabihf (32-bit)
590s 
590s R is free software and comes with ABSOLUTELY NO WARRANTY.
590s You are welcome to redistribute it under certain conditions.
590s Type 'license()' or 'licence()' for distribution details.
590s 
590s R is a collaborative project with many contributors.
590s Type 'contributors()' for more information and
590s 'citation()' on how to cite R or R packages in publications.
590s 
590s Type 'demo()' for some demos, 'help()' for on-line help, or
590s 'help.start()' for an HTML browser interface to help.
590s Type 'q()' to quit R.
590s 
591s > library("matrixStats")
591s > 
591s > ## Create isFALSE() if running on an old version of R
591s > if (!exists("isFALSE", mode="function")) {
591s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
591s + }
591s > 
591s > rowWeightedMeans_R <- function(x, w, na.rm = FALSE, ..., useNames = NA) {
591s +   res <- apply(x, MARGIN = 1L, FUN = weighted.mean, w = w, na.rm = na.rm, ...)
591s +   
591s +   # Keep naming support consistency same as rowWeightedMeans()
591s +   idxs <- which(is.na(w) | w != 0)
591s +   nw <- length(idxs)
591s +   if (na.rm) na.rm <- anyMissing(x)
591s +   if ((!is.null(w) && nw == 0L) || isFALSE(na.rm)) {
591s +     if (is.na(useNames) || !useNames) names(res) <- NULL
591s +   }
591s +   else if (isFALSE(useNames)) names(res) <- NULL
591s +   
591s +   res
591s + }
591s > 
591s > colWeightedMeans_R <- function(x, w, na.rm = FALSE, ..., useNames = NA) {
591s +   res <- apply(x, MARGIN = 1L, FUN = weighted.mean, w = w, na.rm = na.rm, ...)
591s +   
591s +   # Keep naming support consistency same as colWeightedMeans()
591s +   idxs <- which(is.na(w) | w != 0)
591s +   nw <- length(idxs)
591s +   if (!is.null(w) && nw == 0L) {
591s +     if (is.na(useNames) || !useNames) names(res) <- NULL
591s +   }
591s +   else if (isFALSE(useNames)) names(res) <- NULL
591s +   
591s +   res
591s + }
591s > 
591s > 
591s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
591s > # Subsetted tests
591s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
591s > source("utils/validateIndicesFramework.R")
591s > # To check names attribute
591s > dimnames <- list(letters[1:6], LETTERS[1:6])
591s > for (mode in c("numeric", "integer", "logical")) {
591s +   x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
591s +   w <- runif(6, min = 0, max = 6)
591s +   storage.mode(x) <- mode
591s +   storage.mode(w) <- if (mode == "logical") "integer" else mode
591s +   if (mode == "numeric") w[1] <- Inf
591s + 
591s +   # Test with and without dimnames on x
591s +   for (setDimnames in c(TRUE, FALSE)) {
591s +     if (setDimnames) dimnames(x) <- dimnames
591s +     else dimnames(x) <- NULL
591s + 
591s +     count <- 0L
591s +     for (rows in index_cases) {
591s +       for (cols in index_cases) {
591s +         count <- count + 1L
591s +         na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
591s +         useNames <- c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)
591s +         useNames <- useNames[count %% length(useNames) + 1]
591s + 
591s +         validateIndicesTestMatrix_w(x, w, rows, cols, 
591s +                                     ftest = rowWeightedMeans, fsure = rowWeightedMeans_R,
591s +                                     na.rm = na.rm, useNames = useNames)
591s +         validateIndicesTestMatrix_w(x, w, rows, cols,
591s +                                     fcoltest = colWeightedMeans, fsure = colWeightedMeans_R,
591s +                                     na.rm = na.rm, useNames = useNames)
591s +       }
591s +     }
591s +   }
591s + }
594s > 
595s 
595s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
595s Copyright (C) 2024 The R Foundation for Statistical Computing
595s Platform: arm-unknown-linux-gnueabihf (32-bit)
595s 
595s R is free software and comes with ABSOLUTELY NO WARRANTY.
595s You are welcome to redistribute it under certain conditions.
595s Type 'license()' or 'licence()' for distribution details.
595s 
595s R is a collaborative project with many contributors.
595s Type 'contributors()' for more information and
595s 'citation()' on how to cite R or R packages in publications.
595s 
595s Type 'demo()' for some demos, 'help()' for on-line help, or
595s 'help.start()' for an HTML browser interface to help.
595s Type 'q()' to quit R.
595s 
595s > library("matrixStats")
595s > 
595s > ## Create isFALSE() if running on an old version of R
595s > if (!exists("isFALSE", mode="function")) {
595s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
595s + }
595s > 
595s > rowWeightedMedians_R <- function(x, w, na.rm = FALSE, ..., useNames = NA) {
595s +   res <- apply(x, MARGIN = 1L, FUN = weightedMedian, w = w, na.rm = na.rm, ...)
595s +   
595s +   # Keep naming support consistency same as rowWeightedMedians()
595s +   if (!is.null(w)) {
595s +     if (isFALSE(useNames)) names(res) <- NULL
595s +   }
595s +   else if (is.na(useNames) || !useNames) names(res) <- NULL
595s +   
595s +   res
595s + }
595s > 
595s > colWeightedMedians_R <- function(x, w, na.rm = FALSE, ..., useNames = NA) {
595s +   res <- apply(x, MARGIN = 2L, FUN = weightedMedian, w = w, na.rm = na.rm, ...)
595s +   
595s +   # Keep naming support consistency same as colWeightedMedians()
595s +   if (!is.null(w)) {
595s +     if (isFALSE(useNames)) names(res) <- NULL
595s +   }
595s +   else if (is.na(useNames) || !useNames) names(res) <- NULL
595s +   
595s +   res
595s + }
595s > 
595s > set.seed(1)
595s > 
595s > x <- matrix(rnorm(20), nrow = 5, ncol = 4)
595s > print(x)
595s            [,1]       [,2]       [,3]        [,4]
595s [1,] -0.6264538 -0.8204684  1.5117812 -0.04493361
595s [2,]  0.1836433  0.4874291  0.3898432 -0.01619026
595s [3,] -0.8356286  0.7383247 -0.6212406  0.94383621
595s [4,]  1.5952808  0.5757814 -2.2146999  0.82122120
595s [5,]  0.3295078 -0.3053884  1.1249309  0.59390132
595s > 
595s > # To check names attribute
595s > dimnames <- list(letters[1:5], LETTERS[1:4])
595s > 
595s > # Non-weighted row medians
595s > x_est0 <- rowMedians(x)
595s > x_est1 <- rowWeightedMedians(x)
595s > stopifnot(all.equal(x_est1, x_est0))
595s > x_est2 <- colWeightedMedians(t(x))
595s > stopifnot(all.equal(x_est2, x_est0))
595s > # Test with and without dimnames on x
595s > for (setDimnames in c(TRUE, FALSE)) {
595s +   if (setDimnames) dimnames(x) <- dimnames
595s +   else dimnames(x) <- NULL
595s +   # Check names attribute
595s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
595s +     x_est0 <- rowMedians(x, useNames = useNames)
595s +     x_est1 <- rowWeightedMedians(x, useNames = useNames)
595s +     x_est2 <- colWeightedMedians(t(x), useNames = useNames)
595s +     stopifnot(all.equal(x_est1, x_est0))
595s +     stopifnot(all.equal(x_est2, x_est0))
595s +   }
595s + }
595s > 
595s > 
595s > # Weighted row medians (uniform weights)
595s > w <- rep(2.5, times = ncol(x))
595s > x_est0 <- rowMedians(x)
595s > x_est1 <- rowWeightedMedians(x, w = w)
595s > stopifnot(all.equal(x_est1, x_est0))
595s > x_est2 <- colWeightedMedians(t(x), w = w)
595s > stopifnot(all.equal(x_est2, x_est0))
595s > # Test with and without dimnames on x
595s > for (setDimnames in c(TRUE, FALSE)) {
595s +   if (setDimnames) dimnames(x) <- dimnames
595s +   else dimnames(x) <- NULL    
595s +   # Check names attribute
595s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
595s +     x_est0 <- rowWeightedMedians_R(x, w = w, useNames = useNames)
595s +     x_est1 <- rowWeightedMedians(x, w = w, useNames = useNames)
595s +     stopifnot(all.equal(x_est1, x_est0))
595s +     x_est0 <- colWeightedMedians_R(t(x), w = w, useNames = useNames)
595s +     x_est1 <- colWeightedMedians(t(x), w = w, useNames = useNames)
595s +     stopifnot(all.equal(x_est1, x_est0))
595s +   }
595s + }
595s > 
595s > 
595s > # Weighted row medians (excluding some columns)
595s > w <- c(1, 1, 0, 1)
595s > x_est0 <- rowMedians(x[, (w == 1), drop = FALSE])
595s > x_est1 <- rowWeightedMedians(x, w = w)
595s > stopifnot(all.equal(x_est1, x_est0))
595s > x_est2 <- colWeightedMedians(t(x), w = w)
595s > stopifnot(all.equal(x_est2, x_est0))
595s > # Test with and without dimnames on x
595s > for (setDimnames in c(TRUE, FALSE)) {
595s +   if (setDimnames) dimnames(x) <- dimnames
595s +   else dimnames(x) <- NULL    
595s +   # Check names attribute
595s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
595s +     x_est0 <- rowWeightedMedians_R(x, w = w, useNames = useNames)
595s +     x_est1 <- rowWeightedMedians(x, w = w, useNames = useNames)
595s +     stopifnot(all.equal(x_est1, x_est0))
595s +     x_est0 <- colWeightedMedians_R(t(x), w = w, useNames = useNames)
595s +     x_est1 <- colWeightedMedians(t(x), w = w, useNames = useNames)
595s +     stopifnot(all.equal(x_est1, x_est0))
595s +   }
595s + }
595s > 
595s > # Weighted row medians (excluding some columns)
595s > w <- c(0, 1, 0, 0)
595s > x_est0 <- rowMedians(x[, (w == 1), drop = FALSE])
595s > x_est1 <- rowWeightedMedians(x, w = w)
595s > stopifnot(all.equal(x_est1, x_est0))
595s > x_est2 <- colWeightedMedians(t(x), w = w)
595s > stopifnot(all.equal(x_est2, x_est0))
595s > # Test with and without dimnames on x
595s > for (setDimnames in c(TRUE, FALSE)) {
595s +   if (setDimnames) dimnames(x) <- dimnames
595s +   else dimnames(x) <- NULL    
595s +   # Check names attribute
595s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
595s +     x_est0 <- rowWeightedMedians_R(x, w = w, useNames = useNames)
595s +     x_est1 <- rowWeightedMedians(x, w = w, useNames = useNames)
595s +     stopifnot(all.equal(x_est1, x_est0))
595s +     x_est0 <- colWeightedMedians_R(t(x), w = w, useNames = useNames)
595s +     x_est1 <- colWeightedMedians(t(x), w = w, useNames = useNames)
595s +     stopifnot(all.equal(x_est1, x_est0))
595s +   }
595s + }
595s > 
595s > # Weighted row medians (all zero weights)
595s > w <- c(0, 0, 0, 0)
595s > x_est0 <- rowMedians(x[, (w == 1), drop = FALSE])
595s > x_est1 <- rowWeightedMedians(x, w = w)
595s > stopifnot(all.equal(x_est1, x_est0))
595s > x_est2 <- colWeightedMedians(t(x), w = w)
595s > stopifnot(all.equal(x_est2, x_est0))
595s > # Test with and without dimnames on x
595s > for (setDimnames in c(TRUE, FALSE)) {
595s +   if (setDimnames) dimnames(x) <- dimnames
595s +   else dimnames(x) <- NULL    
595s +   # Check names attribute
595s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
595s +     x_est0 <- rowWeightedMedians_R(x, w = w, useNames = useNames)
595s +     x_est1 <- rowWeightedMedians(x, w = w, useNames = useNames)
595s +     stopifnot(all.equal(x_est1, x_est0))
595s +     x_est0 <- colWeightedMedians_R(t(x), w = w, useNames = useNames)
595s +     x_est1 <- colWeightedMedians(t(x), w = w, useNames = useNames)
595s +     stopifnot(all.equal(x_est1, x_est0))
595s +   }
595s + }
595s > 
595s > # Weighted medians by rows and columns
595s > w <- 1:4
595s > x_est1 <- rowWeightedMedians(x, w = w)
595s > x_est2 <- colWeightedMedians(t(x), w = w)
595s > stopifnot(all.equal(x_est2, x_est1))
595s > # Test with and without dimnames on x
595s > for (setDimnames in c(TRUE, FALSE)) {
595s +   if (setDimnames) dimnames(x) <- dimnames
595s +   else dimnames(x) <- NULL    
595s +   # Check names attribute
595s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
595s +     x_est0 <- rowWeightedMedians_R(x, w = w, useNames = useNames)
595s +     x_est1 <- rowWeightedMedians(x, w = w, useNames = useNames)
595s +     stopifnot(all.equal(x_est1, x_est0))
595s +     x_est0 <- colWeightedMedians_R(t(x), w = w, useNames = useNames)
595s +     x_est1 <- colWeightedMedians(t(x), w = w, useNames = useNames)
595s +     stopifnot(all.equal(x_est1, x_est0))
595s +   }
595s + }
595s > 
595s > 
595s > # Weighted row medians with missing values
595s > x_est0 <- apply(x, MARGIN = 1L, FUN = weightedMedian, w = w, na.rm = TRUE)
595s > print(x_est0)
595s [1] -0.04493361  0.23519330  0.73832471  0.65759463  0.59390132
595s > x_est1 <- rowWeightedMedians(x, w = w, na.rm = TRUE)
595s > print(x_est1)
595s [1] -0.04493361  0.23519330  0.73832471  0.65759463  0.59390132
595s > stopifnot(all.equal(x_est1, x_est0))
595s > x_est2 <- colWeightedMedians(t(x), w = w)
595s > stopifnot(all.equal(x_est2, x_est0))
595s > # Test with and without dimnames on x
595s > for (setDimnames in c(TRUE, FALSE)) {
595s +   if (setDimnames) dimnames(x) <- dimnames
595s +   else dimnames(x) <- NULL    
595s +   # Check names attribute
595s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
595s +     x_est0 <- rowWeightedMedians_R(x, w = w, na.rm = TRUE, useNames = useNames)
595s +     x_est1 <- rowWeightedMedians(x, w = w, na.rm = TRUE, useNames = useNames)
595s +     stopifnot(all.equal(x_est1, x_est0))
595s +     x_est0 <- colWeightedMedians_R(t(x), w = w, na.rm = TRUE, useNames = useNames)
595s +     x_est1 <- colWeightedMedians(t(x), w = w, na.rm = TRUE, useNames = useNames)
595s +     stopifnot(all.equal(x_est1, x_est0))
595s +   }
595s + }
595s > 
595s > # Weighted medians by rows and columns
595s > w <- 1:4
595s > x_est1 <- rowWeightedMedians(x, w = w, na.rm = TRUE)
595s > x_est2 <- colWeightedMedians(t(x), w = w, na.rm = TRUE)
595s > stopifnot(all.equal(x_est2, x_est1))
595s > # Test with and without dimnames on x
595s > for (setDimnames in c(TRUE, FALSE)) {
595s +   if (setDimnames) dimnames(x) <- dimnames
595s +   else dimnames(x) <- NULL    
595s +   # Check names attribute
595s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
595s +     x_est0 <- rowWeightedMedians_R(x, w = w, na.rm = TRUE, useNames = useNames)
595s +     x_est1 <- rowWeightedMedians(x, w = w, na.rm = TRUE, useNames = useNames)
595s +     stopifnot(all.equal(x_est1, x_est0))
595s +     x_est0 <- colWeightedMedians_R(t(x), w = w, na.rm = TRUE, useNames = useNames)
595s +     x_est1 <- colWeightedMedians(t(x), w = w, na.rm = TRUE, useNames = useNames)
595s +     stopifnot(all.equal(x_est1, x_est0))
595s +   }
595s + }
595s > 
595s > 
595s > # Inf weight
595s > x <- matrix(1:2, nrow = 1, ncol = 2)
595s > w <- c(7, Inf)
595s > x_est1 <- rowWeightedMedians(x, w = w)
595s > x_est2 <- colWeightedMedians(t(x), w = w)
595s > stopifnot(identical(2, x_est1))
595s > stopifnot(identical(2, x_est2))
595s > # Test with and without dimnames on x
595s > dimnames <- list("a", LETTERS[1:2])
595s > for (setDimnames in c(TRUE, FALSE)) {
595s +   if (setDimnames) dimnames(x) <- dimnames
595s +   else dimnames(x) <- NULL    
595s +   # Check names attribute
595s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
595s +     x_est0 <- rowWeightedMedians_R(x, w = w, useNames = useNames)
595s +     x_est1 <- rowWeightedMedians(x, w = w, useNames = useNames)
595s +     stopifnot(all.equal(x_est1, x_est0))
595s +     x_est0 <- colWeightedMedians_R(t(x), w = w, useNames = useNames)
595s +     x_est1 <- colWeightedMedians(t(x), w = w, useNames = useNames)
595s +     stopifnot(all.equal(x_est1, x_est0))
595s +   }
595s + }
595s > 
596s 
596s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
596s Copyright (C) 2024 The R Foundation for Statistical Computing
596s Platform: arm-unknown-linux-gnueabihf (32-bit)
596s 
596s R is free software and comes with ABSOLUTELY NO WARRANTY.
596s You are welcome to redistribute it under certain conditions.
596s Type 'license()' or 'licence()' for distribution details.
596s 
596s R is a collaborative project with many contributors.
596s Type 'contributors()' for more information and
596s 'citation()' on how to cite R or R packages in publications.
596s 
596s Type 'demo()' for some demos, 'help()' for on-line help, or
596s 'help.start()' for an HTML browser interface to help.
596s Type 'q()' to quit R.
596s 
596s > library("matrixStats")
596s > 
596s > ## Create isFALSE() if running on an old version of R
596s > if (!exists("isFALSE", mode="function")) {
596s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
596s + }
596s > 
596s > rowWeightedMedians_R <- function(x, w, na.rm = FALSE, ..., useNames = NA) {
596s +   res <- apply(x, MARGIN = 1L, FUN = weightedMedian, w = w, na.rm = na.rm, ...)
596s +   
596s +   # Keep naming support consistency same as rowWeightedMedians()
596s +   if (!is.null(w)) {
596s +     if (isFALSE(useNames)) names(res) <- NULL
596s +   }
596s +   else if (is.na(useNames) || !useNames) names(res) <- NULL
596s +   
596s +   res
596s + }
596s > 
596s > 
596s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
596s > # Subsetted tests
596s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
596s > source("utils/validateIndicesFramework.R")
596s > # To check names attribute
596s > dimnames <- list(letters[1:6], LETTERS[1:6])
596s > for (mode in c("numeric", "integer", "logical")) {
596s +   x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
596s +   w <- runif(6, min = 0, max = 6)
596s +   storage.mode(x) <- mode
596s +   storage.mode(w) <- if (mode == "logical") "integer" else mode
596s +   if (mode == "numeric") w[1] <- Inf
596s + 
596s +   # Test with and without dimnames on x
596s +   for (setDimnames in c(TRUE, FALSE)) {
596s +     if (setDimnames) dimnames(x) <- dimnames
596s +     else dimnames(x) <- NULL
596s + 
596s +     count <- 0L
596s +     for (rows in index_cases) {
596s +       for (cols in index_cases) {
596s +         count <- count + 1L
596s +         na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
596s +         useNames <- c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)
596s +         useNames <- useNames[count %% length(useNames) + 1]
596s + 
596s +         validateIndicesTestMatrix_w(x, w, rows, cols,
596s +                                     ftest = rowWeightedMedians,
596s +                                     fsure = rowWeightedMedians_R,
596s +                                     na.rm = na.rm, useNames = useNames)
596s +         validateIndicesTestMatrix_w(x, w, rows, cols,
596s +                                     fcoltest = colWeightedMedians,
596s +                                     fsure = rowWeightedMedians_R,
596s +                                     na.rm = na.rm, useNames = useNames)
596s +       }
596s +     }
596s +   }
596s + }
599s > 
599s 
599s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
599s Copyright (C) 2024 The R Foundation for Statistical Computing
599s Platform: arm-unknown-linux-gnueabihf (32-bit)
599s 
599s R is free software and comes with ABSOLUTELY NO WARRANTY.
599s You are welcome to redistribute it under certain conditions.
599s Type 'license()' or 'licence()' for distribution details.
599s 
599s R is a collaborative project with many contributors.
599s Type 'contributors()' for more information and
599s 'citation()' on how to cite R or R packages in publications.
599s 
599s Type 'demo()' for some demos, 'help()' for on-line help, or
599s 'help.start()' for an HTML browser interface to help.
599s Type 'q()' to quit R.
599s 
600s > library("matrixStats")
600s > 
600s > set.seed(1)
600s > 
600s > x <- matrix(rnorm(20), nrow = 5L, ncol = 4L)
600s > print(x)
600s            [,1]       [,2]       [,3]        [,4]
600s [1,] -0.6264538 -0.8204684  1.5117812 -0.04493361
600s [2,]  0.1836433  0.4874291  0.3898432 -0.01619026
600s [3,] -0.8356286  0.7383247 -0.6212406  0.94383621
600s [4,]  1.5952808  0.5757814 -2.2146999  0.82122120
600s [5,]  0.3295078 -0.3053884  1.1249309  0.59390132
600s > 
600s > # To check names attribute
600s > dimnames <- list(letters[1:5], LETTERS[1:4])
600s > 
600s > # Weighted row variances (uniform weights - all w = 1)
600s > # Non-weighted row variances
600s > x_est0 <- rowVars(x)
600s > w <- rep(1, times = ncol(x))
600s > x_est1 <- rowWeightedVars(x, w = w)
600s > print(x_est1)
600s [1] 1.11767161 0.05022969 0.83582537 2.76819528 0.35351857
600s > stopifnot(all.equal(x_est1, x_est0))
600s > x_est2 <- colWeightedVars(t(x), w = w)
600s > stopifnot(all.equal(x_est2, x_est0))
600s > # Check names attribute
600s > dimnames(x) <- dimnames
600s > x_est1 <- rowWeightedVars(x, w = w, useNames = FALSE)
600s > x_est2 <- colWeightedVars(t(x), w = w, useNames = FALSE)
600s > stopifnot(all.equal(x_est1, x_est0))
600s > stopifnot(all.equal(x_est2, x_est0))
600s > x_est0 <- rowVars(x, useNames = TRUE)
600s > if (!matrixStats:::isUseNamesNADefunct()) {
600s +   x_est1 <- rowWeightedVars(x, w = w, useNames = NA)
600s +   x_est2 <- colWeightedVars(t(x), w = w, useNames = NA)
600s +   stopifnot(all.equal(x_est1, x_est0))
600s +   stopifnot(all.equal(x_est2, x_est0))
600s + }
600s > x_est1 <- rowWeightedVars(x, w = w, useNames = TRUE)
600s > x_est2 <- colWeightedVars(t(x), w = w, useNames = TRUE)
600s > stopifnot(all.equal(x_est1, x_est0))
600s > stopifnot(all.equal(x_est2, x_est0))
600s > dimnames(x) <- NULL
600s > 
600s > 
600s > # Weighted row variances (uniform weights - all w = 3)
600s > x3 <- cbind(x, x, x)
600s > x_est0 <- rowVars(x3)
600s > w <- rep(3, times = ncol(x))
600s > x_est1 <- rowWeightedVars(x, w = w)
600s > print(x_est1)
600s [1] 0.91445859 0.04109702 0.68385712 2.26488705 0.28924246
600s > stopifnot(all.equal(x_est1, x_est0))
600s > x_est2 <- colWeightedVars(t(x), w = w)
600s > stopifnot(all.equal(x_est2, x_est0))
600s > # Check names attribute
600s > dimnames(x) <- dimnames
600s > x_est1 <- rowWeightedVars(x, w = w, useNames = FALSE)
600s > x_est2 <- colWeightedVars(t(x), w = w, useNames = FALSE)
600s > stopifnot(all.equal(x_est1, x_est0))
600s > stopifnot(all.equal(x_est2, x_est0))
600s > x3 <- cbind(x, x, x)
600s > x_est0 <- rowVars(x3, useNames = TRUE)
600s > if (!matrixStats:::isUseNamesNADefunct()) {
600s +   x_est1 <- rowWeightedVars(x, w = w, useNames = NA)
600s +   x_est2 <- colWeightedVars(t(x), w = w, useNames = NA)
600s +   stopifnot(all.equal(x_est1, x_est0))
600s +   stopifnot(all.equal(x_est2, x_est0))
600s + }
600s > x_est1 <- rowWeightedVars(x, w = w, useNames = TRUE)
600s > x_est2 <- colWeightedVars(t(x), w = w, useNames = TRUE)
600s > stopifnot(all.equal(x_est1, x_est0))
600s > stopifnot(all.equal(x_est2, x_est0))
600s > dimnames(x) <- NULL
600s > 
600s > 
600s > # Weighted row variances (excluding some columns)
600s > w <- c(1, 1, 0, 1)
600s > x_est0 <- rowVars(x[, (w == 1), drop = FALSE])
600s > x_est1 <- rowWeightedVars(x, w = w)
600s > print(x_est1)
600s [1] 0.16287693 0.06430861 0.94767651 0.28313135 0.21361984
600s > stopifnot(all.equal(x_est1, x_est0))
600s > x_est2 <- colWeightedVars(t(x), w = w)
600s > stopifnot(all.equal(x_est2, x_est0))
600s > # Check names attribute
600s > dimnames(x) <- dimnames
600s > x_est1 <- rowWeightedVars(x, w = w, useNames = FALSE)
600s > x_est2 <- colWeightedVars(t(x), w = w, useNames = FALSE)
600s > stopifnot(all.equal(x_est1, x_est0))
600s > stopifnot(all.equal(x_est2, x_est0))
600s > x_est0 <- rowVars(x[, (w == 1), drop = FALSE], useNames = TRUE)
600s > if (!matrixStats:::isUseNamesNADefunct()) {
600s +   x_est1 <- rowWeightedVars(x, w = w, useNames = NA)
600s +   x_est2 <- colWeightedVars(t(x), w = w, useNames = NA)
600s +   stopifnot(all.equal(x_est1, x_est0))
600s +   stopifnot(all.equal(x_est2, x_est0))
600s + }
600s > x_est1 <- rowWeightedVars(x, w = w, useNames = TRUE)
600s > x_est2 <- colWeightedVars(t(x), w = w, useNames = TRUE)
600s > stopifnot(all.equal(x_est1, x_est0))
600s > stopifnot(all.equal(x_est2, x_est0))
600s > dimnames(x) <- NULL
600s > 
600s > 
600s > # Weighted row variances (excluding some columns)
600s > w <- c(0, 1, 0, 0)
600s > x_est0 <- rowVars(x[, (w == 1), drop = FALSE])
600s > x_est1 <- rowWeightedVars(x, w = w)
600s > #stopifnot(all.equal(x_est1, x_est0))
600s > x_est2 <- colWeightedVars(t(x), w = w)
600s > stopifnot(all.equal(x_est2, x_est1))
600s > # Check names attribute
600s > dimnames(x) <- dimnames
600s > x_est1 <- rowWeightedVars(x, w = w, useNames = FALSE)
600s > x_est2 <- colWeightedVars(t(x), w = w, useNames = FALSE)
600s > stopifnot(all.equal(x_est1, x_est0))
600s > stopifnot(all.equal(x_est2, x_est0))
600s > x_est0 <- rowVars(x[, (w == 1), drop = FALSE], useNames = TRUE)
600s > if (!matrixStats:::isUseNamesNADefunct()) {
600s +   x_est1 <- rowWeightedVars(x, w = w, useNames = NA)
600s +   x_est2 <- colWeightedVars(t(x), w = w, useNames = NA)
600s +   stopifnot(all.equal(x_est1, x_est0))
600s +   stopifnot(all.equal(x_est2, x_est0))
600s + }
600s > x_est1 <- rowWeightedVars(x, w = w, useNames = TRUE)
600s > x_est2 <- colWeightedVars(t(x), w = w, useNames = TRUE)
600s > stopifnot(all.equal(x_est1, x_est0))
600s > stopifnot(all.equal(x_est2, x_est0))
600s > dimnames(x) <- NULL
600s > 
600s > 
600s > # Weighted row variances (all zero weights)
600s > w <- c(0, 0, 0, 0)
600s > x_est0 <- rowVars(x[, (w == 1), drop = FALSE])
600s > x_est1 <- rowWeightedVars(x, w = w)
600s > stopifnot(all.equal(x_est1, x_est0))
600s > x_est2 <- colWeightedVars(t(x), w = w)
600s > stopifnot(all.equal(x_est2, x_est0))
600s > # Check names attribute
600s > dimnames(x) <- dimnames
600s > x_est1 <- rowWeightedVars(x, w = w, useNames = FALSE)
600s > x_est2 <- colWeightedVars(t(x), w = w, useNames = FALSE)
600s > stopifnot(all.equal(x_est1, x_est0))
600s > stopifnot(all.equal(x_est2, x_est0))
600s > x_est0 <- rowVars(x[, (w == 1), drop = FALSE], useNames = TRUE)
600s > if (!matrixStats:::isUseNamesNADefunct()) {
600s +   x_est1 <- rowWeightedVars(x, w = w, useNames = NA)
600s +   x_est2 <- colWeightedVars(t(x), w = w, useNames = NA)
600s +   stopifnot(all.equal(x_est1, x_est0))
600s +   stopifnot(all.equal(x_est2, x_est0))
600s + }
600s > x_est1 <- rowWeightedVars(x, w = w, useNames = TRUE)
600s > x_est2 <- colWeightedVars(t(x), w = w, useNames = TRUE)
600s > stopifnot(all.equal(x_est1, x_est0))
600s > stopifnot(all.equal(x_est2, x_est0))
600s > dimnames(x) <- NULL
600s > 
600s > # Weighted variances by rows and columns
600s > w <- 1:4
600s > # Test with and without dimnames on x
600s > for (setDimnames in c(TRUE, FALSE)) {
600s +   if (setDimnames) dimnames(x) <- dimnames
600s +   else dimnames(x) <- NULL    
600s +   # Check names attribute
600s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
600s +     x_est1 <- rowWeightedVars(x, w = w, useNames = useNames)
600s +     print(x_est1)
600s +     x_est2 <- colWeightedVars(t(x), w = w, useNames = useNames)
600s +     stopifnot(all.equal(x_est2, x_est1))
600s +   }
600s + }
600s          a          b          c          d          e 
600s 0.90747094 0.05040463 0.65089440 2.28697479 0.27902734 
600s [1] 0.90747094 0.05040463 0.65089440 2.28697479 0.27902734
600s [1] 0.90747094 0.05040463 0.65089440 2.28697479 0.27902734
600s [1] 0.90747094 0.05040463 0.65089440 2.28697479 0.27902734
600s > 
600s > 
600s > x[sample(length(x), size = 0.3 * length(x))] <- NA
600s > print(x)
600s            [,1]      [,2]       [,3]        [,4]
600s [1,] -0.6264538        NA  1.5117812 -0.04493361
600s [2,]  0.1836433        NA         NA -0.01619026
600s [3,] -0.8356286 0.7383247 -0.6212406  0.94383621
600s [4,]  1.5952808        NA -2.2146999  0.82122120
600s [5,]  0.3295078        NA         NA  0.59390132
600s > 
600s > # Non-weighted row variances with missing values
600s > x_est0 <- rowVars(x, na.rm = TRUE)
600s > x_est1 <- rowWeightedVars(x, w = rep(1, times = ncol(x)), na.rm = TRUE)
600s > print(x_est1)
600s [1] 1.22226258 0.01996673 0.83582537 4.05532299 0.03495197
600s > stopifnot(all.equal(x_est1, x_est0))
600s > x_est2 <- colWeightedVars(t(x), w = rep(1, times = ncol(x)), na.rm = TRUE)
600s > stopifnot(all.equal(x_est2, x_est0))
600s > # Check names attribute
600s > dimnames(x) <- dimnames
600s > x_est1 <- rowWeightedVars(x, w = rep(1, times = ncol(x)), na.rm = TRUE, useNames = FALSE)
600s > x_est2 <- colWeightedVars(t(x), w = rep(1, times = ncol(x)), na.rm = TRUE, useNames = FALSE)
600s > stopifnot(all.equal(x_est1, x_est0))
600s > stopifnot(all.equal(x_est2, x_est0))
600s > x_est0 <- rowVars(x, na.rm = TRUE, useNames = TRUE)
600s > x_est1 <- rowWeightedVars(x, w = rep(1, times = ncol(x)), na.rm = TRUE, useNames = TRUE)
600s > x_est2 <- colWeightedVars(t(x), w = rep(1, times = ncol(x)), na.rm = TRUE, useNames = TRUE)
600s > stopifnot(all.equal(x_est1, x_est0))
600s > stopifnot(all.equal(x_est2, x_est0))
600s > dimnames(x) <- NULL
600s > 
600s > 
600s > # Weighted row variances with missing values
600s > # Test with and without dimnames on x
600s > for (setDimnames in c(TRUE, FALSE)) {
600s +   if (setDimnames) dimnames(x) <- dimnames
600s +   else dimnames(x) <- NULL    
600s +   # Check names attribute
600s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
600s +     x_est1 <- rowWeightedVars(x, w = w, na.rm = TRUE, useNames = useNames)
600s +     print(x_est1)
600s +     x_est2 <- colWeightedVars(t(x), w = w, na.rm = TRUE, useNames = useNames)
600s +     stopifnot(all.equal(x_est2, x_est1))
600s +   }
600s + }
600s           a           b           c           d           e 
600s 0.788377504 0.007986693 0.650894398 2.795470241 0.013980790 
600s [1] 0.788377504 0.007986693 0.650894398 2.795470241 0.013980790
600s [1] 0.788377504 0.007986693 0.650894398 2.795470241 0.013980790
600s [1] 0.788377504 0.007986693 0.650894398 2.795470241 0.013980790
600s > 
600s > 
600s > # Weighted variances by rows and columns
600s > w <- 1:4
600s > # Test with and without dimnames on x
600s > for (setDimnames in c(TRUE, FALSE)) {
600s +   if (setDimnames) dimnames(x) <- dimnames
600s +   else dimnames(x) <- NULL    
600s +   # Check names attribute
600s +   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
600s +     x_est1 <- rowWeightedVars(x, w = w, na.rm = TRUE, useNames = useNames)
600s +     print(x_est1)
600s +     x_est2 <- colWeightedVars(t(x), w = w, na.rm = TRUE, useNames = useNames)
600s +     stopifnot(all.equal(x_est2, x_est1))
600s +   }
600s + }
600s           a           b           c           d           e 
600s 0.788377504 0.007986693 0.650894398 2.795470241 0.013980790 
600s [1] 0.788377504 0.007986693 0.650894398 2.795470241 0.013980790
600s [1] 0.788377504 0.007986693 0.650894398 2.795470241 0.013980790
600s [1] 0.788377504 0.007986693 0.650894398 2.795470241 0.013980790
600s > 
600s > 
600s > # Weighted row standard deviation (excluding some columns)
600s > w <- c(1, 1, 0, 1)
600s > ## FIXME: rowVars()/rowSds() needs na.rm = FALSE (wrong default)
600s > x_est0 <- rowSds(x[, (w == 1), drop = FALSE], na.rm = FALSE)
600s > x_est1 <- rowWeightedSds(x, w = w)
600s > print(x_est1)
600s [1]        NA        NA 0.9734868        NA        NA
600s > stopifnot(all.equal(x_est1, x_est0))
600s > x_est2 <- colWeightedSds(t(x), w = w, na.rm = FALSE)
600s > stopifnot(all.equal(x_est2, x_est0))
600s > # Check names attribute
600s > dimnames(x) <- dimnames
600s > x_est1 <- rowWeightedSds(x, w = w, na.rm = FALSE, useNames = FALSE)
600s > x_est2 <- colWeightedSds(t(x), w = w, na.rm = FALSE, useNames = FALSE)
600s > stopifnot(all.equal(x_est1, x_est0))
600s > stopifnot(all.equal(x_est2, x_est0))
600s > x_est0 <- rowSds(x[, (w == 1), drop = FALSE], na.rm = FALSE, useNames = TRUE)
600s > if (!matrixStats:::isUseNamesNADefunct()) {
600s +   x_est1 <- rowWeightedSds(x, w = w, na.rm = FALSE, useNames = NA)
600s +   x_est2 <- colWeightedSds(t(x), w = w, na.rm = FALSE, useNames = NA)
600s +   stopifnot(all.equal(x_est1, x_est0))
600s +   stopifnot(all.equal(x_est2, x_est0))
600s + }  
600s > x_est1 <- rowWeightedSds(x, w = w, na.rm = FALSE, useNames = TRUE)
600s > x_est2 <- colWeightedSds(t(x), w = w, na.rm = FALSE, useNames = TRUE)
600s > stopifnot(all.equal(x_est1, x_est0))
600s > stopifnot(all.equal(x_est2, x_est0))
600s > dimnames(x) <- NULL
600s > 
600s > 
600s > # Weighted row MADs (excluding some columns)
600s > w <- c(1, 1, 0, 1)
600s > x_est0 <- rowMads(x[, (w == 1), drop = FALSE])
600s > x_est1 <- rowWeightedMads(x, w = w)
600s > print(x_est1)
600s [1]        NA        NA 0.3046914        NA        NA
600s > stopifnot(all.equal(x_est1, x_est0))
600s > x_est2 <- colWeightedMads(t(x), w = w)
600s > stopifnot(all.equal(x_est2, x_est0))
600s > # Check names attribute
600s > dimnames(x) <- dimnames
600s > x_est1 <- rowWeightedMads(x, w = w, useNames = FALSE)
600s > x_est2 <- colWeightedMads(t(x), w = w, useNames = FALSE)
600s > stopifnot(all.equal(x_est1, x_est0))
600s > stopifnot(all.equal(x_est2, x_est0))
600s > x_est0 <- rowMads(x[, (w == 1), drop = FALSE], useNames = TRUE)
600s > if (!matrixStats:::isUseNamesNADefunct()) {
600s +   x_est1 <- rowWeightedMads(x, w = w, useNames = NA)
600s +   x_est2 <- colWeightedMads(t(x), w = w, useNames = NA)
600s +   stopifnot(all.equal(x_est1, x_est0))
600s +   stopifnot(all.equal(x_est2, x_est0))
600s + }
600s > x_est1 <- rowWeightedMads(x, w = w, useNames = TRUE)
600s > x_est2 <- colWeightedMads(t(x), w = w, useNames = TRUE)
600s > stopifnot(all.equal(x_est1, x_est0))
600s > stopifnot(all.equal(x_est2, x_est0))
600s > dimnames(x) <- NULL
600s > 
600s 
600s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
600s Copyright (C) 2024 The R Foundation for Statistical Computing
600s Platform: arm-unknown-linux-gnueabihf (32-bit)
600s 
600s R is free software and comes with ABSOLUTELY NO WARRANTY.
600s You are welcome to redistribute it under certain conditions.
600s Type 'license()' or 'licence()' for distribution details.
600s 
600s R is a collaborative project with many contributors.
600s Type 'contributors()' for more information and
600s 'citation()' on how to cite R or R packages in publications.
600s 
600s Type 'demo()' for some demos, 'help()' for on-line help, or
600s 'help.start()' for an HTML browser interface to help.
600s Type 'q()' to quit R.
600s 
600s > library("matrixStats")
600s > 
600s > fcns <- list(
600s +   weightedVar = c(rowWeightedVars, colWeightedVars),
600s +   weightedSd = c(rowWeightedSds, colWeightedSds),
600s +   weightedMad = c(rowWeightedMads, colWeightedMads)
600s + )
600s > 
600s > 
600s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
600s > # Subsetted tests
600s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
600s > source("utils/validateIndicesFramework.R")
600s > # To check names attribute
600s > dimnames <- list(letters[1:6], LETTERS[1:6])
600s > for (fcn in names(fcns)) {
600s +   cat(sprintf("subsetted tests on matrix %s()...\n", fcn))
600s +   row_fcn <- fcns[[fcn]][[1]]
600s +   col_fcn <- fcns[[fcn]][[2]]
600s + 
600s +   for (mode in c("numeric", "integer")) {
600s +     x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
600s +     w <- runif(6, min = 0, max = 6)
600s +     storage.mode(x) <- mode
600s +     storage.mode(w) <- mode
600s +     if (mode == "numeric") w[1] <- Inf
600s + 
600s +     # Test with and without dimnames on x
600s +     for (setDimnames in c(TRUE, FALSE)) {
600s +       if (setDimnames) dimnames(x) <- dimnames
600s +       else dimnames(x) <- NULL
600s + 
600s +       count <- 0L
600s +       for (rows in index_cases) {
600s +         for (cols in index_cases) {
600s +           count <- count + 1L
600s +           na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
600s +           useNames <- c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)
600s +           useNames <- useNames[count %% length(useNames) + 1]
600s + 
600s +           validateIndicesTestMatrix_w(x, w, rows, cols,
600s +                                       ftest = row_fcn, fsure = row_fcn,
600s +                                       na.rm = na.rm, useNames = useNames)
600s +           validateIndicesTestMatrix_w(x, w, rows, cols,
600s +                                       fcoltest = col_fcn, fsure = row_fcn,
600s +                                       na.rm = na.rm, useNames = useNames)
600s +         }
600s +       }
600s +     }
600s +   }
600s +   cat(sprintf("%s()...DONE\n", fcn))
600s + }
600s subsetted tests on matrix weightedVar()...
603s weightedVar()...DONE
603s subsetted tests on matrix weightedSd()...
606s weightedSd()...DONE
606s subsetted tests on matrix weightedMad()...
608s weightedMad()...DONE
608s > 
608s 
608s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
608s Copyright (C) 2024 The R Foundation for Statistical Computing
608s Platform: arm-unknown-linux-gnueabihf (32-bit)
608s 
608s R is free software and comes with ABSOLUTELY NO WARRANTY.
608s You are welcome to redistribute it under certain conditions.
608s Type 'license()' or 'licence()' for distribution details.
608s 
608s R is a collaborative project with many contributors.
608s Type 'contributors()' for more information and
608s 'citation()' on how to cite R or R packages in publications.
608s 
608s Type 'demo()' for some demos, 'help()' for on-line help, or
608s 'help.start()' for an HTML browser interface to help.
608s Type 'q()' to quit R.
608s 
608s > library("matrixStats")
608s > 
608s > signTabulate0 <- function(x, ...) {
608s +   nneg <- sum(x < 0, na.rm = TRUE)
608s +   nzero <- sum(x == 0, na.rm = TRUE)
608s +   npos <- sum(x > 0, na.rm = TRUE)
608s +   nna <- sum(is.na(x))
608s +   nneginf <- sum(is.infinite(x) & x < 0, na.rm = TRUE)
608s +   nposinf <- sum(is.infinite(x) & x > 0, na.rm = TRUE)
608s +   res <- c(nneg, nzero, npos, nna, nneginf, nposinf)
608s +   res <- as.double(res)
608s +   names(res) <- c("-1", "0", "+1", "NA", "-Inf", "+Inf")
608s +   if (is.integer(x)) res <- res[1:4]
608s +   res
608s + } # signTabulate0()
608s > 
608s > 
608s > # Simulate data
608s > set.seed(0xBEEF)
608s > n <- 100L
608s Doubles:
608s > x <- runif(n)
608s > x[sample(n, size = 0.1 * n)] <- 0
608s > x[sample(n, size = 0.1 * n)] <- NA_real_
608s > x[sample(n, size = 0.1 * n)] <- -Inf
608s > x[sample(n, size = 0.1 * n)] <- +Inf
608s > 
608s > # Doubles
608s > message("Doubles:")
608s > counts0 <- signTabulate0(x)
608s > print(counts0)
608s   -1    0   +1   NA -Inf +Inf 
608s    9    7   77    7    9   10 
608s > counts1 <- signTabulate(x)
608s > print(counts1)
608s   -1    0   +1   NA -Inf +Inf 
608s    9    7   77    7    9   10 
608s > stopifnot(identical(counts1, counts0))
608s > 
608s > # Integers
608s > message("Integers:")
608s Integers:
608s > x <- suppressWarnings(as.integer(x))
608s > counts0 <- signTabulate0(x)
608s > print(counts0)
608s -1  0 +1 NA 
608s  0 74  0 26 
608s > counts1 <- signTabulate(x)
608s > print(counts1)
608s -1  0 +1 NA 
608s  0 74  0 26 
608s > stopifnot(identical(counts1, counts0))
608s > 
608s 
608s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
608s Copyright (C) 2024 The R Foundation for Statistical Computing
608s Platform: arm-unknown-linux-gnueabihf (32-bit)
608s 
608s R is free software and comes with ABSOLUTELY NO WARRANTY.
608s You are welcome to redistribute it under certain conditions.
608s Type 'license()' or 'licence()' for distribution details.
608s 
608s R is a collaborative project with many contributors.
608s Type 'contributors()' for more information and
608s 'citation()' on how to cite R or R packages in publications.
608s 
608s Type 'demo()' for some demos, 'help()' for on-line help, or
608s 'help.start()' for an HTML browser interface to help.
608s Type 'q()' to quit R.
608s 
609s > library("matrixStats")
609s > 
609s > signTabulate0 <- function(x, ...) {
609s +   nneg <- sum(x < 0, na.rm = TRUE)
609s +   nzero <- sum(x == 0, na.rm = TRUE)
609s +   npos <- sum(x > 0, na.rm = TRUE)
609s +   nna <- sum(is.na(x))
609s +   nneginf <- sum(is.infinite(x) & x < 0, na.rm = TRUE)
609s +   nposinf <- sum(is.infinite(x) & x > 0, na.rm = TRUE)
609s +   res <- c(nneg, nzero, npos, nna, nneginf, nposinf)
609s +   res <- as.double(res)
609s +   names(res) <- c("-1", "0", "+1", "NA", "-Inf", "+Inf")
609s +   if (is.integer(x)) res <- res[1:4]
609s +   res
609s + } # signTabulate0()
609s > 
609s > 
609s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
609s > # Subsetted tests
609s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
609s > source("utils/validateIndicesFramework.R")
609s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
609s > x[2:3, 4:5] <- +Inf
609s > x[4:5, 1:2] <- -Inf
609s > for (idxs in index_cases) {
609s +   validateIndicesTestVector(x, idxs,
609s +                             ftest = signTabulate, fsure = signTabulate0)
609s + }
609s > 
609s 
609s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
609s Copyright (C) 2024 The R Foundation for Statistical Computing
609s Platform: arm-unknown-linux-gnueabihf (32-bit)
609s 
609s R is free software and comes with ABSOLUTELY NO WARRANTY.
609s You are welcome to redistribute it under certain conditions.
609s Type 'license()' or 'licence()' for distribution details.
609s 
609s R is a collaborative project with many contributors.
609s Type 'contributors()' for more information and
609s 'citation()' on how to cite R or R packages in publications.
609s 
609s Type 'demo()' for some demos, 'help()' for on-line help, or
609s 'help.start()' for an HTML browser interface to help.
609s Type 'q()' to quit R.
609s 
609s > library("matrixStats")
609s > options(warn = 1)
609s > 
609s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
609s > # Consistency checks
609s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
609s > set.seed(1)
609s > 
609s > sum2_R <- function(x, na.rm = FALSE, idxs = NULL) {
609s +   if (is.null(idxs)) {
609s +     sum(x, na.rm = na.rm)
609s +   } else {
609s +     sum(x[idxs], na.rm = na.rm)
609s +   }
609s + } # sum2_R()
609s > 
609s > 
609s > cat("Consistency checks:\n")
609s Consistency checks:
609s > for (kk in 1:20) {
609s +   cat("Random test #", kk, "\n", sep = "")
609s + 
609s +   # Simulate data in a matrix of any shape
609s +   n <- sample(1e3, size = 1L)
609s +   x <- rnorm(n, sd = 100)
609s + 
609s +   # Add NAs?
609s +   if ((kk %% 4) %in% c(3, 0)) {
609s +     cat("Adding NAs\n")
609s +     nna <- sample(n, size = 1L)
609s +     na_values <- c(NA_real_, NaN)
609s +     t <- sample(na_values, size = nna, replace = TRUE)
609s +     x[sample(length(x), size = nna)] <- t
609s +   }
609s + 
609s +   # Integer or double?
609s +   if ((kk %% 4) %in% c(2, 0)) {
609s +     cat("Coercing to integers\n")
609s +     storage.mode(x) <- "integer"
609s +   }
609s + 
609s +   na.rm <- sample(c(TRUE, FALSE), size = 1L)
609s + 
609s +   # Sum over all
609s +   y0 <- sum2_R(x, na.rm = na.rm)
609s +   y1 <- sum2(x, na.rm = na.rm)
609s +   stopifnot(all.equal(y1, y0))
609s + 
609s +   # Sum over subset
609s +   nidxs <- sample(n, size = 1L)
609s +   idxs <- sample(n, size = nidxs)
609s +   y0 <- sum2_R(x, na.rm = na.rm, idxs = idxs)
609s +   y1 <- sum2(x, na.rm = na.rm, idxs = idxs)
609s +   stopifnot(all.equal(y1, y0))
609s + 
609s +   if (storage.mode(x) == "integer") {
609s +     storage.mode(x) <- "logical"
609s +     
609s +     y0 <- sum2_R(x, na.rm = na.rm)
609s +     y1 <- sum2(x, na.rm = na.rm)
609s +     stopifnot(all.equal(y1, y0))
609s +     
609s +     y0 <- sum2_R(x, na.rm = na.rm, idxs = idxs)
609s +     y1 <- sum2(x, na.rm = na.rm, idxs = idxs)
609s +     stopifnot(all.equal(y1, y0))
609s +   }
609s + } # for (kk ...)
609s Random test #1
609s Random test #2
609s Coercing to integers
609s Random test #3
609s Adding NAs
609s Random test #4
609s Adding NAs
609s Coercing to integers
609s Random test #5
609s Random test #6
609s Coercing to integers
609s Random test #7
609s Adding NAs
609s Random test #8
609s Adding NAs
609s Coercing to integers
609s Random test #9
609s Random test #10
609s Coercing to integers
609s Random test #11
609s Adding NAs
609s Random test #12
609s Adding NAs
609s Coercing to integers
609s Random test #13
609s Random test #14
609s Coercing to integers
609s Random test #15
609s Adding NAs
609s Random test #16
610s Adding NAs
610s Coercing to integers
610s Random test #17
610s Random test #18
610s Coercing to integers
610s Random test #19
610s Adding NAs
610s Random test #20
610s Adding NAs
610s Coercing to integers
610s > 
610s > 
610s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
610s > # All missing values
610s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
610s > for (n in 0:2) {
610s +   for (na.rm in c(FALSE, TRUE)) {
610s +     x <- rep(NA_real_, times = n)
610s +     y0 <- sum(x, na.rm = na.rm)
610s +     y <- sum2(x, na.rm = na.rm)
610s +     stopifnot(all.equal(y, y0))
610s + 
610s +     x <- rep(NA_integer_, times = n)
610s +     y0 <- sum(x, na.rm = na.rm)
610s +     y <- sum2(x, na.rm = na.rm)
610s +     stopifnot(all.equal(y, y0))
610s +     
610s +     x <- rep(NA, times = n)
610s +     y0 <- sum(x, na.rm = na.rm)
610s +     y <- sum2(x, na.rm = na.rm)
610s +     stopifnot(all.equal(y, y0))
610s +   }
610s + }
610s > 
610s > 
610s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
610s > # Special cases
610s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
610s > for (na.rm in c(FALSE, TRUE)) {
610s +   # Summing over zero elements (integers)
610s +   x <- integer(0)
610s +   s1 <- sum(x, na.rm = na.rm)
610s +   s2 <- sum2(x, na.rm = na.rm)
610s +   stopifnot(identical(s1, s2))
610s + 
610s +   x <- 1:10
610s +   idxs <- integer(0)
610s +   s1 <- sum(x[idxs], na.rm = na.rm)
610s +   s2 <- sum2(x, idxs = idxs, na.rm = na.rm)
610s +   stopifnot(identical(s1, s2))
610s + 
610s +   # Summing over NA_integer_:s
610s +   x <- rep(NA_integer_, times = 10L)
610s +   s1 <- sum(x, na.rm = na.rm)
610s +   s2 <- sum2(x, na.rm = na.rm)
610s +   stopifnot(identical(s1, s2))
610s + 
610s +   x <- rep(NA_integer_, times = 10L)
610s +   idxs <- 1:5
610s +   s1 <- sum(x[idxs], na.rm = na.rm)
610s +   s2 <- sum2(x, idxs = idxs, na.rm = na.rm)
610s +   stopifnot(identical(s1, s2))
610s + 
610s + 
610s +   # Summing over zero elements (doubles)
610s +   x <- double(0)
610s +   s1 <- sum(x)
610s +   s2 <- sum2(x)
610s +   stopifnot(
610s +     identical(s1, 0),
610s +     identical(s1, s2)
610s +   )
610s + 
610s +   x <- as.double(1:10)
610s +   idxs <- integer(0)
610s +   s1 <- sum(x[idxs])
610s +   s2 <- sum2(x, idxs = idxs)
610s +   stopifnot(
610s +     identical(s1, 0),
610s +     identical(s1, s2)
610s +   )
610s + 
610s +   # Summing over NA_real_:s
610s +   x <- rep(NA_real_, times = 10L)
610s +   s1 <- sum(x, na.rm = na.rm)
610s +   s2 <- sum2(x, na.rm = na.rm)
610s +   stopifnot(
610s +     !na.rm || s1 == 0,
610s +     identical(s1, s2)
610s +   )
610s + 
610s +   x <- rep(NA_real_, times = 10L)
610s +   idxs <- 1:5
610s +   s1 <- sum(x[idxs], na.rm = na.rm)
610s +   s2 <- sum2(x, idxs = idxs, na.rm = na.rm)
610s +   stopifnot(
610s +     !na.rm || s1 == 0,
610s +     identical(s1, s2)
610s +   )
610s + 
610s +   # Summing over -Inf:s
610s +   x <- rep(-Inf, times = 3L)
610s +   s1 <- sum(x, na.rm = na.rm)
610s +   s2 <- sum2(x, na.rm = na.rm)
610s +   stopifnot(
610s +     is.infinite(s1) && s1 < 0,
610s +     identical(s1, s2)
610s +   )
610s + 
610s +   # Summing over +Inf:s
610s +   x <- rep(+Inf, times = 3L)
610s +   s1 <- sum(x, na.rm = na.rm)
610s +   s2 <- sum2(x, na.rm = na.rm)
610s +   stopifnot(identical(s1, s2))
610s +   stopifnot(
610s +     is.infinite(s1) && s1 > 0,
610s +     identical(s1, s2)
610s +   )
610s + 
610s +   # Summing over mix of -Inf:s and +Inf:s
610s +   x <- rep(c(-Inf, +Inf), times = 3L)
610s +   s1 <- sum(x, na.rm = na.rm)
610s +   s2 <- sum2(x, na.rm = na.rm)
610s +   stopifnot(
610s +     is.nan(s1),
610s +     identical(s1, s2)
610s +   )
610s + 
610s +   # Summing over mix of -Inf:s and +Inf:s and numerics
610s +   x <- rep(c(-Inf, +Inf, 3.14), times = 2L)
610s +   s1 <- sum(x, na.rm = na.rm)
610s +   s2 <- sum2(x, na.rm = na.rm)
610s +   stopifnot(
610s +     is.nan(s1),
610s +     identical(s1, s2)
610s +   )
610s + 
610s +   # Summing over mix of NaN, NA, +Inf, and numerics
610s +   x <- c(NaN, NA, +Inf, 3.14)
610s +   s1 <- sum(x, na.rm = na.rm)
610s +   s2 <- sum2(x, na.rm = na.rm)
610s +   if (na.rm) {
610s +     stopifnot(
610s +       is.infinite(s1) && s1 > 0,
610s +       identical(s2, s1)
610s +     )
610s +   } else {
610s +     stopifnot(is.na(s1), is.na(s2))
610s +     ## NOTE, due to compiler optimization, it is not guaranteed that NA is
610s +     ## returned here (as one would expect). NaN might very well be returned,
610s +     ## when both NA and NaN are involved.  This is an accepted feature in R,
610s +     ## which is documented in help("is.nan").  See also
610s +     ## https://stat.ethz.ch/pipermail/r-devel/2017-April/074009.html.
610s +     ## Thus, we cannot guarantee that s1 is identical to s0.
610s +   }
610s + 
610s +   # Summing over mix of NaN, NA, +Inf, and numerics
610s +   x <- c(NA, NaN, +Inf, 3.14)
610s +   s1 <- sum(x, na.rm = na.rm)
610s +   s2 <- sum2(x, na.rm = na.rm)
610s +   if (na.rm) {
610s +     stopifnot(
610s +       is.infinite(s1) && s1 > 0,
610s +       identical(s2, s1)
610s +     )
610s +   } else {
610s +     stopifnot(is.na(s1), is.na(s2))
610s +     ## NOTE, due to compiler optimization, it is not guaranteed that NA is
610s +     ## returned here (as one would expect). NaN might very well be returned,
610s +     ## when both NA and NaN are involved.  This is an accepted feature in R,
610s +     ## which is documented in help("is.nan").  See also
610s +     ## https://stat.ethz.ch/pipermail/r-devel/2017-April/074009.html.
610s +     ## Thus, we cannot guarantee that s1 is identical to s0.
610s +   }
610s + }
610s > 
610s > 
610s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
610s > # Summing of large integers
610s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
610s > x <- c(.Machine$integer.max, 1L, -.Machine$integer.max)
610s > 
610s > # Total gives integer overflow
610s > s1 <- sum(x[1:2])                        # NA_integer_ w/ warning
610s > s2 <- sum2(x[1:2])                       # NA_integer_ w/ warning
610s > stopifnot(
610s +   getRversion() >= "3.5.0" || identical(s1, NA_integer_),
610s +   identical(s2, NA_integer_)
610s + )
610s Warning in sum2(x[1:2]) :
610s   Integer overflow. Use sum2(..., mode = "double") to avoid this.
610s > 
610s > ## Assert above warning
610s > res <- tryCatch({
610s +   s2 <- sum2(x[1:2])
610s + }, warning = identity)
610s > stopifnot(inherits(res, "warning"))
610s > 
610s > 
610s > # Total gives integer overflow (coerce to numeric)
610s > s1 <- sum(as.numeric(x[1:2]))            # 2147483648
610s > s2 <- sum2(as.numeric(x[1:2]))           # 2147483648
610s > s3 <- sum2(x[1:2], mode = "double")      # 2147483648
610s > stopifnot(
610s +   identical(s1, 2147483648),
610s +   identical(s1, s2),
610s +   identical(s1, s3)
610s + )
610s > 
610s > # Cumulative sum would give integer overflow but not the total
610s > s1 <- sum(x)                              # 1L
610s > s2 <- sum2(x)                             # 1L
610s > stopifnot(
610s +   identical(s1, 1L),
610s +   identical(s1, s2)
610s + )
610s > 
610s > # Input is double but coersing result to integer
610s > x <- c(1, 2, 3.1)
610s > s1 <- sum2(x)
610s > s2 <- sum2(x, mode = "integer")
610s Warning in sum2(x, mode = "integer") :
610s   sum2(x, mode = "integer") called with typeof(x) == "double"; did you mean to use as.integer(sum2(x))?
610s > stopifnot(
610s +   identical(as.integer(s1), s2)
610s + )
610s > 
610s > ## Assert above warning
610s > res <- tryCatch({
610s +   s2 <- sum2(x, mode = "integer")
610s + }, warning = identity)
610s > stopifnot(inherits(res, "warning"))
610s > 
610s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
610s > # Summing of large doubles
610s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
610s > ## Double overflow
610s > x <- rep(.Machine$double.xmax, times = 2L)
610s > y0 <- sum(x)
610s > print(y0)
610s [1] Inf
610s > y <- sum2(x)
610s > print(y)
610s [1] Inf
610s > stopifnot(
610s +   is.infinite(y) && y > 0,
610s +   identical(y, y0)
610s + )
610s > 
610s > x <- rep(-.Machine$double.xmax, times = 2L)
610s > y0 <- sum(x)
610s > print(y0)
610s [1] -Inf
610s > y <- sum2(x)
610s > print(y)
610s [1] -Inf
610s > stopifnot(
610s +   is.infinite(y) && y < 0,
610s +   identical(y, y0)
610s + )
610s > 
610s > 
610s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
610s > # Argument 'idxs'
610s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
610s > x <- 1:10
610s > idxs_list <- list(
610s +   integer = 1:5,
610s +   double = as.double(1:5),
610s +   logical = (x <= 5)
610s + )
610s > 
610s > for (idxs in idxs_list) {
610s +   cat("idxs:\n")
610s +   str(idxs)
610s +   s1 <- sum(x[idxs], na.rm = TRUE)
610s +   s2 <- sum2(x, idxs = idxs, na.rm = TRUE)
610s +   stopifnot(identical(s1, s2))
610s + }
610s idxs:
610s  int [1:5] 1 2 3 4 5
610s idxs:
610s  num [1:5] 1 2 3 4 5
610s idxs:
610s  logi [1:10] TRUE TRUE TRUE TRUE TRUE FALSE ...
610s > 
610s 
610s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
610s Copyright (C) 2024 The R Foundation for Statistical Computing
610s Platform: arm-unknown-linux-gnueabihf (32-bit)
610s 
610s R is free software and comes with ABSOLUTELY NO WARRANTY.
610s You are welcome to redistribute it under certain conditions.
610s Type 'license()' or 'licence()' for distribution details.
610s 
610s R is a collaborative project with many contributors.
610s Type 'contributors()' for more information and
610s 'citation()' on how to cite R or R packages in publications.
610s 
610s Type 'demo()' for some demos, 'help()' for on-line help, or
610s 'help.start()' for an HTML browser interface to help.
610s Type 'q()' to quit R.
610s 
610s > library("matrixStats")
610s > 
610s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
610s > # Subsetted tests
610s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
610s > source("utils/validateIndicesFramework.R")
610s > x <- runif(6, min = -6, max = 6)
610s > storage.mode(x) <- "integer"
610s > for (idxs in index_cases) {
610s +   validateIndicesTestVector(x, idxs,
610s +                             ftest = sum2, fsure = sum,
610s +                             na.rm = FALSE)
610s +   validateIndicesTestVector(x, idxs,
610s +                             ftest = sum2, fsure = sum,
610s +                             na.rm = TRUE)
610s + }
610s > 
611s 
611s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
611s Copyright (C) 2024 The R Foundation for Statistical Computing
611s Platform: arm-unknown-linux-gnueabihf (32-bit)
611s 
611s R is free software and comes with ABSOLUTELY NO WARRANTY.
611s You are welcome to redistribute it under certain conditions.
611s Type 'license()' or 'licence()' for distribution details.
611s 
611s R is a collaborative project with many contributors.
611s Type 'contributors()' for more information and
611s 'citation()' on how to cite R or R packages in publications.
611s 
611s Type 'demo()' for some demos, 'help()' for on-line help, or
611s 'help.start()' for an HTML browser interface to help.
611s Type 'q()' to quit R.
611s 
611s > library(matrixStats)
611s > source("utils/validateIndicesFramework.R")
611s > 
611s > oopts <- options(matrixStats.validateIndices = "ignore")
611s > 
611s > ftest <- function(x, idxs) validateIndices(idxs, length(x))
611s > 
611s > x <- 1:6
611s > for (idxs in index_cases) {
611s +   for (mode in c("integer", "numeric", "logical")) {
611s +     if (!is.null(idxs)) {
611s +       suppressWarnings({storage.mode(idxs) <- mode})
611s +     }
611s +     validateIndicesTestVector(x, idxs, ftest = ftest, fsure = identity)
611s +   }
611s + }
611s > 
611s > ftest <- function(x, idxs) validateIndices(idxs, length(x))
611s > 
611s > for (idxs in index_error_cases) {
611s +   validateIndicesTestVector(x, idxs, ftest = ftest, fsure = identity)
611s + }
611s > 
611s > 
611s > ftest <- function(x, rows, cols) {
611s +   vr <- validateIndices(rows, dim(x)[1], FALSE)
611s +   vc <- validateIndices(cols, dim(x)[2], FALSE)
611s + 
611s +   stopifnot(all((vr > 0 & vr <= dim(x)[1]) | is.na(vr)))
611s +   stopifnot(all((vc > 0 & vc <= dim(x)[2]) | is.na(vc)))
611s +   suppressWarnings(x <- x[vr, vc, drop = FALSE])
611s +   x
611s + }
611s > 
611s > x <- matrix(1:36, nrow = 6, ncol = 6)
611s > for (rows in index_cases) {
611s +   for (cols in index_cases) {
611s +     validateIndicesTestMatrix(x, rows, cols, ftest = ftest, fsure = identity)
611s +   }
611s + }
611s > 
611s > # Testing for 64-bit builds (64 bits = 8 bytes)
611s > if (.Machine$sizeof.pointer == 8L) {
611s +   validateIndices(c(1.25*2^40, 3, 1*2^38, 1, 1.4*2^39), maxIdx = 1*2^41)
611s + }
611s > 
611s > options(oopts)
611s > 
612s 
612s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
612s Copyright (C) 2024 The R Foundation for Statistical Computing
612s Platform: arm-unknown-linux-gnueabihf (32-bit)
612s 
612s R is free software and comes with ABSOLUTELY NO WARRANTY.
612s You are welcome to redistribute it under certain conditions.
612s Type 'license()' or 'licence()' for distribution details.
612s 
612s R is a collaborative project with many contributors.
612s Type 'contributors()' for more information and
612s 'citation()' on how to cite R or R packages in publications.
612s 
612s Type 'demo()' for some demos, 'help()' for on-line help, or
612s 'help.start()' for an HTML browser interface to help.
612s Type 'q()' to quit R.
612s 
612s > library("matrixStats")
612s > 
612s > set.seed(1)
612s > x <- rnorm(1e4)
612s > 
612s > 
612s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
612s > # Variance estimators
612s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
612s > sigma2_a <- var(x)
612s > cat(sprintf("var(x) = %g\n", sigma2_a))
612s var(x) = 1.02487
612s > 
612s > sigma2_b <- varDiff(x)
612s > cat(sprintf("varDiff(x) = %g\n", sigma2_b))
612s varDiff(x) = 1.01224
612s > 
612s > d <- abs(sigma2_b - sigma2_a)
612s > cat(sprintf("Absolute difference = %g\n", d))
612s Absolute difference = 0.0126268
612s > stopifnot(d < 0.02)
612s > 
612s > 
612s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
612s > # Standard deviation estimators
612s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
612s > sigma_a <- sd(x)
612s > cat(sprintf("sd(x) = %g\n", sigma_a))
612s sd(x) = 1.01236
612s > 
612s > sigma_b <- sdDiff(x)
612s > cat(sprintf("sdDiff(x) = %g\n", sigma_b))
612s sdDiff(x) = 1.0061
612s > 
612s > d <- abs(sigma_b - sigma_a)
612s > cat(sprintf("Absolute difference = %g\n", d))
612s Absolute difference = 0.00625567
612s > stopifnot(d < 0.01)
612s > 
612s > # Sanity checks
612s > stopifnot(abs(sigma2_a - sigma_a ^ 2) < 1e-9)
612s > stopifnot(abs(sigma2_b - sigma_b ^ 2) < 1e-9)
612s > 
612s > 
612s > sigma_a2 <- mad(x)
612s > cat(sprintf("mad(x) = %g\n", sigma_a2))
612s mad(x) = 0.998376
612s > 
612s > sigma_b2 <- madDiff(x)
612s > cat(sprintf("madDiff(x) = %g\n", sigma_b2))
612s madDiff(x) = 1.02513
612s > 
612s > d <- abs(sigma_b2 - sigma_a2)
612s > cat(sprintf("Absolute difference = %g\n", d))
612s Absolute difference = 0.0267497
612s > stopifnot(d < 0.05)
612s > 
612s > 
612s > sigma_a3 <- IQR(x)
612s > cat(sprintf("IQR(x) = %g\n", sigma_a3))
612s IQR(x) = 1.35105
612s > 
612s > sigma_b3 <- iqrDiff(x)
612s > cat(sprintf("iqrDiff(x) = %g\n", sigma_b3))
612s iqrDiff(x) = 1.37797
612s > 
612s > d <- abs(sigma_b3 - sigma_a3)
612s > cat(sprintf("Absolute difference = %g\n", d))
612s Absolute difference = 0.0269152
612s > stopifnot(d < 0.05)
612s > 
612s > 
612s > 
612s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
612s > # Trimmed estimators
612s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
612s > y <- x
612s > outliers <- sample(length(x), size = 0.1 * length(x))
612s > y[outliers] <- 100 * y[outliers]
612s > 
612s > sigma_ao <- sd(y[-outliers])
612s > cat(sprintf("sd(y) = %g\n", sigma_ao))
612s sd(y) = 1.01166
612s > 
612s > sigma_bo <- sdDiff(y[-outliers])
612s > cat(sprintf("sdDiff(y) = %g\n", sigma_bo))
612s sdDiff(y) = 1.00743
612s > 
612s > d <- abs(sigma_b - sigma_a)
612s > cat(sprintf("Absolute difference = %g\n", d))
612s Absolute difference = 0.00625567
612s > stopifnot(d < 0.01)
612s > 
612s > sigma_bot <- sdDiff(y, trim = 0.05)
612s > cat(sprintf("sdDiff(y, trim = 0.05) = %g\n", sigma_bot))
612s sdDiff(y, trim = 0.05) = 7.74327
612s > 
612s > d <- abs(sigma_bot - sigma_a)
612s > cat(sprintf("Absolute difference = %g\n", d))
612s Absolute difference = 6.73091
612s > #stopifnot(d < 1e-3)
612s > 
612s > sigma_cot <- madDiff(y, trim = 0.05)
612s > cat(sprintf("madDiff(y, trim = 0.05) = %g\n", sigma_cot))
612s madDiff(y, trim = 0.05) = 1.15278
612s > 
612s > sigma_dot <- iqrDiff(y, trim = 0.05)
612s > cat(sprintf("iqrDiff(y, trim = 0.05) = %g\n", sigma_dot))
612s iqrDiff(y, trim = 0.05) = 1.55762
612s > 
612s > 
612s > fcns <- list(
612s +   varDiff = varDiff,
612s +   sdDiff  = sdDiff,
612s +   madDiff = madDiff,
612s +   iqrDiff = iqrDiff
612s + )
612s > 
612s > for (name in names(fcns)) {
612s +   cat(sprintf("%s()...\n", name))
612s +   fcn <- fcns[[name]]
612s + 
612s +   for (mode in c("integer", "double")) {
612s +     cat("mode: ", mode, "", sep = "")
612s +     for (n in 0:3) {
612s +       x <- runif(n, min = -5, max = 5)
612s +       storage.mode(x) <- mode
612s +       str(x)
612s + 
612s +       y <- fcn(x)
612s +       yt <- fcn(x, trim = 0.1)
612s +       str(list("non-trimmed" = y, trimmed = yt))
612s +     } # for (mode ...)
612s +   }
612s + 
612s +   cat(sprintf("%s()...DONE\n", name))
612s + } # for (name ...)
612s varDiff()...
612s mode: integer int(0) 
612s List of 2
612s  $ non-trimmed: num NA
612s  $ trimmed    : num NA
612s  int -4
612s List of 2
612s  $ non-trimmed: num NA
612s  $ trimmed    : num NA
612s  int [1:2] 3 2
612s List of 2
612s  $ non-trimmed: num NA
612s  $ trimmed    : num NA
612s  int [1:3] 1 4 -1
612s List of 2
612s  $ non-trimmed: num 16
612s  $ trimmed    : num 16
612s mode: double num(0) 
612s List of 2
612s  $ non-trimmed: num NA
612s  $ trimmed    : num NA
612s  num -0.794
612s List of 2
612s  $ non-trimmed: num NA
612s  $ trimmed    : num NA
612s  num [1:2] 0.897 -3.728
612s List of 2
612s  $ non-trimmed: num NA
612s  $ trimmed    : num NA
612s  num [1:3] 2.07 -1.13 1.94
612s List of 2
612s  $ non-trimmed: num 9.83
612s  $ trimmed    : num 9.83
612s varDiff()...DONE
612s sdDiff()...
612s mode: integer int(0) 
612s List of 2
612s  $ non-trimmed: num NA
612s  $ trimmed    : num NA
612s  int 2
612s List of 2
612s  $ non-trimmed: num NA
612s  $ trimmed    : num NA
612s  int [1:2] -4 1
612s List of 2
612s  $ non-trimmed: num NA
612s  $ trimmed    : num NA
612s  int [1:3] -2 1 -1
612s List of 2
612s  $ non-trimmed: num 2.5
612s  $ trimmed    : num 2.5
612s mode: double num(0) 
612s List of 2
612s  $ non-trimmed: num NA
612s  $ trimmed    : num NA
612s  num -3.78
612s List of 2
612s  $ non-trimmed: num NA
612s  $ trimmed    : num NA
612s  num [1:2] -2.04 2.38
612s List of 2
612s  $ non-trimmed: num NA
612s  $ trimmed    : num NA
612s  num [1:3] 1.42 -2.14 1.14
612s List of 2
612s  $ non-trimmed: num 3.42
612s  $ trimmed    : num 3.42
612s sdDiff()...DONE
612s madDiff()...
612s mode: integer int(0) 
612s List of 2
612s  $ non-trimmed: num NA
612s  $ trimmed    : num NA
612s  int -1
612s List of 2
612s  $ non-trimmed: num NA
612s  $ trimmed    : num NA
612s  int [1:2] -1 4
612s List of 2
612s  $ non-trimmed: num NA
612s  $ trimmed    : num NA
612s  int [1:3] -1 0 -3
612s List of 2
612s  $ non-trimmed: num 2.1
612s  $ trimmed    : num 2.1
612s mode: double num(0) 
612s List of 2
612s  $ non-trimmed: num NA
612s  $ trimmed    : num NA
612s  num -1.13
612s List of 2
612s  $ non-trimmed: num NA
612s  $ trimmed    : num NA
612s  num [1:2] -1.7 -1.21
612s List of 2
612s  $ non-trimmed: num NA
612s  $ trimmed    : num NA
612s  num [1:3] -2.39 -0.464 3.086
612s List of 2
612s  $ non-trimmed: num 0.851
612s  $ trimmed    : num 0.851
612s madDiff()...DONE
612s iqrDiff()...
612s mode: integer int(0) 
612s List of 2
612s  $ non-trimmed: num NA
612s  $ trimmed    : num NA
612s  int 3
612s List of 2
612s  $ non-trimmed: num 0
612s  $ trimmed    : num 0
612s  int [1:2] -3 4
612s List of 2
612s  $ non-trimmed: num 0
612s  $ trimmed    : num 0
612s  int [1:3] 0 -2 -2
612s List of 2
612s  $ non-trimmed: num 0.707
612s  $ trimmed    : num 0.707
612s mode: double num(0) 
612s List of 2
612s  $ non-trimmed: num NA
612s  $ trimmed    : num NA
612s  num -4.46
612s List of 2
612s  $ non-trimmed: num 0
612s  $ trimmed    : num 0
612s  num [1:2] 3.67 1.02
612s List of 2
612s  $ non-trimmed: num 0
612s  $ trimmed    : num 0
612s  num [1:3] -0.537 -2.733 2.857
612s List of 2
612s  $ non-trimmed: num 2.75
612s  $ trimmed    : num 2.75
612s iqrDiff()...DONE
612s > 
612s 
612s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
612s Copyright (C) 2024 The R Foundation for Statistical Computing
612s Platform: arm-unknown-linux-gnueabihf (32-bit)
612s 
612s R is free software and comes with ABSOLUTELY NO WARRANTY.
612s You are welcome to redistribute it under certain conditions.
612s Type 'license()' or 'licence()' for distribution details.
612s 
612s R is a collaborative project with many contributors.
612s Type 'contributors()' for more information and
612s 'citation()' on how to cite R or R packages in publications.
612s 
612s Type 'demo()' for some demos, 'help()' for on-line help, or
612s 'help.start()' for an HTML browser interface to help.
612s Type 'q()' to quit R.
612s 
613s > library("matrixStats")
613s > 
613s > fcns <- list(
613s +   varDiff = varDiff,
613s +   sdDiff  = sdDiff,
613s +   madDiff = madDiff,
613s +   iqrDiff = iqrDiff
613s + )
613s > 
613s > 
613s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
613s > # Subsetted tests
613s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
613s > source("utils/validateIndicesFramework.R")
613s > for (name in names(fcns)) {
613s +   cat(sprintf("subsetted tests on %s()...\n", name))
613s +   fcn <- fcns[[name]]
613s + 
613s +   for (mode in c("numeric", "integer")) {
613s +     x <- runif(6, min = -6, max = 6)
613s +     storage.mode(x) <- mode
613s +     trim <- runif(1, min = 0, max = 0.5)
613s +     if (mode == "numeric") x[1] <- Inf
613s + 
613s +     for (diff in 1:2) {
613s +       for (idxs in index_cases) {
613s +         validateIndicesTestVector(x, idxs,
613s +                                   ftest = fcn, fsure = fcn,
613s +                                   na.rm = TRUE, diff = diff, trim = trim)
613s +         validateIndicesTestVector(x, idxs,
613s +                                   ftest = fcn, fsure = fcn,
613s +                                   na.rm = FALSE, diff = diff, trim = trim)
613s +       }
613s +     }
613s +   }
613s +   cat(sprintf("%s()...DONE\n", name))
613s + }
613s subsetted tests on varDiff()...
613s varDiff()...DONE
613s subsetted tests on sdDiff()...
613s sdDiff()...DONE
613s subsetted tests on madDiff()...
613s madDiff()...DONE
613s subsetted tests on iqrDiff()...
613s iqrDiff()...DONE
613s > 
613s 
613s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
613s Copyright (C) 2024 The R Foundation for Statistical Computing
613s Platform: arm-unknown-linux-gnueabihf (32-bit)
613s 
613s R is free software and comes with ABSOLUTELY NO WARRANTY.
613s You are welcome to redistribute it under certain conditions.
613s Type 'license()' or 'licence()' for distribution details.
613s 
613s R is a collaborative project with many contributors.
613s Type 'contributors()' for more information and
613s 'citation()' on how to cite R or R packages in publications.
613s 
613s Type 'demo()' for some demos, 'help()' for on-line help, or
613s 'help.start()' for an HTML browser interface to help.
613s Type 'q()' to quit R.
613s 
613s > library("matrixStats")
614s > 
614s > for (mode in c("logical", "integer", "double")) {
614s +   cat("mode: ", mode, "", sep = "")
614s +   n <- 2L
614s +   x <- runif(n, min = -5, max = 5)
614s +   if (mode == "logical") {
614s +     x <- x > 0
614s +   }
614s +   storage.mode(x) <- mode
614s +   str(x)
614s + 
614s +   cat("All weights are 1\n")
614s +   w <- rep(1, times = n)
614s +   m0 <- weighted.mean(x, w)
614s +   m1 <- weightedMean(x, w)
614s +   str(list(m0 = m0, m1 = m1))
614s +   stopifnot(identical(m1, m0))
614s + 
614s +   cat("First weight is 5\n")
614s +   # Pull the mean towards zero
614s +   w[1] <- 5
614s +   str(w)
614s +   m0 <- weighted.mean(x, w)
614s +   m1 <- weightedMean(x, w)
614s +   str(list(m0 = m0, m1 = m1))
614s +   stopifnot(identical(m1, m0))
614s + 
614s +   cat("All weights are 0\n")
614s +   # All weights set to zero
614s +   w <- rep(0, times = n)
614s +   m0 <- weighted.mean(x, w)
614s +   m1 <- weightedMean(x, w)
614s +   str(list(m0 = m0, m1 = m1))
614s +   stopifnot(identical(m1, m0))
614s + 
614s +   cat("First weight is 8.5\n")
614s +   # Put even more weight on the zero
614s +   w[1] <- 8.5
614s +   m0 <- weighted.mean(x, w)
614s +   m1 <- weightedMean(x, w)
614s +   str(list(m0 = m0, m1 = m1))
614s +   stopifnot(identical(m1, m0))
614s + 
614s +   cat("First weight is Inf\n")
614s +   # All weight on the first value
614s +   w[1] <- Inf
614s +   m0 <- weighted.mean(x, w)
614s +   m1 <- weightedMean(x, w)
614s +   str(list(m0 = m0, m1 = m1))
614s +   stopifnot(identical(m1, m0))
614s + 
614s +   cat("Last weight is Inf\n")
614s +   # All weight on the last value
614s +   w[1] <- 1
614s +   w[n] <- Inf
614s +   m0 <- weighted.mean(x, w)
614s +   m1 <- weightedMean(x, w)
614s +   str(list(m0 = m0, m1 = m1))
614s +   stopifnot(identical(m1, m0))
614s + } # for (mode ...)
614s mode: logical logi [1:2] TRUE TRUE
614s All weights are 1
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s First weight is 5
614s  num [1:2] 5 1
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s All weights are 0
614s List of 2
614s  $ m0: num NaN
614s  $ m1: num NaN
614s First weight is 8.5
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s First weight is Inf
614s List of 2
614s  $ m0: num NaN
614s  $ m1: num NaN
614s Last weight is Inf
614s List of 2
614s  $ m0: num NaN
614s  $ m1: num NaN
614s mode: integer int [1:2] -3 0
614s All weights are 1
614s List of 2
614s  $ m0: num -1.5
614s  $ m1: num -1.5
614s First weight is 5
614s  num [1:2] 5 1
614s List of 2
614s  $ m0: num -2.5
614s  $ m1: num -2.5
614s All weights are 0
614s List of 2
614s  $ m0: num NaN
614s  $ m1: num NaN
614s First weight is 8.5
614s List of 2
614s  $ m0: num -3
614s  $ m1: num -3
614s First weight is Inf
614s List of 2
614s  $ m0: num NaN
614s  $ m1: num NaN
614s Last weight is Inf
614s List of 2
614s  $ m0: num NaN
614s  $ m1: num NaN
614s mode: double num [1:2] -3.8 3.02
614s All weights are 1
614s List of 2
614s  $ m0: num -0.389
614s  $ m1: num -0.389
614s First weight is 5
614s  num [1:2] 5 1
614s List of 2
614s  $ m0: num -2.66
614s  $ m1: num -2.66
614s All weights are 0
614s List of 2
614s  $ m0: num NaN
614s  $ m1: num NaN
614s First weight is 8.5
614s List of 2
614s  $ m0: num -3.8
614s  $ m1: num -3.8
614s First weight is Inf
614s List of 2
614s  $ m0: num NaN
614s  $ m1: num NaN
614s Last weight is Inf
614s List of 2
614s  $ m0: num NaN
614s  $ m1: num NaN
614s > 
614s > 
614s > message("*** Testing for missing values")
614s *** Testing for missing values
614s > # NA tests
614s > xs <- list(A = c(1, 2, 3), B = c(NA, 2, 3), C = c(NA, 2, 3))
614s > ws <- list(A = c(1, 1, 1), B = c(NA, 1, 1), C = c(1, NA, 1))
614s > ## NOTE: The (B, B) case with na.rm = TRUE is interesting because
614s > ## even if NAs in 'w' are not dropped by na.rm = TRUE, this one
614s > ## is because 'x' is dropped and therefore that first element
614s > ## is skipped in the computation.  It basically does
614s > ##   keep <- !is.na(x); x <- x[keep]; w <- w[keep]
614s > ## without looking at 'w'.
614s > for (x in xs) {
614s +   for (mode in c("logical", "integer", "double")) {
614s +     storage.mode(x) <- mode
614s +     for (w in ws) {
614s +       for (na.rm in c(FALSE, TRUE)) {
614s +         cat(sprintf("mode: %s, na.rm = %s\n", mode, na.rm))
614s +         str(list(x = x, w = w))
614s +         m0 <- weighted.mean(x, w, na.rm = na.rm)
614s +         m1 <- weightedMean(x, w, na.rm = na.rm)
614s +         str(list(m0 = m0, m1 = m1))
614s +         stopifnot(all.equal(m1, m0))
614s +       }
614s +     }
614s +   }
614s + }
614s mode: logical, na.rm = FALSE
614s List of 2
614s  $ x: logi [1:3] TRUE TRUE TRUE
614s  $ w: num [1:3] 1 1 1
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s mode: logical, na.rm = TRUE
614s List of 2
614s  $ x: logi [1:3] TRUE TRUE TRUE
614s  $ w: num [1:3] 1 1 1
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s mode: logical, na.rm = FALSE
614s List of 2
614s  $ x: logi [1:3] TRUE TRUE TRUE
614s  $ w: num [1:3] NA 1 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: logical, na.rm = TRUE
614s List of 2
614s  $ x: logi [1:3] TRUE TRUE TRUE
614s  $ w: num [1:3] NA 1 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: logical, na.rm = FALSE
614s List of 2
614s  $ x: logi [1:3] TRUE TRUE TRUE
614s  $ w: num [1:3] 1 NA 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: logical, na.rm = TRUE
614s List of 2
614s  $ x: logi [1:3] TRUE TRUE TRUE
614s  $ w: num [1:3] 1 NA 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: integer, na.rm = FALSE
614s List of 2
614s  $ x: int [1:3] 1 1 1
614s  $ w: num [1:3] 1 1 1
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s mode: integer, na.rm = TRUE
614s List of 2
614s  $ x: int [1:3] 1 1 1
614s  $ w: num [1:3] 1 1 1
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s mode: integer, na.rm = FALSE
614s List of 2
614s  $ x: int [1:3] 1 1 1
614s  $ w: num [1:3] NA 1 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: integer, na.rm = TRUE
614s List of 2
614s  $ x: int [1:3] 1 1 1
614s  $ w: num [1:3] NA 1 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: integer, na.rm = FALSE
614s List of 2
614s  $ x: int [1:3] 1 1 1
614s  $ w: num [1:3] 1 NA 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: integer, na.rm = TRUE
614s List of 2
614s  $ x: int [1:3] 1 1 1
614s  $ w: num [1:3] 1 NA 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: double, na.rm = FALSE
614s List of 2
614s  $ x: num [1:3] 1 1 1
614s  $ w: num [1:3] 1 1 1
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s mode: double, na.rm = TRUE
614s List of 2
614s  $ x: num [1:3] 1 1 1
614s  $ w: num [1:3] 1 1 1
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s mode: double, na.rm = FALSE
614s List of 2
614s  $ x: num [1:3] 1 1 1
614s  $ w: num [1:3] NA 1 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: double, na.rm = TRUE
614s List of 2
614s  $ x: num [1:3] 1 1 1
614s  $ w: num [1:3] NA 1 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: double, na.rm = FALSE
614s List of 2
614s  $ x: num [1:3] 1 1 1
614s  $ w: num [1:3] 1 NA 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: double, na.rm = TRUE
614s List of 2
614s  $ x: num [1:3] 1 1 1
614s  $ w: num [1:3] 1 NA 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: logical, na.rm = FALSE
614s List of 2
614s  $ x: logi [1:3] NA TRUE TRUE
614s  $ w: num [1:3] 1 1 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: logical, na.rm = TRUE
614s List of 2
614s  $ x: logi [1:3] NA TRUE TRUE
614s  $ w: num [1:3] 1 1 1
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s mode: logical, na.rm = FALSE
614s List of 2
614s  $ x: logi [1:3] NA TRUE TRUE
614s  $ w: num [1:3] NA 1 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: logical, na.rm = TRUE
614s List of 2
614s  $ x: logi [1:3] NA TRUE TRUE
614s  $ w: num [1:3] NA 1 1
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s mode: logical, na.rm = FALSE
614s List of 2
614s  $ x: logi [1:3] NA TRUE TRUE
614s  $ w: num [1:3] 1 NA 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: logical, na.rm = TRUE
614s List of 2
614s  $ x: logi [1:3] NA TRUE TRUE
614s  $ w: num [1:3] 1 NA 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: integer, na.rm = FALSE
614s List of 2
614s  $ x: int [1:3] NA 1 1
614s  $ w: num [1:3] 1 1 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: integer, na.rm = TRUE
614s List of 2
614s  $ x: int [1:3] NA 1 1
614s  $ w: num [1:3] 1 1 1
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s mode: integer, na.rm = FALSE
614s List of 2
614s  $ x: int [1:3] NA 1 1
614s  $ w: num [1:3] NA 1 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: integer, na.rm = TRUE
614s List of 2
614s  $ x: int [1:3] NA 1 1
614s  $ w: num [1:3] NA 1 1
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s mode: integer, na.rm = FALSE
614s List of 2
614s  $ x: int [1:3] NA 1 1
614s  $ w: num [1:3] 1 NA 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: integer, na.rm = TRUE
614s List of 2
614s  $ x: int [1:3] NA 1 1
614s  $ w: num [1:3] 1 NA 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: double, na.rm = FALSE
614s List of 2
614s  $ x: num [1:3] NA 1 1
614s  $ w: num [1:3] 1 1 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: double, na.rm = TRUE
614s List of 2
614s  $ x: num [1:3] NA 1 1
614s  $ w: num [1:3] 1 1 1
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s mode: double, na.rm = FALSE
614s List of 2
614s  $ x: num [1:3] NA 1 1
614s  $ w: num [1:3] NA 1 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: double, na.rm = TRUE
614s List of 2
614s  $ x: num [1:3] NA 1 1
614s  $ w: num [1:3] NA 1 1
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s mode: double, na.rm = FALSE
614s List of 2
614s  $ x: num [1:3] NA 1 1
614s  $ w: num [1:3] 1 NA 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: double, na.rm = TRUE
614s List of 2
614s  $ x: num [1:3] NA 1 1
614s  $ w: num [1:3] 1 NA 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: logical, na.rm = FALSE
614s List of 2
614s  $ x: logi [1:3] NA TRUE TRUE
614s  $ w: num [1:3] 1 1 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: logical, na.rm = TRUE
614s List of 2
614s  $ x: logi [1:3] NA TRUE TRUE
614s  $ w: num [1:3] 1 1 1
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s mode: logical, na.rm = FALSE
614s List of 2
614s  $ x: logi [1:3] NA TRUE TRUE
614s  $ w: num [1:3] NA 1 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: logical, na.rm = TRUE
614s List of 2
614s  $ x: logi [1:3] NA TRUE TRUE
614s  $ w: num [1:3] NA 1 1
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s mode: logical, na.rm = FALSE
614s List of 2
614s  $ x: logi [1:3] NA TRUE TRUE
614s  $ w: num [1:3] 1 NA 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: logical, na.rm = TRUE
614s List of 2
614s  $ x: logi [1:3] NA TRUE TRUE
614s  $ w: num [1:3] 1 NA 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: integer, na.rm = FALSE
614s List of 2
614s  $ x: int [1:3] NA 1 1
614s  $ w: num [1:3] 1 1 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: integer, na.rm = TRUE
614s List of 2
614s  $ x: int [1:3] NA 1 1
614s  $ w: num [1:3] 1 1 1
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s mode: integer, na.rm = FALSE
614s List of 2
614s  $ x: int [1:3] NA 1 1
614s  $ w: num [1:3] NA 1 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: integer, na.rm = TRUE
614s List of 2
614s  $ x: int [1:3] NA 1 1
614s  $ w: num [1:3] NA 1 1
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s mode: integer, na.rm = FALSE
614s List of 2
614s  $ x: int [1:3] NA 1 1
614s  $ w: num [1:3] 1 NA 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: integer, na.rm = TRUE
614s List of 2
614s  $ x: int [1:3] NA 1 1
614s  $ w: num [1:3] 1 NA 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: double, na.rm = FALSE
614s List of 2
614s  $ x: num [1:3] NA 1 1
614s  $ w: num [1:3] 1 1 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: double, na.rm = TRUE
614s List of 2
614s  $ x: num [1:3] NA 1 1
614s  $ w: num [1:3] 1 1 1
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s mode: double, na.rm = FALSE
614s List of 2
614s  $ x: num [1:3] NA 1 1
614s  $ w: num [1:3] NA 1 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: double, na.rm = TRUE
614s List of 2
614s  $ x: num [1:3] NA 1 1
614s  $ w: num [1:3] NA 1 1
614s List of 2
614s  $ m0: num 1
614s  $ m1: num 1
614s mode: double, na.rm = FALSE
614s List of 2
614s  $ x: num [1:3] NA 1 1
614s  $ w: num [1:3] 1 NA 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s mode: double, na.rm = TRUE
614s List of 2
614s  $ x: num [1:3] NA 1 1
614s  $ w: num [1:3] 1 NA 1
614s List of 2
614s  $ m0: num NA
614s  $ m1: num NA
614s > 
614s 
614s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
614s Copyright (C) 2024 The R Foundation for Statistical Computing
614s Platform: arm-unknown-linux-gnueabihf (32-bit)
614s 
614s R is free software and comes with ABSOLUTELY NO WARRANTY.
614s You are welcome to redistribute it under certain conditions.
614s Type 'license()' or 'licence()' for distribution details.
614s 
614s R is a collaborative project with many contributors.
614s Type 'contributors()' for more information and
614s 'citation()' on how to cite R or R packages in publications.
614s 
614s Type 'demo()' for some demos, 'help()' for on-line help, or
614s 'help.start()' for an HTML browser interface to help.
614s Type 'q()' to quit R.
614s 
615s > library("matrixStats")
615s > 
615s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
615s > # Subsetted tests
615s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
615s > source("utils/validateIndicesFramework.R")
615s > for (mode in c("numeric", "integer")) {
615s +   x <- runif(6, min = -6, max = 6)
615s +   w <- runif(6, min = 0, max = 6)
615s +   storage.mode(x) <- mode
615s +   storage.mode(w) <- mode
615s +   if (mode == "numeric") w[1] <- Inf
615s + 
615s +   for (idxs in index_cases) {
615s +     validateIndicesTestVector_w(x, w, idxs,
615s +                                 ftest = weightedMean, fsure = weighted.mean,
615s +                                 na.rm = TRUE, refine = TRUE)
615s +     validateIndicesTestVector_w(x, w, idxs,
615s +                                 ftest = weightedMean, fsure = weighted.mean,
615s +                                 na.rm = FALSE, refine = TRUE)
615s +   }
615s + }
615s > 
615s 
615s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
615s Copyright (C) 2024 The R Foundation for Statistical Computing
615s Platform: arm-unknown-linux-gnueabihf (32-bit)
615s 
615s R is free software and comes with ABSOLUTELY NO WARRANTY.
615s You are welcome to redistribute it under certain conditions.
615s Type 'license()' or 'licence()' for distribution details.
615s 
615s R is a collaborative project with many contributors.
615s Type 'contributors()' for more information and
615s 'citation()' on how to cite R or R packages in publications.
615s 
615s Type 'demo()' for some demos, 'help()' for on-line help, or
615s 'help.start()' for an HTML browser interface to help.
615s Type 'q()' to quit R.
615s 
615s > library("matrixStats")
615s > 
615s > x <- 1:5
615s > y <- weightedMedian(x)
615s > y <- weightedMedian(x, w = c(NA, Inf, NA, Inf, NA), na.rm = TRUE)
615s > print(y)
615s [1] 3
615s > 
615s > y <- weightedMedian(x, w = c(NA, Inf, NA, Inf, NA), na.rm = FALSE)
615s > print(y)
615s [1] NA
615s > stopifnot(is.na(y))
615s > 
615s > x <- 1:10
615s > n <- length(x)
615s > 
615s > y1 <- median(x)                           # 5.5
615s > y2 <- weightedMedian(x)                   # 5.5
615s > stopifnot(all.equal(y1, y2))
615s > 
615s > 
615s > w <- rep(1, times = n)
615s > y1 <- weightedMedian(x, w)                 # 5.5 (default)
615s > y2a <- weightedMedian(x, ties = "weighted")  # 5.5 (default)
615s > y2b <- weightedMedian(x, ties = "min")       # 5
615s > y2c <- weightedMedian(x, ties = "max")       # 6
615s > stopifnot(all.equal(y2a, y1))
615s > 
615s > y3 <- weightedMedian(x, w)                # 5.5 (default)
615s > 
615s > 
615s > # Pull the median towards zero
615s > w[1] <- 5
615s > y1 <- weightedMedian(x, w)                # 3.5
615s > y <- c(rep(0, times = w[1]), x[-1])       # Only possible for integer weights
615s > y2 <- median(y)                           # 3.5
615s > stopifnot(all.equal(y1, y2))
615s > 
615s > # Put even more weight on the zero
615s > w[1] <- 8.5
615s > y <- weightedMedian(x, w)                # 2
615s > 
615s > # All weight on the first value
615s > w[1] <- Inf
615s > y <- weightedMedian(x, w)                # 1
615s > 
615s > # All weight on the last value
615s > w[1] <- 1
615s > w[n] <- Inf
615s > y <- weightedMedian(x, w)                # 10
615s > 
615s > # All weights set to zero
615s > w <- rep(0, times = n)
615s > y <- weightedMedian(x, w)                # NA
615s > 
615s > x <- 1:4
615s > w <- rep(1, times = 4)
615s > for (mode in c("integer", "double")) {
615s +   storage.mode(x) <- mode
615s +   for (ties in c("weighted", "mean", "min", "max")) {
615s +     cat(sprintf("ties = %s\n", ties))
615s +     y <- weightedMedian(x, w, ties = ties)
615s +   }
615s + }
615s ties = weighted
615s ties = mean
615s ties = min
615s ties = max
615s ties = weighted
615s ties = mean
615s ties = min
615s ties = max
615s > 
615s > set.seed(0x42)
615s > 
615s > y <- weightedMedian(x = double(0L))
615s > print(y)
615s [1] NA
615s > stopifnot(length(y) == 1L)
615s > stopifnot(is.na(y))
615s > 
615s > y <- weightedMedian(x = x[1])
615s > print(y)
615s [1] 1
615s > stopifnot(length(y) == 1L)
615s > stopifnot(all.equal(y, x[1]))
615s > 
615s > 
615s > n <- 1e3
615s > x <- runif(n)
615s > w <- runif(n, min = 0, max = 1)
615s > for (mode in c("integer", "double")) {
615s +   storage.mode(x) <- mode
615s +   for (ties in c("weighted", "mean", "min", "max")) {
615s +     y <- weightedMedian(x, w, ties = ties)
615s +     cat(sprintf("mode = %s, ties = %s, result = %g\n", mode, ties, y))
615s +   }
615s + }
615s mode = integer, ties = weighted, result = 0
615s mode = integer, ties = mean, result = 0
615s mode = integer, ties = min, result = 0
615s mode = integer, ties = max, result = 0
615s mode = double, ties = weighted, result = 0
615s mode = double, ties = mean, result = 0
615s mode = double, ties = min, result = 0
615s mode = double, ties = max, result = 0
615s > 
615s > 
615s > # A large vector
615s > n <- 1e5
615s > x <- runif(n)
615s > w <- runif(n, min = 0, max = 1)
615s > y <- weightedMedian(x, w)
615s > 
615s > y <- weightedMedian(x, w, ties = "min")
615s > 
615s > 
615s > # Single Number
615s > xs <- c(1, NA_integer_)
615s > ws <- c(1, NA_integer_)
615s > for (x in xs) {
615s +   for (w in ws) {
615s +     y <- weightedMedian(x = x, w = w)
615s +     if (is.na(w)) z <- NA_real_
615s +     else z <- x[1]
615s +     stopifnot(all.equal(y, z))
615s +   }
615s + }
615s > 
615s > ## Logical
615s > x1 <- c(TRUE, FALSE, TRUE)
615s > w0 <- c(0, 0, 0)
615s > stopifnot(!is.finite(weightedMedian(x1, w0)),
615s +           !is.infinite(weightedMedian(x1, w0)))
615s > 
615s > w1 <- c(1, 1, 1)
615s > stopifnot(weightedMedian(x1, w1) == 1)
615s > 
615s > w2 <- c(1, 2, 3)
615s > stopifnot(weightedMedian(x1, w2) == 1)
615s > 
615s > ### NA
615s > stopifnot(is.na(weightedMedian(c(TRUE, FALSE, NA),
615s +                                c(1, 2, 3))),
615s +           all.equal(weightedMedian(c(TRUE, FALSE, NA),
615s +                                    c(1, 2, 3),
615s +                                    na.rm = TRUE),
615s +                     weightedMedian(c(TRUE, FALSE),
615s +                                    c(1, 2))))
615s > ### Identical to as.integer()
615s > x <- rcauchy(100)
615s > w <- abs(rcauchy(100))
615s > stopifnot(all.equal(weightedMedian(x > 0, w),
615s +                     weightedMedian(as.integer(x > 0), w)))
615s > 
615s > 
615s > 
616s 
616s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
616s Copyright (C) 2024 The R Foundation for Statistical Computing
616s Platform: arm-unknown-linux-gnueabihf (32-bit)
616s 
616s R is free software and comes with ABSOLUTELY NO WARRANTY.
616s You are welcome to redistribute it under certain conditions.
616s Type 'license()' or 'licence()' for distribution details.
616s 
616s R is a collaborative project with many contributors.
616s Type 'contributors()' for more information and
616s 'citation()' on how to cite R or R packages in publications.
616s 
616s Type 'demo()' for some demos, 'help()' for on-line help, or
616s 'help.start()' for an HTML browser interface to help.
616s Type 'q()' to quit R.
616s 
616s > library("matrixStats")
616s > 
616s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
616s > # Subsetted tests
616s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
616s > source("utils/validateIndicesFramework.R")
616s > for (mode in c("numeric", "integer")) {
616s +   x <- runif(6, min = -6, max = 6)
616s +   w <- runif(6, min = 0, max = 6)
616s +   storage.mode(x) <- mode
616s +   storage.mode(w) <- mode
616s +   if (mode == "numeric") w[1] <- Inf
616s + 
616s +   for (idxs in index_cases) {
616s +     validateIndicesTestVector_w(x, w, idxs,
616s +                                 ftest = weightedMedian,
616s +                                 fsure = weightedMedian,
616s +                                 na.rm = TRUE)
616s +     validateIndicesTestVector_w(x, w, idxs,
616s +                                 ftest = weightedMedian,
616s +                                 fsure = weightedMedian,
616s +                                 na.rm = FALSE)
616s + 
616s +     for (ties in c("weighted", "mean", "min", "max")) {
616s +       validateIndicesTestVector_w(x, w, idxs,
616s +                                   ftest = weightedMedian,
616s +                                   fsure = weightedMedian,
616s +                                   na.rm = TRUE, ties = ties)
616s +       validateIndicesTestVector_w(x, w, idxs,
616s +                                   ftest = weightedMedian,
616s +                                   fsure = weightedMedian,
616s +                                   na.rm = FALSE, ties = ties)
616s +     }
616s +   }
616s + }
616s > 
616s 
616s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
616s Copyright (C) 2024 The R Foundation for Statistical Computing
616s Platform: arm-unknown-linux-gnueabihf (32-bit)
616s 
616s R is free software and comes with ABSOLUTELY NO WARRANTY.
616s You are welcome to redistribute it under certain conditions.
616s Type 'license()' or 'licence()' for distribution details.
616s 
616s R is a collaborative project with many contributors.
616s Type 'contributors()' for more information and
616s 'citation()' on how to cite R or R packages in publications.
616s 
616s Type 'demo()' for some demos, 'help()' for on-line help, or
616s 'help.start()' for an HTML browser interface to help.
616s Type 'q()' to quit R.
616s 
617s > library("matrixStats")
617s > 
617s > weightedVar_R <- function(x, w) {
617s +   mu <- weighted.mean(x, w = w)
617s +   sum(w * (x - mu) ^ 2) / (sum(w) - 1)
617s + }
617s > 
617s > 
617s > n <- 10
617s > x <- as.double(1:n)
617s > 
617s > message("*** weightedVar() ...")
617s > 
617s > message("- Zero elements")
617s *** weightedVar() ...
617s > m0 <- var(integer(0))
617s > m1 <- weightedVar(integer(0), w = integer(0))
617s > str(list(m0 = m0, m1 = m1))
617s - Zero elements
617s List of 2
617s  $ m0: num NA
617s  $ m1: int NA
617s > stopifnot(all.equal(m1, m0))
617s > 
617s > 
617s > message("- One elements")
617s > m0 <- var(1)
617s > m1 <- weightedVar(1)
617s > str(list(m0 = m0, m1 = m1))
617s List of 2
617s  $ m0:- One elements
617s  num NA
617s  $ m1:- Uniform weights (all w = 1)
617s  num NA
617s > stopifnot(all.equal(m1, m0))
617s > 
617s > 
617s > message("- Uniform weights (all w = 1)")
617s > m0 <- var(x)
617s > w <- rep(1, times = n)
617s > m1 <- weightedVar(x, w = w)
617s > str(list(m0 = m0, m1 = m1))
617s List of 2
617s - Uniform weights (all w = 3)
617s - Uniform weights on the first five elements
617s - Uniform weights on every second elements
617s  $ m0: num 9.17
617s  $ m1: num 9.17
617s > stopifnot(all.equal(m1, m0))
617s > 
617s > 
617s > message("- Uniform weights (all w = 3)")
617s > m0 <- var(rep(x, each = 3))
617s > w <- rep(3, times = n)
617s > m1 <- weightedVar(x, w = w)
617s > str(list(m0 = m0, m1 = m1))
617s List of 2
617s  $ m0: num 8.53
617s  $ m1: num 8.53
617s > stopifnot(all.equal(m1, m0))
617s > 
617s > 
617s > message("- Uniform weights on the first five elements")
617s > idxs <- 1:5
617s > m0 <- var(x[1:5])
617s > w <- rep(0, times = n)
617s > w[idxs] <- 1
617s > m1 <- weightedVar(x, w = w)
617s > str(list(m0 = m0, m1 = m1))
617s List of 2
617s  $ m0: num 2.5
617s  $ m1: num 2.5
617s > stopifnot(all.equal(m1, m0))
617s > 
617s > 
617s > message("- Uniform weights on every second elements")
617s > idxs <- seq(from = 1, to = n, by = 2)
617s > m0 <- var(x[idxs])
617s > w <- rep(0, times = n)
617s > w[idxs] <- 1
617s > m1 <- weightedVar(x, w = w)
617s > str(list(m0 = m0, m1 = m1))
617s List of 2
617s  $ m0:- All weights are zero
617s  num 10
617s  $ m1: num 10
617s - Infinite weight on first element
617s - Missing-value weight on first element
617s > stopifnot(all.equal(m1, m0))
617s > 
617s > 
617s > message("- All weights are zero")
617s > idxs <- integer(0L)
617s > m0 <- var(x[idxs])
617s > w <- rep(0, times = n)
617s > w[idxs] <- 1
617s > m1 <- weightedVar(x, w = w)
617s > str(list(m0 = m0, m1 = m1))
617s List of 2
617s  $ m0: num NA
617s  $ m1: num NA
617s > stopifnot(all.equal(m1, m0))
617s > 
617s > message("- Infinite weight on first element")
617s > idxs <- 1L
617s > m0 <- var(x[idxs])
617s > w <- rep(0, times = n)
617s > w[idxs] <- Inf
617s > m1 <- weightedVar(x, w = w)
617s > str(list(m0 = m0, m1 = m1))
617s List of 2
617s  $ m0: num NA
617s  $ m1: num NA
617s > stopifnot(all.equal(m1, m0))
617s > 
617s > message("- Missing-value weight on first element")
617s > idxs <- 1L
617s > w <- rep(1, times = n)
617s > w[idxs] <- NA_real_
617s > m1 <- weightedVar(x, w = w)
617s > str(list(m1 = m1))
617s List of 1
617s  $ m1: num NA
617s > stopifnot(identical(m1, NA_real_))
617s > 
617s > 
617s > message("- Frequency weights")
617s > 
617s > ## From https://en.wikipedia.org/wiki/Weighted_arithmetic_mean
617s > y <-  c(2, 2, 4, 5, 5, 5)
617s > x <- unique(y)
617s > w <- table(y)
617s > stopifnot(names(w) == x)
617s > 
617s > m0 <- weightedVar(x, w = w)
617s > m1 <- var(y)
617s > stopifnot(all.equal(m1, m0))
617s > m2 <- weightedVar(x, w = w)
617s > str(list(m0 = m0, m1 = m1, m2 = m2))
617s List of 3
617s  $ m0: num 2.17
617s  $ m1:- Frequency weights
617s  num 2.17
617s  $ m2: num 2.17
617s > stopifnot(all.equal(m2, m0))
617s > 
617s > ## From https://github.com/HenrikBengtsson/matrixStats/issues/72
617s > large <- c(21, 8, 26, 1, 15, 33, 12, 25, 0, 84)
617s > years <- c(41706, 9301, 33678, 3082, 27040, 44188, 10049, 30591, 2275, 109831)
617s > 
617s > m0 <- weightedVar(large, w = years)
617s > m1 <- weightedVar(large, w = years)
617s > str(list(m0 = m0, m1 = m1))
617s List of 2
617s  $ m0: num 899
617s *** weightedVar() ... DONE
617s  $ m1: num 899
617s > stopifnot(all.equal(m1, m0))
617s > 
617s > message("*** weightedVar() ... DONE")
617s > 
617s 
617s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
617s Copyright (C) 2024 The R Foundation for Statistical Computing
617s Platform: arm-unknown-linux-gnueabihf (32-bit)
617s 
617s R is free software and comes with ABSOLUTELY NO WARRANTY.
617s You are welcome to redistribute it under certain conditions.
617s Type 'license()' or 'licence()' for distribution details.
617s 
617s R is a collaborative project with many contributors.
617s Type 'contributors()' for more information and
617s 'citation()' on how to cite R or R packages in publications.
617s 
617s Type 'demo()' for some demos, 'help()' for on-line help, or
617s 'help.start()' for an HTML browser interface to help.
617s Type 'q()' to quit R.
617s 
617s > library("matrixStats")
617s > 
617s > fcns <- list(
617s +   weightedVar = weightedVar,
617s +   weightedSd  = weightedSd,
617s +   weightedMad = weightedMad
617s + )
617s > 
617s > for (name in names(fcns)) {
617s +   cat(sprintf("%s()...\n", name))
617s +   fcn <- fcns[[name]]
617s + 
617s +   for (mode in c("integer", "double")) {
617s +     cat("mode: ", mode, "\n", sep = "")
617s +     n <- 15L
617s +     x <- runif(n, min = -5, max = 5)
617s +     storage.mode(x) <- mode
617s +     str(x)
617s + 
617s +     for (add_na in c(FALSE, TRUE)) {
617s +       cat("add_na: ", add_na, "\n", sep = "")
617s +       if (add_na) {
617s +         x[c(5, 7)] <- NA
617s +       }
617s +       str(x)
617s + 
617s +       for (na.rm in c(FALSE, TRUE)) {
617s +         cat("na.rm: ", na.rm, "\n", sep = "")
617s + 
617s +         cat("Weights are not specified (all are 1)\n")
617s +         m1 <- fcn(x, na.rm = na.rm)
617s +         str(list(m1 = m1))
617s + 
617s +         cat("All weights are 1\n")
617s +         w <- rep(1, times = n)
617s +         m1 <- fcn(x, w, na.rm = na.rm)
617s +         str(list(m1 = m1))
617s + 
617s +         cat("First weight is 5\n")
617s +         # Pull the mean towards zero
617s +         w[1] <- 5
617s +         str(w)
617s +         m1 <- fcn(x, w, na.rm = na.rm)
617s +         str(list(m1 = m1))
617s + 
617s +         cat("All weights are 0\n")
617s +         # All weights set to zero
617s +         w <- rep(0, times = n)
617s +         m1 <- fcn(x, w, na.rm = na.rm)
617s +         str(list(m1 = m1))
617s + 
617s +         cat("First weight is 8.5\n")
617s +         # Put even more weight on the zero
617s +         w[1] <- 8.5
617s +         m1 <- fcn(x, w, na.rm = na.rm)
617s +         str(list(m1 = m1))
617s + 
617s +         cat("First weight is Inf\n")
617s +         # All weight on the first value
617s +         w[1] <- Inf
617s +         m1 <- fcn(x, w, na.rm = na.rm)
617s +         str(list(m1 = m1))
617s + 
617s +         cat("Last weight is Inf\n")
617s +         # All weight on the last value
617s +         w[1] <- 1
617s +         w[n] <- Inf
617s +         m1 <- fcn(x, w, na.rm = na.rm)
617s +         str(list(m1 = m1))
617s + 
617s +         cat("Last weight is NA\n")
617s +         # All weight on the last value
617s +         w[1] <- 1
617s +         w[n] <- NA_real_
617s +         m1 <- fcn(x, w, na.rm = na.rm)
617s +         str(list(m1 = m1))
617s +       } # for (na.rm ...)
617s +     } # for (add_na ...)
617s +   } # for (mode ...)
617s + 
617s +   cat(sprintf("%s()...DONE\n", name))
617s + } # for (name ...)
617s weightedVar()...
617s mode: integer
617s  int [1:15] 0 0 2 -4 -3 -4 2 0 -3 0 ...
617s add_na: FALSE
617s  int [1:15] 0 0 2 -4 -3 -4 2 0 -3 0 ...
617s na.rm: FALSE
617s Weights are not specified (all are 1)
617s List of 1
617s  $ m1: num 7.24
617s All weights are 1
617s List of 1
617s  $ m1: num 7.24
617s First weight is 5
617s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
617s List of 1
617s  $ m1: num 5.71
617s All weights are 0
617s List of 1
617s  $ m1: int NA
617s First weight is 8.5
617s List of 1
617s  $ m1: int NA
617s First weight is Inf
617s List of 1
617s  $ m1: int NA
617s Last weight is Inf
617s List of 1
617s  $ m1: int NA
617s Last weight is NA
617s List of 1
617s  $ m1: int NA
617s na.rm: TRUE
617s Weights are not specified (all are 1)
617s List of 1
617s  $ m1: num 7.24
617s All weights are 1
617s List of 1
617s  $ m1: num 7.24
617s First weight is 5
617s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
617s List of 1
617s  $ m1: num 5.71
617s All weights are 0
617s List of 1
617s  $ m1: int NA
617s First weight is 8.5
617s List of 1
617s  $ m1: int NA
617s First weight is Inf
617s List of 1
617s  $ m1: int NA
617s Last weight is Inf
617s List of 1
617s  $ m1: int NA
617s Last weight is NA
617s List of 1
617s  $ m1: int NA
617s add_na: TRUE
617s  int [1:15] 0 0 2 -4 NA -4 NA 0 -3 0 ...
617s na.rm: FALSE
617s Weights are not specified (all are 1)
617s List of 1
617s  $ m1: int NA
617s All weights are 1
617s List of 1
617s  $ m1: int NA
617s First weight is 5
617s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
617s List of 1
617s  $ m1: int NA
617s All weights are 0
617s List of 1
617s  $ m1: int NA
617s First weight is 8.5
617s List of 1
617s  $ m1: int NA
617s First weight is Inf
617s List of 1
617s  $ m1: int NA
617s Last weight is Inf
617s List of 1
617s  $ m1: int NA
617s Last weight is NA
617s List of 1
617s  $ m1: int NA
617s na.rm: TRUE
617s Weights are not specified (all are 1)
617s List of 1
617s  $ m1: num 7.4
617s All weights are 1
617s List of 1
617s  $ m1: num 7.4
617s First weight is 5
617s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
617s List of 1
617s  $ m1: num 5.64
617s All weights are 0
617s List of 1
617s  $ m1: int NA
617s First weight is 8.5
617s List of 1
617s  $ m1: int NA
617s First weight is Inf
617s List of 1
617s  $ m1: int NA
617s Last weight is Inf
617s List of 1
617s  $ m1: int NA
617s Last weight is NA
617s List of 1
617s  $ m1: int NA
617s mode: double
617s  num [1:15] -0.259 3.368 2.272 -2.357 1.886 ...
617s add_na: FALSE
617s  num [1:15] -0.259 3.368 2.272 -2.357 1.886 ...
617s na.rm: FALSE
617s Weights are not specified (all are 1)
617s List of 1
617s  $ m1: num 8.96
617s All weights are 1
617s List of 1
617s  $ m1: num 8.96
617s First weight is 5
617s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
617s List of 1
617s  $ m1: num 6.97
617s All weights are 0
617s List of 1
617s  $ m1: num NA
617s First weight is 8.5
617s List of 1
618s  $ m1: num NA
618s First weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is NA
618s List of 1
618s  $ m1: num NA
618s na.rm: TRUE
618s Weights are not specified (all are 1)
618s List of 1
618s  $ m1: num 8.96
618s All weights are 1
618s List of 1
618s  $ m1: num 8.96
618s First weight is 5
618s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
618s List of 1
618s  $ m1: num 6.97
618s All weights are 0
618s List of 1
618s  $ m1: num NA
618s First weight is 8.5
618s List of 1
618s  $ m1: num NA
618s First weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is NA
618s List of 1
618s  $ m1: num NA
618s add_na: TRUE
618s  num [1:15] -0.259 3.368 2.272 -2.357 NA ...
618s na.rm: FALSE
618s Weights are not specified (all are 1)
618s List of 1
618s  $ m1: num NA
618s All weights are 1
618s List of 1
618s  $ m1: num NA
618s First weight is 5
618s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
618s List of 1
618s  $ m1: num NA
618s All weights are 0
618s List of 1
618s  $ m1: num NA
618s First weight is 8.5
618s List of 1
618s  $ m1: num NA
618s First weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is NA
618s List of 1
618s  $ m1: num NA
618s na.rm: TRUE
618s Weights are not specified (all are 1)
618s List of 1
618s  $ m1: num 8.89
618s All weights are 1
618s List of 1
618s  $ m1: num 8.89
618s First weight is 5
618s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
618s List of 1
618s  $ m1: num 6.69
618s All weights are 0
618s List of 1
618s  $ m1: num NA
618s First weight is 8.5
618s List of 1
618s  $ m1: num NA
618s First weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is NA
618s List of 1
618s  $ m1: num NA
618s weightedVar()...DONE
618s weightedSd()...
618s mode: integer
618s  int [1:15] -3 -2 4 -4 2 -2 -1 -2 3 -4 ...
618s add_na: FALSE
618s  int [1:15] -3 -2 4 -4 2 -2 -1 -2 3 -4 ...
618s na.rm: FALSE
618s Weights are not specified (all are 1)
618s List of 1
618s  $ m1: num 2.61
618s All weights are 1
618s List of 1
618s  $ m1: num 2.61
618s First weight is 5
618s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
618s List of 1
618s  $ m1: num 2.4
618s All weights are 0
618s List of 1
618s  $ m1: num NA
618s First weight is 8.5
618s List of 1
618s  $ m1: num NA
618s First weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is NA
618s List of 1
618s  $ m1: num NA
618s na.rm: TRUE
618s Weights are not specified (all are 1)
618s List of 1
618s  $ m1: num 2.61
618s All weights are 1
618s List of 1
618s  $ m1: num 2.61
618s First weight is 5
618s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
618s List of 1
618s  $ m1: num 2.4
618s All weights are 0
618s List of 1
618s  $ m1: num NA
618s First weight is 8.5
618s List of 1
618s  $ m1: num NA
618s First weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is NA
618s List of 1
618s  $ m1: num NA
618s add_na: TRUE
618s  int [1:15] -3 -2 4 -4 NA -2 NA -2 3 -4 ...
618s na.rm: FALSE
618s Weights are not specified (all are 1)
618s List of 1
618s  $ m1: num NA
618s All weights are 1
618s List of 1
618s  $ m1: num NA
618s First weight is 5
618s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
618s List of 1
618s  $ m1: num NA
618s All weights are 0
618s List of 1
618s  $ m1: num NA
618s First weight is 8.5
618s List of 1
618s  $ m1: num NA
618s First weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is NA
618s List of 1
618s  $ m1: num NA
618s na.rm: TRUE
618s Weights are not specified (all are 1)
618s List of 1
618s  $ m1: num 2.63
618s All weights are 1
618s List of 1
618s  $ m1: num 2.63
618s First weight is 5
618s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
618s List of 1
618s  $ m1: num 2.36
618s All weights are 0
618s List of 1
618s  $ m1: num NA
618s First weight is 8.5
618s List of 1
618s  $ m1: num NA
618s First weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is NA
618s List of 1
618s  $ m1: num NA
618s mode: double
618s  num [1:15] -4.18 4.28 -2.42 1 2.87 ...
618s add_na: FALSE
618s  num [1:15] -4.18 4.28 -2.42 1 2.87 ...
618s na.rm: FALSE
618s Weights are not specified (all are 1)
618s List of 1
618s  $ m1: num 3.12
618s All weights are 1
618s List of 1
618s  $ m1: num 3.12
618s First weight is 5
618s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
618s List of 1
618s  $ m1: num 3.18
618s All weights are 0
618s List of 1
618s  $ m1: num NA
618s First weight is 8.5
618s List of 1
618s  $ m1: num NA
618s First weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is NA
618s List of 1
618s  $ m1: num NA
618s na.rm: TRUE
618s Weights are not specified (all are 1)
618s List of 1
618s  $ m1: num 3.12
618s All weights are 1
618s List of 1
618s  $ m1: num 3.12
618s First weight is 5
618s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
618s List of 1
618s  $ m1: num 3.18
618s All weights are 0
618s List of 1
618s  $ m1: num NA
618s First weight is 8.5
618s List of 1
618s  $ m1: num NA
618s First weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is NA
618s List of 1
618s  $ m1: num NA
618s add_na: TRUE
618s  num [1:15] -4.18 4.28 -2.42 1 NA ...
618s na.rm: FALSE
618s Weights are not specified (all are 1)
618s List of 1
618s  $ m1: num NA
618s All weights are 1
618s List of 1
618s  $ m1: num NA
618s First weight is 5
618s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
618s List of 1
618s  $ m1: num NA
618s All weights are 0
618s List of 1
618s  $ m1: num NA
618s First weight is 8.5
618s List of 1
618s  $ m1: num NA
618s First weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is NA
618s List of 1
618s  $ m1: num NA
618s na.rm: TRUE
618s Weights are not specified (all are 1)
618s List of 1
618s  $ m1: num 3.2
618s All weights are 1
618s List of 1
618s  $ m1: num 3.2
618s First weight is 5
618s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
618s List of 1
618s  $ m1: num 3.17
618s All weights are 0
618s List of 1
618s  $ m1: num NA
618s First weight is 8.5
618s List of 1
618s  $ m1: num NA
618s First weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is Inf
618s List of 1
618s  $ m1: num NA
618s Last weight is NA
618s List of 1
618s  $ m1: num NA
618s weightedSd()...DONE
618s weightedMad()...
618s mode: integer
618s  int [1:15] -1 0 -3 -1 2 -3 4 1 3 4 ...
618s add_na: FALSE
618s  int [1:15] -1 0 -3 -1 2 -3 4 1 3 4 ...
618s na.rm: FALSE
618s Weights are not specified (all are 1)
618s List of 1
618s  $ m1: num 1.48
618s All weights are 1
618s List of 1
618s  $ m1: num 1.48
618s First weight is 5
618s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
618s List of 1
618s  $ m1: num 1.48
618s All weights are 0
618s List of 1
618s  $ m1: int NA
618s First weight is 8.5
618s List of 1
618s  $ m1: int 0
618s First weight is Inf
618s List of 1
618s  $ m1: int 0
618s Last weight is Inf
618s List of 1
618s  $ m1: int 0
618s Last weight is NA
618s List of 1
618s  $ m1: int NA
618s na.rm: TRUE
618s Weights are not specified (all are 1)
618s List of 1
618s  $ m1: num 1.48
618s All weights are 1
618s List of 1
618s  $ m1: num 1.48
618s First weight is 5
618s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
618s List of 1
618s  $ m1: num 1.48
618s All weights are 0
618s List of 1
618s  $ m1: int NA
618s First weight is 8.5
618s List of 1
618s  $ m1: int 0
618s First weight is Inf
618s List of 1
618s  $ m1: int 0
618s Last weight is Inf
618s List of 1
618s  $ m1: int 0
618s Last weight is NA
618s List of 1
618s  $ m1: int NA
618s add_na: TRUE
618s  int [1:15] -1 0 -3 -1 NA -3 NA 1 3 4 ...
618s na.rm: FALSE
618s Weights are not specified (all are 1)
618s List of 1
618s  $ m1: num NA
618s All weights are 1
618s List of 1
618s  $ m1: int NA
618s First weight is 5
618s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
618s List of 1
618s  $ m1: int NA
618s All weights are 0
618s List of 1
618s  $ m1: int NA
618s First weight is 8.5
618s List of 1
618s  $ m1: int 0
618s First weight is Inf
618s List of 1
618s  $ m1: int 0
618s Last weight is Inf
618s List of 1
618s  $ m1: int 0
618s Last weight is NA
618s List of 1
618s  $ m1: int NA
618s na.rm: TRUE
618s Weights are not specified (all are 1)
618s List of 1
618s  $ m1: num 1.48
618s All weights are 1
618s List of 1
618s  $ m1: num 1.48
618s First weight is 5
618s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
618s List of 1
618s  $ m1: num 1.48
618s All weights are 0
618s List of 1
618s  $ m1: int NA
618s First weight is 8.5
618s List of 1
618s  $ m1: int 0
618s First weight is Inf
618s List of 1
618s  $ m1: int 0
618s Last weight is Inf
618s List of 1
618s  $ m1: int 0
618s Last weight is NA
618s List of 1
618s  $ m1: int NA
618s mode: double
618s  num [1:15] -2.29 2.99 3.58 2.94 -1.72 ...
618s add_na: FALSE
618s  num [1:15] -2.29 2.99 3.58 2.94 -1.72 ...
618s na.rm: FALSE
618s Weights are not specified (all are 1)
618s List of 1
618s  $ m1: num 2.69
618s All weights are 1
618s List of 1
618s  $ m1: num 2.69
618s First weight is 5
618s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
618s List of 1
618s  $ m1: num 3.85
618s All weights are 0
618s List of 1
618s  $ m1: num NA
618s First weight is 8.5
618s List of 1
618s  $ m1: num 0
618s First weight is Inf
618s List of 1
618s  $ m1: num 0
618s Last weight is Inf
618s List of 1
618s  $ m1: num 0
618s Last weight is NA
618s List of 1
618s  $ m1: num NA
618s na.rm: TRUE
618s Weights are not specified (all are 1)
618s List of 1
618s  $ m1: num 2.69
618s All weights are 1
618s List of 1
618s  $ m1: num 2.69
618s First weight is 5
618s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
618s List of 1
618s  $ m1: num 3.85
618s All weights are 0
618s List of 1
618s  $ m1: num NA
618s First weight is 8.5
618s List of 1
618s  $ m1: num 0
618s First weight is Inf
618s List of 1
618s  $ m1: num 0
618s Last weight is Inf
618s List of 1
618s  $ m1: num 0
618s Last weight is NA
618s List of 1
618s  $ m1: num NA
618s add_na: TRUE
618s  num [1:15] -2.29 2.99 3.58 2.94 NA ...
618s na.rm: FALSE
618s Weights are not specified (all are 1)
618s List of 1
618s  $ m1: num NA
618s All weights are 1
618s List of 1
618s  $ m1: num NA
618s First weight is 5
618s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
618s List of 1
618s  $ m1: num NA
618s All weights are 0
618s List of 1
618s  $ m1: num NA
618s First weight is 8.5
618s List of 1
618s  $ m1: num 0
618s First weight is Inf
618s List of 1
618s  $ m1: num 0
618s Last weight is Inf
618s List of 1
618s  $ m1: num 0
618s Last weight is NA
618s List of 1
618s  $ m1: num NA
618s na.rm: TRUE
618s Weights are not specified (all are 1)
618s List of 1
618s  $ m1: num 1.8
618s All weights are 1
618s List of 1
618s  $ m1: num 1.8
618s First weight is 5
618s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
618s List of 1
618s  $ m1: num 3.98
618s All weights are 0
618s List of 1
618s  $ m1: num NA
618s First weight is 8.5
618s List of 1
618s  $ m1: num 0
618s First weight is Inf
618s List of 1
618s  $ m1: num 0
618s Last weight is Inf
618s List of 1
618s  $ m1: num 0
618s Last weight is NA
618s List of 1
618s  $ m1: num NA
618s weightedMad()...DONE
618s > 
618s 
618s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
618s Copyright (C) 2024 The R Foundation for Statistical Computing
618s Platform: arm-unknown-linux-gnueabihf (32-bit)
618s 
618s R is free software and comes with ABSOLUTELY NO WARRANTY.
618s You are welcome to redistribute it under certain conditions.
618s Type 'license()' or 'licence()' for distribution details.
618s 
618s R is a collaborative project with many contributors.
618s Type 'contributors()' for more information and
618s 'citation()' on how to cite R or R packages in publications.
618s 
618s Type 'demo()' for some demos, 'help()' for on-line help, or
618s 'help.start()' for an HTML browser interface to help.
618s Type 'q()' to quit R.
618s 
618s > library("matrixStats")
618s > 
618s > fcns <- list(
618s +   weightedVar = weightedVar,
618s +   weightedSd  = weightedSd,
618s +   weightedMad = weightedMad
618s + )
618s > 
618s > 
618s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
618s > # Subsetted tests
618s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
618s > source("utils/validateIndicesFramework.R")
618s > for (name in names(fcns)) {
618s +   cat(sprintf("subsetted tests on %s()...\n", name))
618s +   fcn <- fcns[[name]]
618s + 
618s +   for (mode in c("numeric", "integer")) {
618s +     x <- runif(6, min = -6, max = 6)
618s +     w <- runif(6, min = 0, max = 6)
618s +     storage.mode(x) <- mode
618s +     storage.mode(w) <- mode
618s +     if (mode == "numeric") w[1] <- Inf
618s + 
618s +     for (idxs in index_cases) {
618s +       validateIndicesTestVector_w(x, w, idxs,
618s +                                   ftest = fcn, fsure = fcn,
618s +                                   na.rm = TRUE)
618s +       validateIndicesTestVector_w(x, w, idxs,
618s +                                   ftest = fcn, fsure = fcn,
618s +                                   na.rm = FALSE)
618s +     }
618s +   }
618s +   cat(sprintf("%s()...DONE\n", name))
618s + }
618s subsetted tests on weightedVar()...
618s weightedVar()...DONE
618s subsetted tests on weightedSd()...
619s weightedSd()...DONE
619s subsetted tests on weightedMad()...
619s weightedMad()...DONE
619s > 
619s 
619s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
619s Copyright (C) 2024 The R Foundation for Statistical Computing
619s Platform: arm-unknown-linux-gnueabihf (32-bit)
619s 
619s R is free software and comes with ABSOLUTELY NO WARRANTY.
619s You are welcome to redistribute it under certain conditions.
619s Type 'license()' or 'licence()' for distribution details.
619s 
619s R is a collaborative project with many contributors.
619s Type 'contributors()' for more information and
619s 'citation()' on how to cite R or R packages in publications.
619s 
619s Type 'demo()' for some demos, 'help()' for on-line help, or
619s 'help.start()' for an HTML browser interface to help.
619s Type 'q()' to quit R.
619s 
619s > library("matrixStats")
619s > 
619s > x_OP_y_R <- function(x, y, OP, na.rm = FALSE) {
619s +   if (na.rm) {
619s +     xnok <- is.na(x)
619s +     ynok <- is.na(y)
619s +     anok <- xnok & ynok
619s +     unit <- switch(OP,
619s +       "+" = 0,
619s +       "-" = NA_real_,
619s +       "*" = 1,
619s +       "/" = NA_real_,
619s +       stop("Unknown 'OP' operator: ", OP)
619s +     )
619s +     x[xnok] <- unit
619s +     y[ynok] <- unit
619s +   }
619s + 
619s +   ans <- switch(OP,
619s +     "+" = x + y,
619s +     "-" = x - y,
619s +     "*" = x * y,
619s +     "/" = x / y,
619s +     stop("Unknown 'OP' operator: ", OP)
619s +   )
619s + 
619s +   if (na.rm) {
619s +     ans[anok] <- NA_real_
619s +   }
619s + 
619s +   ans
619s + } # x_OP_y_R()
619s > 
619s > 
619s > 
619s > t_tx_OP_y_R <- function(x, y, OP, na.rm = FALSE) {
619s +   t(x_OP_y_R(x = t(x), y = y, OP = OP, na.rm = na.rm))
619s + }
619s > 
619s > 
619s > 
619s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
619s > # No missing values
619s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
619s > x <- matrix(1:16, nrow = 4, ncol = 4)
619s > y <- 1:nrow(x)
619s > storage.mode(y) <- storage.mode(x)
619s > 
619s > for (OP in c("+", "-", "*", "/")) {
619s +   for (na.rm in c(FALSE, TRUE)) {
619s +     cat(sprintf("OP = '%s', na.rm = %s\n", OP, na.rm))
619s + 
619s +     a0 <- x_OP_y_R(x, y, OP, na.rm = na.rm)
619s +     a1 <- x_OP_y(x, y, OP, na.rm = na.rm)
619s +     str(a1)
619s +     stopifnot(all.equal(a1, a0))
619s + 
619s +     b0 <- t_tx_OP_y_R(x, y, OP, na.rm = na.rm)
619s +     b1 <- t_tx_OP_y(x, y, OP, na.rm = na.rm)
619s +     str(b1)
619s +     stopifnot(all.equal(b1, b0))
619s +   }
619s + }
619s OP = '+', na.rm = FALSE
619s  int [1:4, 1:4] 2 4 6 8 6 8 10 12 10 12 ...
619s  int [1:4, 1:4] 2 3 4 5 7 8 9 10 12 13 ...
619s OP = '+', na.rm = TRUE
619s  int [1:4, 1:4] 2 4 6 8 6 8 10 12 10 12 ...
619s  int [1:4, 1:4] 2 3 4 5 7 8 9 10 12 13 ...
619s OP = '-', na.rm = FALSE
619s  int [1:4, 1:4] 0 0 0 0 4 4 4 4 8 8 ...
619s  int [1:4, 1:4] 0 1 2 3 3 4 5 6 6 7 ...
619s OP = '-', na.rm = TRUE
619s  int [1:4, 1:4] 0 0 0 0 4 4 4 4 8 8 ...
619s  int [1:4, 1:4] 0 1 2 3 3 4 5 6 6 7 ...
619s OP = '*', na.rm = FALSE
619s  int [1:4, 1:4] 1 4 9 16 5 12 21 32 9 20 ...
619s  int [1:4, 1:4] 1 2 3 4 10 12 14 16 27 30 ...
619s OP = '*', na.rm = TRUE
619s  int [1:4, 1:4] 1 4 9 16 5 12 21 32 9 20 ...
619s  int [1:4, 1:4] 1 2 3 4 10 12 14 16 27 30 ...
619s OP = '/', na.rm = FALSE
619s  num [1:4, 1:4] 1 1 1 1 5 ...
619s  num [1:4, 1:4] 1 2 3 4 2.5 ...
619s OP = '/', na.rm = TRUE
619s  num [1:4, 1:4] 1 1 1 1 5 ...
619s  num [1:4, 1:4] 1 2 3 4 2.5 ...
619s > 
619s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
619s > # Missing values in x, y, or both.
619s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
619s > for (which in c("x", "y", "both")) {
619s +   x <- matrix(1:16, nrow = 4, ncol = 4)
619s +   y <- 1:nrow(x)
619s +   storage.mode(y) <- storage.mode(x)
619s + 
619s +   if (which == "x") {
619s +     x[3:6] <- NA_real_
619s +   } else if (which == "y") {
619s +     y[c(1, 3)] <- NA_real_
619s +   } else if (which == "both") {
619s +     x[3:6] <- NA_real_
619s +     y[c(1, 3)] <- NA_real_
619s +   }
619s + 
619s +   for (OP in c("+", "-", "*", "/")) {
619s +     for (na.rm in c(FALSE, TRUE)) {
619s +       cat(sprintf("OP = '%s', na.rm = %s\n", OP, na.rm))
619s +       a0 <- x_OP_y_R(x, y, OP, na.rm = na.rm)
619s +       a1 <- x_OP_y(x, y, OP, na.rm = na.rm)
619s +       str(a1)
619s +       stopifnot(all.equal(a1, a0))
619s + 
619s +       b0 <- t_tx_OP_y_R(x, y, OP, na.rm = na.rm)
619s +       b1 <- t_tx_OP_y(x, y, OP, na.rm = na.rm)
619s +       str(b1)
619s +       stopifnot(all.equal(b1, b0))
619s +     }
619s +   }
619s + }
619s OP = '+', na.rm = FALSE
619s  num [1:4, 1:4] 2 4 NA NA NA NA 10 12 10 12 ...
619s  num [1:4, 1:4] 2 3 NA NA NA NA 9 10 12 13 ...
619s OP = '+', na.rm = TRUE
619s  num [1:4, 1:4] 2 4 3 4 1 2 10 12 10 12 ...
619s  num [1:4, 1:4] 2 3 1 1 2 2 9 10 12 13 ...
619s OP = '-', na.rm = FALSE
619s  num [1:4, 1:4] 0 0 NA NA NA NA 4 4 8 8 ...
619s  num [1:4, 1:4] 0 1 NA NA NA NA 5 6 6 7 ...
619s OP = '-', na.rm = TRUE
619s  num [1:4, 1:4] 0 0 NA NA NA NA 4 4 8 8 ...
619s  num [1:4, 1:4] 0 1 NA NA NA NA 5 6 6 7 ...
619s OP = '*', na.rm = FALSE
619s  num [1:4, 1:4] 1 4 NA NA NA NA 21 32 9 20 ...
619s  num [1:4, 1:4] 1 2 NA NA NA NA 14 16 27 30 ...
619s OP = '*', na.rm = TRUE
619s  num [1:4, 1:4] 1 4 3 4 1 2 21 32 9 20 ...
619s  num [1:4, 1:4] 1 2 1 1 2 2 14 16 27 30 ...
619s OP = '/', na.rm = FALSE
619s  num [1:4, 1:4] 1 1 NA NA NA ...
619s  num [1:4, 1:4] 1 2 NA NA NA ...
619s OP = '/', na.rm = TRUE
619s  num [1:4, 1:4] 1 1 NA NA NA ...
619s  num [1:4, 1:4] 1 2 NA NA NA ...
619s OP = '+', na.rm = FALSE
619s  num [1:4, 1:4] NA 4 NA 8 NA 8 NA 12 NA 12 ...
619s  num [1:4, 1:4] NA NA NA NA 7 8 9 10 NA NA ...
619s OP = '+', na.rm = TRUE
619s  num [1:4, 1:4] 1 4 3 8 5 8 7 12 9 12 ...
619s  num [1:4, 1:4] 1 2 3 4 7 8 9 10 9 10 ...
619s OP = '-', na.rm = FALSE
619s  num [1:4, 1:4] NA 0 NA 0 NA 4 NA 4 NA 8 ...
619s  num [1:4, 1:4] NA NA NA NA 3 4 5 6 NA NA ...
619s OP = '-', na.rm = TRUE
619s  num [1:4, 1:4] NA 0 NA 0 NA 4 NA 4 NA 8 ...
619s  num [1:4, 1:4] NA NA NA NA 3 4 5 6 NA NA ...
619s OP = '*', na.rm = FALSE
619s  num [1:4, 1:4] NA 4 NA 16 NA 12 NA 32 NA 20 ...
619s  num [1:4, 1:4] NA NA NA NA 10 12 14 16 NA NA ...
619s OP = '*', na.rm = TRUE
619s  num [1:4, 1:4] 1 4 3 16 5 12 7 32 9 20 ...
619s  num [1:4, 1:4] 1 2 3 4 10 12 14 16 9 10 ...
619s OP = '/', na.rm = FALSE
619s  num [1:4, 1:4] NA 1 NA 1 NA 3 NA 2 NA 5 ...
619s  num [1:4, 1:4] NA NA NA NA 2.5 3 3.5 4 NA NA ...
619s OP = '/', na.rm = TRUE
619s  num [1:4, 1:4] NA 1 NA 1 NA 3 NA 2 NA 5 ...
619s  num [1:4, 1:4] NA NA NA NA 2.5 3 3.5 4 NA NA ...
619s OP = '+', na.rm = FALSE
619s  num [1:4, 1:4] NA 4 NA NA NA NA NA 12 NA 12 ...
619s  num [1:4, 1:4] NA NA NA NA NA NA 9 10 NA NA ...
619s OP = '+', na.rm = TRUE
619s  num [1:4, 1:4] 1 4 NA 4 NA 2 7 12 9 12 ...
619s  num [1:4, 1:4] 1 2 NA NA 2 2 9 10 9 10 ...
619s OP = '-', na.rm = FALSE
619s  num [1:4, 1:4] NA 0 NA NA NA NA NA 4 NA 8 ...
619s  num [1:4, 1:4] NA NA NA NA NA NA 5 6 NA NA ...
619s OP = '-', na.rm = TRUE
619s  num [1:4, 1:4] NA 0 NA NA NA NA NA 4 NA 8 ...
619s  num [1:4, 1:4] NA NA NA NA NA NA 5 6 NA NA ...
619s OP = '*', na.rm = FALSE
619s  num [1:4, 1:4] NA 4 NA NA NA NA NA 32 NA 20 ...
619s  num [1:4, 1:4] NA NA NA NA NA NA 14 16 NA NA ...
619s OP = '*', na.rm = TRUE
619s  num [1:4, 1:4] 1 4 NA 4 NA 2 7 32 9 20 ...
619s  num [1:4, 1:4] 1 2 NA NA 2 2 14 16 9 10 ...
619s OP = '/', na.rm = FALSE
619s  num [1:4, 1:4] NA 1 NA NA NA NA NA 2 NA 5 ...
619s  num [1:4, 1:4] NA NA NA NA NA NA 3.5 4 NA NA ...
619s OP = '/', na.rm = TRUE
619s  num [1:4, 1:4] NA 1 NA NA NA NA NA 2 NA 5 ...
619s  num [1:4, 1:4] NA NA NA NA NA NA 3.5 4 NA NA ...
619s > 
619s > 
619s > 
619s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
619s > # Length differences
619s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
619s > x <- matrix(1:8, nrow = 2, ncol = 4)
619s > y <- 1:ncol(x)
619s > storage.mode(y) <- storage.mode(x)
619s > 
619s > for (OP in c("+", "-", "*", "/")) {
619s +   for (na.rm in c(FALSE, TRUE)) {
619s +     cat(sprintf("OP = '%s', na.rm = %s\n", OP, na.rm))
619s + 
619s +     a0 <- x_OP_y_R(x, y, OP, na.rm = na.rm)
619s +     a1 <- x_OP_y(x, y, OP, na.rm = na.rm)
619s +     str(a1)
619s +     stopifnot(all.equal(a1, a0))
619s + 
619s +     b0 <- t_tx_OP_y_R(x, y, OP, na.rm = na.rm)
619s +     b1 <- t_tx_OP_y(x, y, OP, na.rm = na.rm)
619s +     str(b1)
619s +     stopifnot(all.equal(b1, b0))
619s +   }
619s + }
619s OP = '+', na.rm = FALSE
619s  int [1:2, 1:4] 2 4 6 8 6 8 10 12
619s  int [1:2, 1:4] 2 3 5 6 8 9 11 12
619s OP = '+', na.rm = TRUE
619s  int [1:2, 1:4] 2 4 6 8 6 8 10 12
619s  int [1:2, 1:4] 2 3 5 6 8 9 11 12
619s OP = '-', na.rm = FALSE
619s  int [1:2, 1:4] 0 0 0 0 4 4 4 4
619s  int [1:2, 1:4] 0 1 1 2 2 3 3 4
619s OP = '-', na.rm = TRUE
619s  int [1:2, 1:4] 0 0 0 0 4 4 4 4
619s  int [1:2, 1:4] 0 1 1 2 2 3 3 4
619s OP = '*', na.rm = FALSE
619s  int [1:2, 1:4] 1 4 9 16 5 12 21 32
619s  int [1:2, 1:4] 1 2 6 8 15 18 28 32
619s OP = '*', na.rm = TRUE
619s  int [1:2, 1:4] 1 4 9 16 5 12 21 32
619s  int [1:2, 1:4] 1 2 6 8 15 18 28 32
619s OP = '/', na.rm = FALSE
619s  num [1:2, 1:4] 1 1 1 1 5 ...
619s  num [1:2, 1:4] 1 2 1.5 2 1.67 ...
619s OP = '/', na.rm = TRUE
619s  num [1:2, 1:4] 1 1 1 1 5 ...
619s  num [1:2, 1:4] 1 2 1.5 2 1.67 ...
619s > 
619s > 
619s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
619s > # All missing values
619s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
619s > xs <- list(
619s +   A = matrix(1:2, nrow = 2, ncol = 2),
619s +   B = matrix(NA_integer_, nrow = 2, ncol = 2)
619s + )
619s > ys <- list(
619s +   A = 1L,
619s +   B = NA_integer_
619s + )
619s > 
619s > for (x in xs) {
619s +   for (y in ys) {
619s +     for (mode in c("logical", "integer", "double")) {
619s +       storage.mode(x) <- mode
619s +       storage.mode(y) <- mode
619s +       str(list(x = x, y = y))
619s + 
619s +       for (OP in c("+", "-", "*", "/")) {
619s +         for (na.rm in c(FALSE, TRUE)) {
619s +           cat(sprintf("mode = '%s', OP = '%s', na.rm = %s\n", mode, OP, na.rm))
619s +           suppressWarnings({
619s +             z0 <- x_OP_y_R(x, y, OP, na.rm = na.rm)
619s +             z <- x_OP_y(x, y, OP, na.rm = na.rm)
619s +           })
619s +           str(z)
619s +           stopifnot(all.equal(z, z0))
619s +         }
619s +       }
619s +     } # for (mode ...)
619s +   } # for (y ...)
619s + } # for (x ...)
619s List of 2
619s  $ x: logi [1:2, 1:2] TRUE TRUE TRUE TRUE
619s  $ y: logi TRUE
619s mode = 'logical', OP = '+', na.rm = FALSE
619s  int [1:2, 1:2] 2 2 2 2
619s mode = 'logical', OP = '+', na.rm = TRUE
619s  int [1:2, 1:2] 2 2 2 2
619s mode = 'logical', OP = '-', na.rm = FALSE
619s  int [1:2, 1:2] 0 0 0 0
619s mode = 'logical', OP = '-', na.rm = TRUE
619s  int [1:2, 1:2] 0 0 0 0
619s mode = 'logical', OP = '*', na.rm = FALSE
619s  int [1:2, 1:2] 1 1 1 1
619s mode = 'logical', OP = '*', na.rm = TRUE
619s  int [1:2, 1:2] 1 1 1 1
619s mode = 'logical', OP = '/', na.rm = FALSE
619s  num [1:2, 1:2] 1 1 1 1
619s mode = 'logical', OP = '/', na.rm = TRUE
619s  num [1:2, 1:2] 1 1 1 1
619s List of 2
619s  $ x: int [1:2, 1:2] 1 1 1 1
619s  $ y: int 1
619s mode = 'integer', OP = '+', na.rm = FALSE
619s  int [1:2, 1:2] 2 2 2 2
619s mode = 'integer', OP = '+', na.rm = TRUE
619s  int [1:2, 1:2] 2 2 2 2
619s mode = 'integer', OP = '-', na.rm = FALSE
619s  int [1:2, 1:2] 0 0 0 0
619s mode = 'integer', OP = '-', na.rm = TRUE
619s  int [1:2, 1:2] 0 0 0 0
619s mode = 'integer', OP = '*', na.rm = FALSE
619s  int [1:2, 1:2] 1 1 1 1
619s mode = 'integer', OP = '*', na.rm = TRUE
619s  int [1:2, 1:2] 1 1 1 1
619s mode = 'integer', OP = '/', na.rm = FALSE
619s  num [1:2, 1:2] 1 1 1 1
619s mode = 'integer', OP = '/', na.rm = TRUE
619s  num [1:2, 1:2] 1 1 1 1
619s List of 2
619s  $ x: num [1:2, 1:2] 1 1 1 1
620s  $ y: num 1
620s mode = 'double', OP = '+', na.rm = FALSE
620s  num [1:2, 1:2] 2 2 2 2
620s mode = 'double', OP = '+', na.rm = TRUE
620s  num [1:2, 1:2] 2 2 2 2
620s mode = 'double', OP = '-', na.rm = FALSE
620s  num [1:2, 1:2] 0 0 0 0
620s mode = 'double', OP = '-', na.rm = TRUE
620s  num [1:2, 1:2] 0 0 0 0
620s mode = 'double', OP = '*', na.rm = FALSE
620s  num [1:2, 1:2] 1 1 1 1
620s mode = 'double', OP = '*', na.rm = TRUE
620s  num [1:2, 1:2] 1 1 1 1
620s mode = 'double', OP = '/', na.rm = FALSE
620s  num [1:2, 1:2] 1 1 1 1
620s mode = 'double', OP = '/', na.rm = TRUE
620s  num [1:2, 1:2] 1 1 1 1
620s List of 2
620s  $ x: logi [1:2, 1:2] TRUE TRUE TRUE TRUE
620s  $ y: logi NA
620s mode = 'logical', OP = '+', na.rm = FALSE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'logical', OP = '+', na.rm = TRUE
620s  int [1:2, 1:2] 1 1 1 1
620s mode = 'logical', OP = '-', na.rm = FALSE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'logical', OP = '-', na.rm = TRUE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'logical', OP = '*', na.rm = FALSE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'logical', OP = '*', na.rm = TRUE
620s  int [1:2, 1:2] 1 1 1 1
620s mode = 'logical', OP = '/', na.rm = FALSE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'logical', OP = '/', na.rm = TRUE
620s  num [1:2, 1:2] NA NA NA NA
620s List of 2
620s  $ x: int [1:2, 1:2] 1 1 1 1
620s  $ y: int NA
620s mode = 'integer', OP = '+', na.rm = FALSE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'integer', OP = '+', na.rm = TRUE
620s  int [1:2, 1:2] 1 1 1 1
620s mode = 'integer', OP = '-', na.rm = FALSE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'integer', OP = '-', na.rm = TRUE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'integer', OP = '*', na.rm = FALSE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'integer', OP = '*', na.rm = TRUE
620s  int [1:2, 1:2] 1 1 1 1
620s mode = 'integer', OP = '/', na.rm = FALSE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'integer', OP = '/', na.rm = TRUE
620s  num [1:2, 1:2] NA NA NA NA
620s List of 2
620s  $ x: num [1:2, 1:2] 1 1 1 1
620s  $ y: num NA
620s mode = 'double', OP = '+', na.rm = FALSE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'double', OP = '+', na.rm = TRUE
620s  num [1:2, 1:2] 1 1 1 1
620s mode = 'double', OP = '-', na.rm = FALSE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'double', OP = '-', na.rm = TRUE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'double', OP = '*', na.rm = FALSE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'double', OP = '*', na.rm = TRUE
620s  num [1:2, 1:2] 1 1 1 1
620s mode = 'double', OP = '/', na.rm = FALSE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'double', OP = '/', na.rm = TRUE
620s  num [1:2, 1:2] NA NA NA NA
620s List of 2
620s  $ x: logi [1:2, 1:2] NA NA NA NA
620s  $ y: logi TRUE
620s mode = 'logical', OP = '+', na.rm = FALSE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'logical', OP = '+', na.rm = TRUE
620s  int [1:2, 1:2] 1 1 1 1
620s mode = 'logical', OP = '-', na.rm = FALSE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'logical', OP = '-', na.rm = TRUE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'logical', OP = '*', na.rm = FALSE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'logical', OP = '*', na.rm = TRUE
620s  int [1:2, 1:2] 1 1 1 1
620s mode = 'logical', OP = '/', na.rm = FALSE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'logical', OP = '/', na.rm = TRUE
620s  num [1:2, 1:2] NA NA NA NA
620s List of 2
620s  $ x: int [1:2, 1:2] NA NA NA NA
620s  $ y: int 1
620s mode = 'integer', OP = '+', na.rm = FALSE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'integer', OP = '+', na.rm = TRUE
620s  int [1:2, 1:2] 1 1 1 1
620s mode = 'integer', OP = '-', na.rm = FALSE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'integer', OP = '-', na.rm = TRUE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'integer', OP = '*', na.rm = FALSE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'integer', OP = '*', na.rm = TRUE
620s  int [1:2, 1:2] 1 1 1 1
620s mode = 'integer', OP = '/', na.rm = FALSE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'integer', OP = '/', na.rm = TRUE
620s  num [1:2, 1:2] NA NA NA NA
620s List of 2
620s  $ x: num [1:2, 1:2] NA NA NA NA
620s  $ y: num 1
620s mode = 'double', OP = '+', na.rm = FALSE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'double', OP = '+', na.rm = TRUE
620s  num [1:2, 1:2] 1 1 1 1
620s mode = 'double', OP = '-', na.rm = FALSE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'double', OP = '-', na.rm = TRUE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'double', OP = '*', na.rm = FALSE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'double', OP = '*', na.rm = TRUE
620s  num [1:2, 1:2] 1 1 1 1
620s mode = 'double', OP = '/', na.rm = FALSE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'double', OP = '/', na.rm = TRUE
620s  num [1:2, 1:2] NA NA NA NA
620s List of 2
620s  $ x: logi [1:2, 1:2] NA NA NA NA
620s  $ y: logi NA
620s mode = 'logical', OP = '+', na.rm = FALSE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'logical', OP = '+', na.rm = TRUE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'logical', OP = '-', na.rm = FALSE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'logical', OP = '-', na.rm = TRUE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'logical', OP = '*', na.rm = FALSE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'logical', OP = '*', na.rm = TRUE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'logical', OP = '/', na.rm = FALSE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'logical', OP = '/', na.rm = TRUE
620s  num [1:2, 1:2] NA NA NA NA
620s List of 2
620s  $ x: int [1:2, 1:2] NA NA NA NA
620s  $ y: int NA
620s mode = 'integer', OP = '+', na.rm = FALSE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'integer', OP = '+', na.rm = TRUE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'integer', OP = '-', na.rm = FALSE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'integer', OP = '-', na.rm = TRUE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'integer', OP = '*', na.rm = FALSE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'integer', OP = '*', na.rm = TRUE
620s  int [1:2, 1:2] NA NA NA NA
620s mode = 'integer', OP = '/', na.rm = FALSE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'integer', OP = '/', na.rm = TRUE
620s  num [1:2, 1:2] NA NA NA NA
620s List of 2
620s  $ x: num [1:2, 1:2] NA NA NA NA
620s  $ y: num NA
620s mode = 'double', OP = '+', na.rm = FALSE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'double', OP = '+', na.rm = TRUE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'double', OP = '-', na.rm = FALSE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'double', OP = '-', na.rm = TRUE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'double', OP = '*', na.rm = FALSE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'double', OP = '*', na.rm = TRUE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'double', OP = '/', na.rm = FALSE
620s  num [1:2, 1:2] NA NA NA NA
620s mode = 'double', OP = '/', na.rm = TRUE
620s  num [1:2, 1:2] NA NA NA NA
620s > 
620s 
620s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
620s Copyright (C) 2024 The R Foundation for Statistical Computing
620s Platform: arm-unknown-linux-gnueabihf (32-bit)
620s 
620s R is free software and comes with ABSOLUTELY NO WARRANTY.
620s You are welcome to redistribute it under certain conditions.
620s Type 'license()' or 'licence()' for distribution details.
620s 
620s R is a collaborative project with many contributors.
620s Type 'contributors()' for more information and
620s 'citation()' on how to cite R or R packages in publications.
620s 
620s Type 'demo()' for some demos, 'help()' for on-line help, or
620s 'help.start()' for an HTML browser interface to help.
620s Type 'q()' to quit R.
620s 
620s > library("matrixStats")
620s > 
620s > x_OP_y_R <- function(x, y, OP, na.rm = FALSE) {
620s +   if (na.rm) {
620s +     xnok <- is.na(x)
620s +     ynok <- is.na(y)
620s +     anok <- xnok & ynok
620s +     unit <- switch(OP,
620s +       "+" = 0,
620s +       "-" = NA_real_,
620s +       "*" = 1,
620s +       "/" = NA_real_,
620s +       stop("Unknown 'OP' operator: ", OP)
620s +     )
620s +     x[xnok] <- unit
620s +     y[ynok] <- unit
620s +   }
620s + 
620s +   ans <- switch(OP,
620s +     "+" = x + y,
620s +     "-" = x - y,
620s +     "*" = x * y,
620s +     "/" = x / y,
620s +     stop("Unknown 'OP' operator: ", OP)
620s +   )
620s + 
620s +   if (na.rm) {
620s +     ans[anok] <- NA_real_
620s +   }
620s + 
620s +   ans
620s + } # x_OP_y_R()
620s > 
620s > 
620s > t_tx_OP_y_R <- function(x, y, OP, na.rm = FALSE) {
620s +   t(x_OP_y_R(x = t(x), y = y, OP = OP, na.rm = na.rm))
620s + }
620s > 
620s > 
620s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
620s > # Subsetted tests
620s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
620s > source("utils/validateIndicesFramework.R")
620s > for (OP in c("+", "-", "*", "/")) {
620s +   for (mode in c("numeric", "integer", "logical")) {
620s +     x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6L, ncol = 6L)
620s +     y <- runif(6, min = 0, max = 6)
620s +     storage.mode(x) <- mode
620s +     storage.mode(y) <- mode
620s +     if (mode == "numeric") y[1] <- Inf
620s + 
620s +     for (xrows in index_cases) {
620s +       for (xcols in index_cases) {
620s +         if (is.null(xrows)) xrows <- seq_len(nrow(x))
620s +         if (is.null(xcols)) xcols <- seq_len(ncol(x))
620s + 
620s +         for (yidxs in list(xrows, xcols)) {
620s +           for (na.rm in c(TRUE, FALSE)) {
620s + 
620s +             suppressWarnings({
620s +               actual <- tryCatch(
620s +                 x_OP_y(x, y, OP, xrows = xrows, xcols = xcols, yidxs = yidxs,
620s +                        na.rm = na.rm),
620s +                 error = function(c) "error"
620s +               )
620s + 
620s +               expect <- tryCatch(
620s +                 x_OP_y_R(x[xrows, xcols, drop = FALSE], y[yidxs], OP,
620s +                          na.rm = na.rm),
620s +                 error = function(c) "error"
620s +               )
620s +             })
620s +             stopifnot(all.equal(as.vector(actual), as.vector(expect)))
620s + 
620s +             suppressWarnings({
620s +               actual <- tryCatch(
620s +                 t_tx_OP_y(x, y, OP, xrows = xrows, xcols = xcols, yidxs = yidxs,
620s +                           na.rm = na.rm),
620s +                 error = function(c) "error"
620s +               )
620s + 
620s +               expect <- tryCatch(
620s +                 t_tx_OP_y_R(x[xrows, xcols, drop = FALSE], y[yidxs], OP,
620s +                             na.rm = na.rm),
620s +                 error = function(c) "error"
620s +               )
620s +             })
620s +             stopifnot(all.equal(as.vector(actual), as.vector(expect)))
620s +           }
620s +         }
620s +       }
620s +     }
620s +   }
620s + }
634s > 
634s 
634s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
634s Copyright (C) 2024 The R Foundation for Statistical Computing
634s Platform: arm-unknown-linux-gnueabihf (32-bit)
634s 
634s R is free software and comes with ABSOLUTELY NO WARRANTY.
634s You are welcome to redistribute it under certain conditions.
634s Type 'license()' or 'licence()' for distribution details.
634s 
634s R is a collaborative project with many contributors.
634s Type 'contributors()' for more information and
634s 'citation()' on how to cite R or R packages in publications.
634s 
634s Type 'demo()' for some demos, 'help()' for on-line help, or
634s 'help.start()' for an HTML browser interface to help.
634s Type 'q()' to quit R.
634s 
634s > ## These tests need to be last of all tests, otherwise
634s > ## covr::package_coverage() gives an error.
634s > cat("1. Loading package\n")
634s 1. Loading package
634s > loadNamespace("matrixStats")
634s <environment: namespace:matrixStats>
634s > stopifnot("matrixStats" %in% loadedNamespaces())
634s > 
634s > cat("2. Unloading package\n")
634s 2. Unloading package
634s > unloadNamespace("matrixStats")
634s > stopifnot(!"matrixStats" %in% loadedNamespaces())
634s > 
634s > if (FALSE) {
634s +   ## 'covr' gives "Error in library("matrixStats") :
634s +   ## there is no package called 'matrixStats'" here, cf.
634s +   ## https://travis-ci.org/HenrikBengtsson/matrixStats/builds/48015577
634s + 
634s +   cat("3. Attaching package\n")
634s +   library("matrixStats")
634s +   stopifnot("package:matrixStats" %in% search())
634s + 
634s +   cat("4. Detaching package\n")
634s +   detach("package:matrixStats")
634s +   stopifnot(!"package:matrixStats" %in% search())
634s +   stopifnot("matrixStats" %in% loadedNamespaces())
634s + 
634s +   cat("5. Unloading package\n")
634s +   unloadNamespace("matrixStats")
634s +   stopifnot(!"matrixStats" %in% loadedNamespaces())
634s + 
634s +   cat("6. Attaching package (again)\n")
634s +   library("matrixStats")
634s +   stopifnot("package:matrixStats" %in% search())
634s + 
634s +   cat("7. Detaching package (again)\n")
634s +   detach("package:matrixStats")
634s +   stopifnot(!"package:matrixStats" %in% search())
634s +   stopifnot("matrixStats" %in% loadedNamespaces())
634s + }
634s > 
634s > cat("7. DONE\n")
634s 7. DONE
634s > 
635s autopkgtest [08:32:27]: test run-unit-test: -----------------------]
640s run-unit-test        PASS
640s autopkgtest [08:32:32]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
645s autopkgtest [08:32:37]: test pkg-r-autopkgtest: preparing testbed
698s autopkgtest [08:33:30]: testbed dpkg architecture: armhf
700s autopkgtest [08:33:32]: testbed apt version: 2.7.14build2
700s autopkgtest [08:33:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup
702s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [73.9 kB]
703s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [1964 B]
703s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [53.5 kB]
703s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [3388 B]
703s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [497 kB]
703s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf Packages [112 kB]
703s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf Packages [432 kB]
703s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf Packages [1968 B]
703s Fetched 1176 kB in 1s (1040 kB/s)
703s Reading package lists...
722s tee: /proc/self/fd/2: Permission denied
746s Hit:1 http://ftpmaster.internal/ubuntu oracular InRelease
746s Hit:2 http://ftpmaster.internal/ubuntu oracular-updates InRelease
746s Hit:3 http://ftpmaster.internal/ubuntu oracular-security InRelease
747s Hit:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease
749s Reading package lists...
749s Reading package lists...
750s Building dependency tree...
750s Reading state information...
751s Calculating upgrade...
752s The following package was automatically installed and is no longer required:
752s   libatm1t64
752s Use 'apt autoremove' to remove it.
752s The following NEW packages will be installed:
752s   python3-jaraco.context python3-jaraco.functools
752s The following packages will be upgraded:
752s   apparmor apport apport-core-dump-handler apt apt-utils bash-completion curl
752s   dhcpcd-base dpkg dpkg-dev dracut-install eatmydata fwupd gcc-14-base
752s   gir1.2-girepository-2.0 gir1.2-glib-2.0 groff-base initramfs-tools
752s   initramfs-tools-bin initramfs-tools-core iproute2 klibc-utils less libacl1
752s   libapparmor1 libapt-pkg6.0t64 libbpf1 libbsd0 libc-bin libc6 libcap-ng0
752s   libcurl3t64-gnutls libcurl4t64 libdpkg-perl libeatmydata1 libelf1t64
752s   libevent-core-2.1-7t64 libexpat1 libfwupd2 libgcc-s1 libgcrypt20
752s   libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgnutls30t64
752s   libgpg-error-l10n libgpg-error0 libklibc liblocale-gettext-perl liblz4-1
752s   libnss3 libnvme1t64 libpam-modules libpam-modules-bin libpam-runtime
752s   libpam0g libperl5.38t64 libslang2 libsqlite3-0 libstdc++6 libtirpc-common
752s   libtirpc3t64 libuv1t64 libxcb1 locales man-db pastebinit perl perl-base
752s   perl-modules-5.38 python-apt-common python-babel-localedata python3-apport
752s   python3-apt python3-babel python3-blinker python3-httplib2 python3-jinja2
752s   python3-keyring python3-problem-report python3-pyparsing python3-six rsync
752s   tzdata ubuntu-pro-client ubuntu-pro-client-l10n vim-common vim-tiny xxd
753s 89 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
753s Need to get 48.8 MB of archives.
753s After this operation, 267 kB of additional disk space will be used.
753s Get:1 http://ftpmaster.internal/ubuntu oracular/main armhf gcc-14-base armhf 14.1.0-1ubuntu1 [48.4 kB]
753s Get:2 http://ftpmaster.internal/ubuntu oracular/main armhf libgcc-s1 armhf 14.1.0-1ubuntu1 [41.5 kB]
753s Get:3 http://ftpmaster.internal/ubuntu oracular/main armhf libstdc++6 armhf 14.1.0-1ubuntu1 [714 kB]
753s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf libc6 armhf 2.39-0ubuntu8.1 [2828 kB]
753s Get:5 http://ftpmaster.internal/ubuntu oracular/main armhf libgpg-error-l10n all 1.49-2 [8228 B]
753s Get:6 http://ftpmaster.internal/ubuntu oracular/main armhf libgpg-error0 armhf 1.49-2 [62.7 kB]
753s Get:7 http://ftpmaster.internal/ubuntu oracular/main armhf libgcrypt20 armhf 1.10.3-3 [454 kB]
753s Get:8 http://ftpmaster.internal/ubuntu oracular/main armhf liblz4-1 armhf 1.9.4-2 [58.0 kB]
753s Get:9 http://ftpmaster.internal/ubuntu oracular/main armhf libapt-pkg6.0t64 armhf 2.9.3 [1013 kB]
753s Get:10 http://ftpmaster.internal/ubuntu oracular/main armhf dpkg armhf 1.22.6ubuntu10 [1230 kB]
753s Get:11 http://ftpmaster.internal/ubuntu oracular/main armhf libperl5.38t64 armhf 5.38.2-4 [4102 kB]
754s Get:12 http://ftpmaster.internal/ubuntu oracular/main armhf perl armhf 5.38.2-4 [231 kB]
754s Get:13 http://ftpmaster.internal/ubuntu oracular/main armhf perl-base armhf 5.38.2-4 [1671 kB]
754s Get:14 http://ftpmaster.internal/ubuntu oracular/main armhf perl-modules-5.38 all 5.38.2-4 [3110 kB]
754s Get:15 http://ftpmaster.internal/ubuntu oracular/main armhf libc-bin armhf 2.39-0ubuntu8.1 [530 kB]
754s Get:16 http://ftpmaster.internal/ubuntu oracular/main armhf apt armhf 2.9.3 [1397 kB]
754s Get:17 http://ftpmaster.internal/ubuntu oracular/main armhf apt-utils armhf 2.9.3 [217 kB]
754s Get:18 http://ftpmaster.internal/ubuntu oracular/main armhf libgnutls30t64 armhf 3.8.5-2ubuntu1 [958 kB]
754s Get:19 http://ftpmaster.internal/ubuntu oracular/main armhf libpam0g armhf 1.5.3-7ubuntu1 [62.3 kB]
754s Get:20 http://ftpmaster.internal/ubuntu oracular/main armhf libpam-modules-bin armhf 1.5.3-7ubuntu1 [47.0 kB]
754s Get:21 http://ftpmaster.internal/ubuntu oracular/main armhf libpam-modules armhf 1.5.3-7ubuntu1 [266 kB]
754s Get:22 http://ftpmaster.internal/ubuntu oracular/main armhf liblocale-gettext-perl armhf 1.07-7 [14.8 kB]
754s Get:23 http://ftpmaster.internal/ubuntu oracular/main armhf libacl1 armhf 2.3.2-2 [15.1 kB]
754s Get:24 http://ftpmaster.internal/ubuntu oracular/main armhf rsync armhf 3.3.0-1 [414 kB]
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754s Get:26 http://ftpmaster.internal/ubuntu oracular/main armhf python3-apt armhf 2.9.0 [162 kB]
754s Get:27 http://ftpmaster.internal/ubuntu oracular/main armhf python3-pyparsing all 3.1.2-1 [86.4 kB]
754s Get:28 http://ftpmaster.internal/ubuntu oracular/main armhf python3-httplib2 all 0.22.0-1 [30.4 kB]
754s Get:29 http://ftpmaster.internal/ubuntu oracular/main armhf python3-problem-report all 2.28.1-0ubuntu4 [23.9 kB]
754s Get:30 http://ftpmaster.internal/ubuntu oracular/main armhf python3-apport all 2.28.1-0ubuntu4 [92.1 kB]
754s Get:31 http://ftpmaster.internal/ubuntu oracular/main armhf gir1.2-girepository-2.0 armhf 1.80.1-3 [24.7 kB]
754s Get:32 http://ftpmaster.internal/ubuntu oracular/main armhf gir1.2-glib-2.0 armhf 2.80.2-1ubuntu1 [182 kB]
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754s Get:34 http://ftpmaster.internal/ubuntu oracular/main armhf libgirepository-1.0-1 armhf 1.80.1-3 [107 kB]
754s Get:35 http://ftpmaster.internal/ubuntu oracular/main armhf apport-core-dump-handler all 2.28.1-0ubuntu4 [16.9 kB]
754s Get:36 http://ftpmaster.internal/ubuntu oracular/main armhf apport all 2.28.1-0ubuntu4 [83.4 kB]
754s Get:37 http://ftpmaster.internal/ubuntu oracular/main armhf libcap-ng0 armhf 0.8.5-1 [13.6 kB]
754s Get:38 http://ftpmaster.internal/ubuntu oracular/main armhf libpam-runtime all 1.5.3-7ubuntu1 [40.8 kB]
754s Get:39 http://ftpmaster.internal/ubuntu oracular/main armhf dhcpcd-base armhf 1:10.0.6-5 [186 kB]
754s Get:40 http://ftpmaster.internal/ubuntu oracular/main armhf libelf1t64 armhf 0.191-1 [49.8 kB]
754s Get:41 http://ftpmaster.internal/ubuntu oracular/main armhf libbpf1 armhf 1:1.4.1-1 [151 kB]
754s Get:42 http://ftpmaster.internal/ubuntu oracular/main armhf libtirpc-common all 1.3.4+ds-1.3 [8106 B]
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754s Get:44 http://ftpmaster.internal/ubuntu oracular/main armhf iproute2 armhf 6.9.0-1 [1083 kB]
754s Get:45 http://ftpmaster.internal/ubuntu oracular/main armhf less armhf 590-2ubuntu2.1 [131 kB]
754s Get:46 http://ftpmaster.internal/ubuntu oracular/main armhf libapparmor1 armhf 4.0.1-0ubuntu1 [45.5 kB]
754s Get:47 http://ftpmaster.internal/ubuntu oracular/main armhf libbsd0 armhf 0.12.2-1 [36.5 kB]
754s Get:48 http://ftpmaster.internal/ubuntu oracular/main armhf libexpat1 armhf 2.6.2-1 [65.9 kB]
754s Get:49 http://ftpmaster.internal/ubuntu oracular/main armhf libglib2.0-data all 2.80.2-1ubuntu1 [49.3 kB]
754s Get:50 http://ftpmaster.internal/ubuntu oracular/main armhf libslang2 armhf 2.3.3-5 [478 kB]
757s Get:51 http://ftpmaster.internal/ubuntu oracular/main armhf libsqlite3-0 armhf 3.45.3-1 [601 kB]
757s Get:52 http://ftpmaster.internal/ubuntu oracular/main armhf locales all 2.39-0ubuntu8.1 [4234 kB]
757s Get:53 http://ftpmaster.internal/ubuntu oracular/main armhf tzdata all 2024a-4ubuntu1 [274 kB]
757s Get:54 http://ftpmaster.internal/ubuntu oracular/main armhf ubuntu-pro-client-l10n armhf 32.1 [19.4 kB]
757s Get:55 http://ftpmaster.internal/ubuntu oracular/main armhf ubuntu-pro-client armhf 32.1 [230 kB]
757s Get:56 http://ftpmaster.internal/ubuntu oracular/main armhf vim-tiny armhf 2:9.1.0377-1ubuntu1 [670 kB]
757s Get:57 http://ftpmaster.internal/ubuntu oracular/main armhf vim-common all 2:9.1.0377-1ubuntu1 [385 kB]
757s Get:58 http://ftpmaster.internal/ubuntu oracular/main armhf xxd armhf 2:9.1.0377-1ubuntu1 [63.0 kB]
757s Get:59 http://ftpmaster.internal/ubuntu oracular/main armhf apparmor armhf 4.0.1-0ubuntu1 [565 kB]
757s Get:60 http://ftpmaster.internal/ubuntu oracular/main armhf bash-completion all 1:2.14.0-1 [206 kB]
757s Get:61 http://ftpmaster.internal/ubuntu oracular/main armhf groff-base armhf 1.23.0-4 [946 kB]
757s Get:62 http://ftpmaster.internal/ubuntu oracular/main armhf libuv1t64 armhf 1.48.0-4 [83.2 kB]
757s Get:63 http://ftpmaster.internal/ubuntu oracular/main armhf libxcb1 armhf 1.17.0-2 [46.3 kB]
757s Get:64 http://ftpmaster.internal/ubuntu oracular/main armhf man-db armhf 2.12.1-1 [1201 kB]
757s Get:65 http://ftpmaster.internal/ubuntu oracular/main armhf curl armhf 8.5.0-2ubuntu10.1 [219 kB]
757s Get:66 http://ftpmaster.internal/ubuntu oracular/main armhf libcurl4t64 armhf 8.5.0-2ubuntu10.1 [296 kB]
757s Get:67 http://ftpmaster.internal/ubuntu oracular/main armhf dpkg-dev all 1.22.6ubuntu10 [1074 kB]
757s Get:68 http://ftpmaster.internal/ubuntu oracular/main armhf libdpkg-perl all 1.22.6ubuntu10 [269 kB]
757s Get:69 http://ftpmaster.internal/ubuntu oracular/main armhf dracut-install armhf 060+5-8ubuntu1 [34.3 kB]
757s Get:70 http://ftpmaster.internal/ubuntu oracular/main armhf libeatmydata1 armhf 131-2 [7106 B]
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757s Get:72 http://ftpmaster.internal/ubuntu oracular/main armhf libcurl3t64-gnutls armhf 8.5.0-2ubuntu10.1 [290 kB]
757s Get:73 http://ftpmaster.internal/ubuntu oracular/main armhf libfwupd2 armhf 1.9.20-1 [126 kB]
757s Get:74 http://ftpmaster.internal/ubuntu oracular/main armhf fwupd armhf 1.9.20-1 [4368 kB]
757s Get:75 http://ftpmaster.internal/ubuntu oracular/main armhf initramfs-tools all 0.142ubuntu27 [7898 B]
757s Get:76 http://ftpmaster.internal/ubuntu oracular/main armhf initramfs-tools-core all 0.142ubuntu27 [49.5 kB]
757s Get:77 http://ftpmaster.internal/ubuntu oracular/main armhf initramfs-tools-bin armhf 0.142ubuntu27 [20.9 kB]
757s Get:78 http://ftpmaster.internal/ubuntu oracular/main armhf klibc-utils armhf 2.0.13-4ubuntu1 [93.8 kB]
757s Get:79 http://ftpmaster.internal/ubuntu oracular/main armhf libklibc armhf 2.0.13-4ubuntu1 [45.0 kB]
757s Get:80 http://ftpmaster.internal/ubuntu oracular/main armhf libevent-core-2.1-7t64 armhf 2.1.12-stable-10 [82.5 kB]
757s Get:81 http://ftpmaster.internal/ubuntu oracular/main armhf libnss3 armhf 2:3.100-1 [1331 kB]
757s Get:82 http://ftpmaster.internal/ubuntu oracular/main armhf libnvme1t64 armhf 1.9-1 [69.9 kB]
757s Get:83 http://ftpmaster.internal/ubuntu oracular/main armhf pastebinit all 1.7.0-1 [14.9 kB]
757s Get:84 http://ftpmaster.internal/ubuntu oracular/main armhf python3-babel all 2.14.0-1 [96.4 kB]
757s Get:85 http://ftpmaster.internal/ubuntu oracular/main armhf python-babel-localedata all 2.14.0-1 [6385 kB]
757s Get:86 http://ftpmaster.internal/ubuntu oracular/main armhf python3-blinker all 1.8.2-1 [11.4 kB]
757s Get:87 http://ftpmaster.internal/ubuntu oracular/main armhf python3-jaraco.context all 4.3.0-1 [6994 B]
757s Get:88 http://ftpmaster.internal/ubuntu oracular/main armhf python3-jaraco.functools all 4.0.0-1 [10.7 kB]
757s Get:89 http://ftpmaster.internal/ubuntu oracular/main armhf python3-jinja2 all 3.1.3-1 [107 kB]
757s Get:90 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-keyring all 25.2.1-1 [39.9 kB]
757s Get:91 http://ftpmaster.internal/ubuntu oracular/main armhf python3-six all 1.16.0-6 [13.0 kB]
757s Preconfiguring packages ...
757s Fetched 48.8 MB in 3s (17.0 MB/s)
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757s Preparing to unpack .../gcc-14-base_14.1.0-1ubuntu1_armhf.deb ...
757s Unpacking gcc-14-base:armhf (14.1.0-1ubuntu1) over (14-20240412-0ubuntu1) ...
757s Setting up gcc-14-base:armhf (14.1.0-1ubuntu1) ...
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757s Preparing to unpack .../libgcc-s1_14.1.0-1ubuntu1_armhf.deb ...
757s Unpacking libgcc-s1:armhf (14.1.0-1ubuntu1) over (14-20240412-0ubuntu1) ...
757s Setting up libgcc-s1:armhf (14.1.0-1ubuntu1) ...
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758s Preparing to unpack .../libstdc++6_14.1.0-1ubuntu1_armhf.deb ...
758s Unpacking libstdc++6:armhf (14.1.0-1ubuntu1) over (14-20240412-0ubuntu1) ...
758s Setting up libstdc++6:armhf (14.1.0-1ubuntu1) ...
758s (Reading database ... 
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758s Preparing to unpack .../libc6_2.39-0ubuntu8.1_armhf.deb ...
758s Unpacking libc6:armhf (2.39-0ubuntu8.1) over (2.39-0ubuntu8) ...
759s Setting up libc6:armhf (2.39-0ubuntu8.1) ...
760s (Reading database ... 
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760s Preparing to unpack .../libgpg-error-l10n_1.49-2_all.deb ...
760s Unpacking libgpg-error-l10n (1.49-2) over (1.47-3build2) ...
760s Preparing to unpack .../libgpg-error0_1.49-2_armhf.deb ...
760s Unpacking libgpg-error0:armhf (1.49-2) over (1.47-3build2) ...
760s Setting up libgpg-error0:armhf (1.49-2) ...
760s (Reading database ... 
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760s Preparing to unpack .../libgcrypt20_1.10.3-3_armhf.deb ...
760s Unpacking libgcrypt20:armhf (1.10.3-3) over (1.10.3-2build1) ...
760s Setting up libgcrypt20:armhf (1.10.3-3) ...
760s (Reading database ... 
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760s Preparing to unpack .../liblz4-1_1.9.4-2_armhf.deb ...
760s Unpacking liblz4-1:armhf (1.9.4-2) over (1.9.4-1build1) ...
760s Setting up liblz4-1:armhf (1.9.4-2) ...
760s (Reading database ... 
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760s Preparing to unpack .../libapt-pkg6.0t64_2.9.3_armhf.deb ...
760s Unpacking libapt-pkg6.0t64:armhf (2.9.3) over (2.7.14build2) ...
760s Setting up libapt-pkg6.0t64:armhf (2.9.3) ...
760s (Reading database ... 
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760s Preparing to unpack .../dpkg_1.22.6ubuntu10_armhf.deb ...
760s Unpacking dpkg (1.22.6ubuntu10) over (1.22.6ubuntu6) ...
761s Setting up dpkg (1.22.6ubuntu10) ...
762s (Reading database ... 
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762s Preparing to unpack .../libperl5.38t64_5.38.2-4_armhf.deb ...
762s Unpacking libperl5.38t64:armhf (5.38.2-4) over (5.38.2-3.2build2) ...
762s Preparing to unpack .../perl_5.38.2-4_armhf.deb ...
762s Unpacking perl (5.38.2-4) over (5.38.2-3.2build2) ...
763s Preparing to unpack .../perl-base_5.38.2-4_armhf.deb ...
763s Unpacking perl-base (5.38.2-4) over (5.38.2-3.2build2) ...
763s Setting up perl-base (5.38.2-4) ...
763s (Reading database ... 
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763s Preparing to unpack .../perl-modules-5.38_5.38.2-4_all.deb ...
763s Unpacking perl-modules-5.38 (5.38.2-4) over (5.38.2-3.2build2) ...
764s Preparing to unpack .../libc-bin_2.39-0ubuntu8.1_armhf.deb ...
764s Unpacking libc-bin (2.39-0ubuntu8.1) over (2.39-0ubuntu8) ...
764s Setting up libc-bin (2.39-0ubuntu8.1) ...
765s (Reading database ... 
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765s Preparing to unpack .../archives/apt_2.9.3_armhf.deb ...
765s Unpacking apt (2.9.3) over (2.7.14build2) ...
765s Setting up apt (2.9.3) ...
767s (Reading database ... 
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767s Preparing to unpack .../apt-utils_2.9.3_armhf.deb ...
767s Unpacking apt-utils (2.9.3) over (2.7.14build2) ...
767s Preparing to unpack .../libgnutls30t64_3.8.5-2ubuntu1_armhf.deb ...
767s Unpacking libgnutls30t64:armhf (3.8.5-2ubuntu1) over (3.8.3-1.1ubuntu3) ...
767s Setting up libgnutls30t64:armhf (3.8.5-2ubuntu1) ...
767s (Reading database ... 
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767s Preparing to unpack .../libpam0g_1.5.3-7ubuntu1_armhf.deb ...
767s Unpacking libpam0g:armhf (1.5.3-7ubuntu1) over (1.5.3-5ubuntu5) ...
767s Setting up libpam0g:armhf (1.5.3-7ubuntu1) ...
767s (Reading database ... 
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767s Preparing to unpack .../libpam-modules-bin_1.5.3-7ubuntu1_armhf.deb ...
767s Unpacking libpam-modules-bin (1.5.3-7ubuntu1) over (1.5.3-5ubuntu5) ...
768s Setting up libpam-modules-bin (1.5.3-7ubuntu1) ...
768s pam_namespace.service is a disabled or a static unit not running, not starting it.
768s (Reading database ... 
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768s Preparing to unpack .../libpam-modules_1.5.3-7ubuntu1_armhf.deb ...
769s Unpacking libpam-modules:armhf (1.5.3-7ubuntu1) over (1.5.3-5ubuntu5) ...
769s Setting up libpam-modules:armhf (1.5.3-7ubuntu1) ...
769s (Reading database ... 
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769s Preparing to unpack .../liblocale-gettext-perl_1.07-7_armhf.deb ...
769s Unpacking liblocale-gettext-perl (1.07-7) over (1.07-6ubuntu5) ...
769s Preparing to unpack .../libacl1_2.3.2-2_armhf.deb ...
769s Unpacking libacl1:armhf (2.3.2-2) over (2.3.2-1build1) ...
769s Setting up libacl1:armhf (2.3.2-2) ...
769s (Reading database ... 
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769s Preparing to unpack .../00-rsync_3.3.0-1_armhf.deb ...
769s Unpacking rsync (3.3.0-1) over (3.2.7-1ubuntu1) ...
769s Preparing to unpack .../01-python-apt-common_2.9.0_all.deb ...
769s Unpacking python-apt-common (2.9.0) over (2.7.7ubuntu1) ...
769s Preparing to unpack .../02-python3-apt_2.9.0_armhf.deb ...
769s Unpacking python3-apt (2.9.0) over (2.7.7ubuntu1) ...
770s Preparing to unpack .../03-python3-pyparsing_3.1.2-1_all.deb ...
770s Unpacking python3-pyparsing (3.1.2-1) over (3.1.1-1) ...
770s Preparing to unpack .../04-python3-httplib2_0.22.0-1_all.deb ...
770s Unpacking python3-httplib2 (0.22.0-1) over (0.20.4-3) ...
770s Preparing to unpack .../05-python3-problem-report_2.28.1-0ubuntu4_all.deb ...
770s Unpacking python3-problem-report (2.28.1-0ubuntu4) over (2.28.1-0ubuntu2) ...
770s Preparing to unpack .../06-python3-apport_2.28.1-0ubuntu4_all.deb ...
770s Unpacking python3-apport (2.28.1-0ubuntu4) over (2.28.1-0ubuntu2) ...
770s Preparing to unpack .../07-gir1.2-girepository-2.0_1.80.1-3_armhf.deb ...
771s Unpacking gir1.2-girepository-2.0:armhf (1.80.1-3) over (1.80.1-1) ...
771s Preparing to unpack .../08-gir1.2-glib-2.0_2.80.2-1ubuntu1_armhf.deb ...
771s Unpacking gir1.2-glib-2.0:armhf (2.80.2-1ubuntu1) over (2.80.0-6ubuntu1) ...
771s Preparing to unpack .../09-libglib2.0-0t64_2.80.2-1ubuntu1_armhf.deb ...
771s Unpacking libglib2.0-0t64:armhf (2.80.2-1ubuntu1) over (2.80.0-6ubuntu1) ...
771s Preparing to unpack .../10-libgirepository-1.0-1_1.80.1-3_armhf.deb ...
771s Unpacking libgirepository-1.0-1:armhf (1.80.1-3) over (1.80.1-1) ...
771s Preparing to unpack .../11-apport-core-dump-handler_2.28.1-0ubuntu4_all.deb ...
771s Unpacking apport-core-dump-handler (2.28.1-0ubuntu4) over (2.28.1-0ubuntu2) ...
771s Preparing to unpack .../12-apport_2.28.1-0ubuntu4_all.deb ...
771s Unpacking apport (2.28.1-0ubuntu4) over (2.28.1-0ubuntu2) ...
771s Preparing to unpack .../13-libcap-ng0_0.8.5-1_armhf.deb ...
771s Unpacking libcap-ng0:armhf (0.8.5-1) over (0.8.4-2build2) ...
771s Setting up libcap-ng0:armhf (0.8.5-1) ...
771s (Reading database ... 
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771s Preparing to unpack .../libpam-runtime_1.5.3-7ubuntu1_all.deb ...
771s Unpacking libpam-runtime (1.5.3-7ubuntu1) over (1.5.3-5ubuntu5) ...
771s Setting up libpam-runtime (1.5.3-7ubuntu1) ...
772s (Reading database ... 
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772s Preparing to unpack .../00-dhcpcd-base_1%3a10.0.6-5_armhf.deb ...
772s Unpacking dhcpcd-base (1:10.0.6-5) over (1:10.0.6-1ubuntu3) ...
772s Preparing to unpack .../01-libelf1t64_0.191-1_armhf.deb ...
772s Unpacking libelf1t64:armhf (0.191-1) over (0.190-1.1build4) ...
772s Preparing to unpack .../02-libbpf1_1%3a1.4.1-1_armhf.deb ...
772s Unpacking libbpf1:armhf (1:1.4.1-1) over (1:1.3.0-2build2) ...
772s Preparing to unpack .../03-libtirpc-common_1.3.4+ds-1.3_all.deb ...
772s Unpacking libtirpc-common (1.3.4+ds-1.3) over (1.3.4+ds-1.1build1) ...
772s Preparing to unpack .../04-libtirpc3t64_1.3.4+ds-1.3_armhf.deb ...
772s Unpacking libtirpc3t64:armhf (1.3.4+ds-1.3) over (1.3.4+ds-1.1build1) ...
772s Preparing to unpack .../05-iproute2_6.9.0-1_armhf.deb ...
773s Unpacking iproute2 (6.9.0-1) over (6.1.0-1ubuntu6) ...
773s dpkg: warning: unable to delete old directory '/etc/iproute2/rt_tables.d': Directory not empty
773s dpkg: warning: unable to delete old directory '/etc/iproute2/rt_protos.d': Directory not empty
773s dpkg: warning: unable to delete old directory '/etc/iproute2': Directory not empty
773s Preparing to unpack .../06-less_590-2ubuntu2.1_armhf.deb ...
773s Unpacking less (590-2ubuntu2.1) over (590-2ubuntu2) ...
773s Preparing to unpack .../07-libapparmor1_4.0.1-0ubuntu1_armhf.deb ...
773s Unpacking libapparmor1:armhf (4.0.1-0ubuntu1) over (4.0.0-beta3-0ubuntu3) ...
774s Preparing to unpack .../08-libbsd0_0.12.2-1_armhf.deb ...
774s Unpacking libbsd0:armhf (0.12.2-1) over (0.12.1-1build1) ...
774s Preparing to unpack .../09-libexpat1_2.6.2-1_armhf.deb ...
774s Unpacking libexpat1:armhf (2.6.2-1) over (2.6.1-2build1) ...
774s Preparing to unpack .../10-libglib2.0-data_2.80.2-1ubuntu1_all.deb ...
774s Unpacking libglib2.0-data (2.80.2-1ubuntu1) over (2.80.0-6ubuntu1) ...
774s Preparing to unpack .../11-libslang2_2.3.3-5_armhf.deb ...
774s Unpacking libslang2:armhf (2.3.3-5) over (2.3.3-3build2) ...
774s Preparing to unpack .../12-libsqlite3-0_3.45.3-1_armhf.deb ...
774s Unpacking libsqlite3-0:armhf (3.45.3-1) over (3.45.1-1ubuntu2) ...
774s Preparing to unpack .../13-locales_2.39-0ubuntu8.1_all.deb ...
774s Unpacking locales (2.39-0ubuntu8.1) over (2.39-0ubuntu8) ...
775s Preparing to unpack .../14-tzdata_2024a-4ubuntu1_all.deb ...
775s Unpacking tzdata (2024a-4ubuntu1) over (2024a-2ubuntu1) ...
775s Preparing to unpack .../15-ubuntu-pro-client-l10n_32.1_armhf.deb ...
775s Unpacking ubuntu-pro-client-l10n (32.1) over (31.2.3) ...
775s Preparing to unpack .../16-ubuntu-pro-client_32.1_armhf.deb ...
775s Unpacking ubuntu-pro-client (32.1) over (31.2.3) ...
776s Preparing to unpack .../17-vim-tiny_2%3a9.1.0377-1ubuntu1_armhf.deb ...
776s Unpacking vim-tiny (2:9.1.0377-1ubuntu1) over (2:9.1.0016-1ubuntu7) ...
776s Preparing to unpack .../18-vim-common_2%3a9.1.0377-1ubuntu1_all.deb ...
776s Unpacking vim-common (2:9.1.0377-1ubuntu1) over (2:9.1.0016-1ubuntu7) ...
776s Preparing to unpack .../19-xxd_2%3a9.1.0377-1ubuntu1_armhf.deb ...
776s Unpacking xxd (2:9.1.0377-1ubuntu1) over (2:9.1.0016-1ubuntu7) ...
776s Preparing to unpack .../20-apparmor_4.0.1-0ubuntu1_armhf.deb ...
778s Unpacking apparmor (4.0.1-0ubuntu1) over (4.0.0-beta3-0ubuntu3) ...
778s Preparing to unpack .../21-bash-completion_1%3a2.14.0-1_all.deb ...
778s Unpacking bash-completion (1:2.14.0-1) over (1:2.11-8) ...
779s Preparing to unpack .../22-groff-base_1.23.0-4_armhf.deb ...
779s Unpacking groff-base (1.23.0-4) over (1.23.0-3build2) ...
779s Preparing to unpack .../23-libuv1t64_1.48.0-4_armhf.deb ...
779s Unpacking libuv1t64:armhf (1.48.0-4) over (1.48.0-1.1build1) ...
779s Preparing to unpack .../24-libxcb1_1.17.0-2_armhf.deb ...
779s Unpacking libxcb1:armhf (1.17.0-2) over (1.15-1ubuntu2) ...
780s Preparing to unpack .../25-man-db_2.12.1-1_armhf.deb ...
780s Unpacking man-db (2.12.1-1) over (2.12.0-4build2) ...
780s Preparing to unpack .../26-curl_8.5.0-2ubuntu10.1_armhf.deb ...
780s Unpacking curl (8.5.0-2ubuntu10.1) over (8.5.0-2ubuntu10) ...
780s Preparing to unpack .../27-libcurl4t64_8.5.0-2ubuntu10.1_armhf.deb ...
780s Unpacking libcurl4t64:armhf (8.5.0-2ubuntu10.1) over (8.5.0-2ubuntu10) ...
780s Preparing to unpack .../28-dpkg-dev_1.22.6ubuntu10_all.deb ...
780s Unpacking dpkg-dev (1.22.6ubuntu10) over (1.22.6ubuntu6) ...
781s Preparing to unpack .../29-libdpkg-perl_1.22.6ubuntu10_all.deb ...
781s Unpacking libdpkg-perl (1.22.6ubuntu10) over (1.22.6ubuntu6) ...
781s Preparing to unpack .../30-dracut-install_060+5-8ubuntu1_armhf.deb ...
781s Unpacking dracut-install (060+5-8ubuntu1) over (060+5-1ubuntu3) ...
781s Preparing to unpack .../31-libeatmydata1_131-2_armhf.deb ...
781s Unpacking libeatmydata1:armhf (131-2) over (131-1ubuntu1) ...
781s Preparing to unpack .../32-eatmydata_131-2_all.deb ...
781s Unpacking eatmydata (131-2) over (131-1ubuntu1) ...
781s Preparing to unpack .../33-libcurl3t64-gnutls_8.5.0-2ubuntu10.1_armhf.deb ...
781s Unpacking libcurl3t64-gnutls:armhf (8.5.0-2ubuntu10.1) over (8.5.0-2ubuntu10) ...
781s Preparing to unpack .../34-libfwupd2_1.9.20-1_armhf.deb ...
781s Unpacking libfwupd2:armhf (1.9.20-1) over (1.9.16-1) ...
781s Preparing to unpack .../35-fwupd_1.9.20-1_armhf.deb ...
782s Unpacking fwupd (1.9.20-1) over (1.9.16-1) ...
782s Preparing to unpack .../36-initramfs-tools_0.142ubuntu27_all.deb ...
782s Unpacking initramfs-tools (0.142ubuntu27) over (0.142ubuntu25) ...
782s Preparing to unpack .../37-initramfs-tools-core_0.142ubuntu27_all.deb ...
782s Unpacking initramfs-tools-core (0.142ubuntu27) over (0.142ubuntu25) ...
782s Preparing to unpack .../38-initramfs-tools-bin_0.142ubuntu27_armhf.deb ...
782s Unpacking initramfs-tools-bin (0.142ubuntu27) over (0.142ubuntu25) ...
782s Preparing to unpack .../39-klibc-utils_2.0.13-4ubuntu1_armhf.deb ...
782s Unpacking klibc-utils (2.0.13-4ubuntu1) over (2.0.13-4) ...
782s Preparing to unpack .../40-libklibc_2.0.13-4ubuntu1_armhf.deb ...
782s Unpacking libklibc:armhf (2.0.13-4ubuntu1) over (2.0.13-4) ...
782s Preparing to unpack .../41-libevent-core-2.1-7t64_2.1.12-stable-10_armhf.deb ...
782s Unpacking libevent-core-2.1-7t64:armhf (2.1.12-stable-10) over (2.1.12-stable-9ubuntu2) ...
782s Preparing to unpack .../42-libnss3_2%3a3.100-1_armhf.deb ...
782s Unpacking libnss3:armhf (2:3.100-1) over (2:3.98-1build1) ...
783s Preparing to unpack .../43-libnvme1t64_1.9-1_armhf.deb ...
783s Unpacking libnvme1t64 (1.9-1) over (1.8-3build1) ...
783s Preparing to unpack .../44-pastebinit_1.7.0-1_all.deb ...
783s Unpacking pastebinit (1.7.0-1) over (1.6.2-1) ...
783s Preparing to unpack .../45-python3-babel_2.14.0-1_all.deb ...
783s Unpacking python3-babel (2.14.0-1) over (2.10.3-3build1) ...
783s Preparing to unpack .../46-python-babel-localedata_2.14.0-1_all.deb ...
783s Unpacking python-babel-localedata (2.14.0-1) over (2.10.3-3build1) ...
784s Preparing to unpack .../47-python3-blinker_1.8.2-1_all.deb ...
784s Unpacking python3-blinker (1.8.2-1) over (1.8.1-1) ...
784s Selecting previously unselected package python3-jaraco.context.
784s Preparing to unpack .../48-python3-jaraco.context_4.3.0-1_all.deb ...
784s Unpacking python3-jaraco.context (4.3.0-1) ...
784s Selecting previously unselected package python3-jaraco.functools.
784s Preparing to unpack .../49-python3-jaraco.functools_4.0.0-1_all.deb ...
784s Unpacking python3-jaraco.functools (4.0.0-1) ...
784s Preparing to unpack .../50-python3-jinja2_3.1.3-1_all.deb ...
785s Unpacking python3-jinja2 (3.1.3-1) over (3.1.2-1ubuntu1) ...
785s Preparing to unpack .../51-python3-keyring_25.2.1-1_all.deb ...
785s Unpacking python3-keyring (25.2.1-1) over (24.3.1-1) ...
785s Preparing to unpack .../52-python3-six_1.16.0-6_all.deb ...
785s Unpacking python3-six (1.16.0-6) over (1.16.0-4) ...
785s Setting up libexpat1:armhf (2.6.2-1) ...
785s Setting up libapparmor1:armhf (4.0.1-0ubuntu1) ...
785s Setting up libxcb1:armhf (1.17.0-2) ...
785s Setting up apt-utils (2.9.3) ...
785s Setting up python3-jaraco.functools (4.0.0-1) ...
786s Setting up python3-jaraco.context (4.3.0-1) ...
786s Setting up libcurl4t64:armhf (8.5.0-2ubuntu10.1) ...
786s Setting up python3-problem-report (2.28.1-0ubuntu4) ...
786s Setting up libtirpc-common (1.3.4+ds-1.3) ...
786s Setting up libsqlite3-0:armhf (3.45.3-1) ...
786s Setting up libuv1t64:armhf (1.48.0-4) ...
786s Setting up libcurl3t64-gnutls:armhf (8.5.0-2ubuntu10.1) ...
786s Setting up less (590-2ubuntu2.1) ...
786s Setting up pastebinit (1.7.0-1) ...
786s Setting up libnss3:armhf (2:3.100-1) ...
786s Setting up locales (2.39-0ubuntu8.1) ...
788s Generating locales (this might take a while)...
793s   en_US.UTF-8... done
793s Generation complete.
793s Setting up xxd (2:9.1.0377-1ubuntu1) ...
793s Setting up libelf1t64:armhf (0.191-1) ...
793s Setting up python-babel-localedata (2.14.0-1) ...
793s Setting up tzdata (2024a-4ubuntu1) ...
794s 
794s Current default time zone: 'Etc/UTC'
794s Local time is now:      Fri May 24 08:35:06 UTC 2024.
794s Universal Time is now:  Fri May 24 08:35:06 UTC 2024.
794s Run 'dpkg-reconfigure tzdata' if you wish to change it.
794s 
794s Setting up python3-six (1.16.0-6) ...
794s Setting up apparmor (4.0.1-0ubuntu1) ...
794s Installing new version of config file /etc/apparmor.d/abstractions/authentication ...
794s Installing new version of config file /etc/apparmor.d/abstractions/samba ...
794s Installing new version of config file /etc/apparmor.d/firefox ...
795s apparmor_parser: Unable to replace "lsb_release".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
795s 
795s apparmor_parser: Unable to replace "kmod".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
795s 
795s apparmor_parser: Unable to replace "nvidia_modprobe".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
795s 
797s Reloading AppArmor profiles 
797s /sbin/apparmor_parser: Unable to replace "1password".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "Discord".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "MongoDB Compass".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "balena-etcher".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "brave".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "buildah".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "busybox".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "cam".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "ch-checkns".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "ch-run".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "chrome".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "element-desktop".  /sbin/apparmor_parser: Unable to replace "crun".  /sbin/apparmor_parser: Unable to replace "devhelp".  /sbin/apparmor_parser: Unable to replace "bwrap".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "vscode".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "epiphany".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "evolution".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "firefox".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "flatpak".  /sbin/apparmor_parser: Unable to replace "foliate".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "geary".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "github-desktop".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "goldendict".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "ipa_verify".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "keybase".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "kchmviewer".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "lc-compliance".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "libcamerify".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "linux-sandbox".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "loupe".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "lxc-attach".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "lxc-create".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "lxc-destroy".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "lxc-execute".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "lxc-stop".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "lxc-usernsexec".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "lxc-unshare".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "msedge".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "mmdebstrap".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "nautilus".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "notepadqq".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "obsidian".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "opam".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "opera".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "podman".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "polypane".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "privacybrowser".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "qmapshack".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "qutebrowser".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "rpm".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "rootlesskit".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "qcam".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "runc".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "pageedit".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "rssguard".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "sbuild".  /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "plasmashell".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "sbuild-abort".  /sbin/apparmor_parser: Unable to replace "sbuild-adduser".  /sbin/apparmor_parser: Unable to replace "sbuild-apt".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "sbuild-distupgrade".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "sbuild-createchroot".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "sbuild-checkpackages".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "sbuild-destroychroot".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "sbuild-clean".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "sbuild-shell".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "sbuild-update".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "sbuild-hold".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "sbuild-unhold".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "scide".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "signal-desktop".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "slack".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "sbuild-upgrade".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "steam".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "lsb_release".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "surfshark".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "stress-ng".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "slirp4netns".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "thunderbird".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "trinity".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "systemd-coredump".  /sbin/apparmor_parser: Unable to replace "tup".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "toybox".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "tuxedo-control-center".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "userbindmount".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "unprivileged_userns".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "kmod".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "nvidia_modprobe".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "uwsgi-core".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "vdens".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "virtiofsd".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "vivaldi-bin".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "vpnns".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "wike".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "unix-chkpwd".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "wpcom".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "/usr/bin/man".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "rsyslogd".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_apt_news".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "/usr/lib/NetworkManager/nm-dhcp-client.action".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
797s /sbin/apparmor_parser: Unable to replace "tcpdump".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
797s 
798s /sbin/apparmor_parser: Unable to replace "transmission-cli".  /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
798s 
798s Error: At least one profile failed to load
798s Setting up libklibc:armhf (2.0.13-4ubuntu1) ...
798s Setting up python3-jinja2 (3.1.3-1) ...
798s Setting up libglib2.0-0t64:armhf (2.80.2-1ubuntu1) ...
798s No schema files found: doing nothing.
798s Setting up libglib2.0-data (2.80.2-1ubuntu1) ...
798s Setting up vim-common (2:9.1.0377-1ubuntu1) ...
798s Setting up libslang2:armhf (2.3.3-5) ...
798s Setting up python3-pyparsing (3.1.2-1) ...
799s Setting up libnvme1t64 (1.9-1) ...
799s Setting up bash-completion (1:2.14.0-1) ...
799s Installing new version of config file /etc/profile.d/bash_completion.sh ...
799s Setting up perl-modules-5.38 (5.38.2-4) ...
799s Setting up dhcpcd-base (1:10.0.6-5) ...
799s Setting up gir1.2-glib-2.0:armhf (2.80.2-1ubuntu1) ...
799s Setting up python-apt-common (2.9.0) ...
799s Setting up dracut-install (060+5-8ubuntu1) ...
799s Setting up groff-base (1.23.0-4) ...
799s Setting up libeatmydata1:armhf (131-2) ...
799s Setting up python3-keyring (25.2.1-1) ...
799s Setting up python3-httplib2 (0.22.0-1) ...
800s Setting up libgirepository-1.0-1:armhf (1.80.1-3) ...
800s Setting up libevent-core-2.1-7t64:armhf (2.1.12-stable-10) ...
800s Setting up curl (8.5.0-2ubuntu10.1) ...
800s Setting up libperl5.38t64:armhf (5.38.2-4) ...
800s Setting up klibc-utils (2.0.13-4ubuntu1) ...
800s Setting up libbsd0:armhf (0.12.2-1) ...
800s Setting up libgpg-error-l10n (1.49-2) ...
800s Setting up liblocale-gettext-perl (1.07-7) ...
800s Setting up libbpf1:armhf (1:1.4.1-1) ...
800s Setting up rsync (3.3.0-1) ...
801s rsync.service is a disabled or a static unit not running, not starting it.
801s Setting up initramfs-tools-bin (0.142ubuntu27) ...
801s Setting up python3-blinker (1.8.2-1) ...
802s Setting up eatmydata (131-2) ...
802s Setting up libtirpc3t64:armhf (1.3.4+ds-1.3) ...
802s Setting up python3-babel (2.14.0-1) ...
802s Setting up python3-apt (2.9.0) ...
803s Setting up iproute2 (6.9.0-1) ...
803s Removing obsolete conffile /etc/iproute2/group ...
803s Removing obsolete conffile /etc/iproute2/rt_realms ...
803s Removing obsolete conffile /etc/iproute2/rt_scopes ...
803s Removing obsolete conffile /etc/iproute2/rt_tables ...
803s Removing obsolete conffile /etc/iproute2/rt_tables.d/README ...
803s Removing obsolete conffile /etc/iproute2/rt_protos.d/README ...
803s Removing obsolete conffile /etc/iproute2/rt_protos ...
803s Removing obsolete conffile /etc/iproute2/rt_dsfield ...
803s Removing obsolete conffile /etc/iproute2/nl_protos ...
803s Removing obsolete conffile /etc/iproute2/ematch_map ...
803s Removing obsolete conffile /etc/iproute2/bpf_pinning ...
803s Setting up libfwupd2:armhf (1.9.20-1) ...
803s Setting up vim-tiny (2:9.1.0377-1ubuntu1) ...
803s Setting up man-db (2.12.1-1) ...
803s Updating database of manual pages ...
806s apparmor_parser: Unable to replace "/usr/bin/man".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
806s 
807s man-db.service is a disabled or a static unit not running, not starting it.
807s Setting up python3-apport (2.28.1-0ubuntu4) ...
808s Setting up perl (5.38.2-4) ...
808s Setting up gir1.2-girepository-2.0:armhf (1.80.1-3) ...
808s Setting up libdpkg-perl (1.22.6ubuntu10) ...
808s Setting up initramfs-tools-core (0.142ubuntu27) ...
808s Setting up ubuntu-pro-client (32.1) ...
808s Installing new version of config file /etc/apparmor.d/ubuntu_pro_apt_news ...
808s apparmor_parser: Unable to replace "ubuntu_pro_apt_news".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
808s 
809s apparmor_parser: Unable to replace "apt_methods".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
809s 
809s apparmor_parser: Unable to replace "ubuntu_pro_esm_cache".  apparmor_parser: Access denied. You need policy admin privileges to manage profiles.
809s 
812s Setting up fwupd (1.9.20-1) ...
813s fwupd-offline-update.service is a disabled or a static unit not running, not starting it.
813s fwupd-refresh.service is a disabled or a static unit not running, not starting it.
813s fwupd.service is a disabled or a static unit not running, not starting it.
813s Setting up ubuntu-pro-client-l10n (32.1) ...
813s Setting up initramfs-tools (0.142ubuntu27) ...
813s update-initramfs: deferring update (trigger activated)
813s Setting up dpkg-dev (1.22.6ubuntu10) ...
813s Setting up apport-core-dump-handler (2.28.1-0ubuntu4) ...
815s Setting up apport (2.28.1-0ubuntu4) ...
815s Installing new version of config file /etc/apport/crashdb.conf ...
817s apport-autoreport.service is a disabled or a static unit not running, not starting it.
817s Processing triggers for dbus (1.14.10-4ubuntu4) ...
817s Processing triggers for libc-bin (2.39-0ubuntu8.1) ...
817s Processing triggers for initramfs-tools (0.142ubuntu27) ...
820s Reading package lists...
820s Building dependency tree...
820s Reading state information...
822s The following packages will be REMOVED:
822s   libatm1t64*
822s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded.
822s After this operation, 94.2 kB disk space will be freed.
823s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 58570 files and directories currently installed.)
823s Removing libatm1t64:armhf (1:2.5.1-5.1build1) ...
823s Processing triggers for libc-bin (2.39-0ubuntu8.1) ...
825s autopkgtest [08:35:37]: rebooting testbed after setup commands that affected boot
910s Reading package lists...
911s Building dependency tree...
911s Reading state information...
912s Starting pkgProblemResolver with broken count: 0
912s Starting 2 pkgProblemResolver with broken count: 0
912s Done
913s The following additional packages will be installed:
913s   build-essential cpp cpp-13 cpp-13-arm-linux-gnueabihf
913s   cpp-arm-linux-gnueabihf dctrl-tools fontconfig fontconfig-config
913s   fonts-dejavu-core fonts-dejavu-mono fonts-glyphicons-halflings fonts-mathjax
913s   g++ g++-13 g++-13-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-13
913s   gcc-13-arm-linux-gnueabihf gcc-13-base gcc-arm-linux-gnueabihf gfortran
913s   gfortran-13 gfortran-13-arm-linux-gnueabihf gfortran-arm-linux-gnueabihf
913s   icu-devtools libasan8 libatomic1 libblas-dev libblas3 libbz2-dev
913s   libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libdatrie1
913s   libdeflate-dev libdeflate0 libfontconfig1 libfreetype6 libgcc-13-dev
913s   libgfortran-13-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b
913s   libice6 libicu-dev libisl23 libjbig0 libjpeg-dev libjpeg-turbo8
913s   libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-bootstrap libjs-highlight.js
913s   libjs-jquery libjs-jquery-datatables libjs-mathjax liblapack-dev liblapack3
913s   liblerc4 liblzma-dev libmpc3 libncurses-dev libpango-1.0-0
913s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre2-16-0
913s   libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3
913s   libpng-dev libreadline-dev libsharpyuv0 libsm6 libstdc++-13-dev libtcl8.6
913s   libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libubsan1 libwebp7
913s   libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64
913s   linux-libc-dev node-normalize.css pkg-r-autopkgtest pkgconf pkgconf-bin
913s   r-base-core r-base-dev r-cran-base64enc r-cran-cli r-cran-colorspace
913s   r-cran-commonmark r-cran-evaluate r-cran-fansi r-cran-farver r-cran-ggplot2
913s   r-cran-glue r-cran-gtable r-cran-highr r-cran-isoband r-cran-knitr
913s   r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-magrittr
913s   r-cran-markdown r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-mgcv
913s   r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-r6
913s   r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8
913s   r-cran-vctrs r-cran-viridislite r-cran-withr r-cran-xfun r-cran-yaml
913s   rpcsvc-proto unzip x11-common xdg-utils zip zlib1g-dev
914s Suggested packages:
914s   cpp-doc gcc-13-locales cpp-13-doc debtags gcc-13-doc gcc-multilib
914s   manpages-dev autoconf automake libtool flex bison gdb gcc-doc
914s   gdb-arm-linux-gnueabihf gfortran-doc gfortran-13-doc libcoarrays-dev
914s   liblapack-doc glibc-doc icu-doc fonts-mathjax-extras fonts-stix
914s   libjs-mathjax-doc liblzma-doc ncurses-doc readline-doc libstdc++-13-doc
914s   tcl8.6 tk8.6 libjs-html5shiv elpa-ess r-doc-info | r-doc-pdf r-mathlib
914s   r-base-html texlive-base texlive-latex-base texlive-plain-generic
914s   texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils
914s   texlive-latex-recommended texlive-latex-extra texinfo r-cran-kernsmooth
914s   r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs
914s   r-cran-dplyr r-cran-png r-cran-jpeg r-cran-rmarkdown r-cran-viridis
914s   r-cran-covr r-cran-magick r-cran-sf r-cran-bit64 r-cran-dbi
914s   r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-stringi
914s   r-cran-survival r-cran-units r-cran-vdiffr r-cran-testthat r-cran-bench
914s   r-cran-blob r-cran-brio r-cran-callr r-cran-crayon r-cran-here r-cran-hms
914s   r-cran-htmltools r-cran-pkgbuild r-cran-pkgload r-cran-purrr r-cran-tidyr
914s Recommended packages:
914s   bzip2-doc manpages manpages-dev libc-devtools javascript-common libpng-tools
914s   r-recommended r-doc-html r-cran-callr r-cran-covr r-cran-crayon
914s   r-cran-digest r-cran-htmltools r-cran-htmlwidgets r-cran-mockery
914s   r-cran-processx r-cran-ps r-cran-rmarkdown r-cran-rprojroot
914s   r-cran-rstudioapi r-cran-testthat r-cran-whoami r-cran-curl r-cran-xml2
914s   r-cran-unitizer r-cran-dplyr r-cran-hexbin r-cran-hmisc r-cran-mapproj
914s   r-cran-maps r-cran-multcomp r-cran-profvis r-cran-quantreg r-cran-ragg
914s   r-cran-rpart r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-dbi
914s   r-cran-rsqlite r-cran-waldo r-cran-testit r-cran-bslib r-cran-codetools
914s   r-cran-formatr r-cran-gridsvg r-cran-jpeg r-cran-magick r-cran-png
914s   r-cran-reticulate r-cran-rgl r-cran-sass r-cran-tikzdevice r-cran-tinytex
914s   r-cran-webshot node-highlight.js r-cran-lintr r-cran-tidyverse r-cran-rcurl
914s   r-cran-r.devices r-cran-r.rsp r-cran-lubridate r-cran-fs r-cran-usethis
914s   r-cran-bit64 r-cran-dichromat r-cran-hms r-cran-stringi r-cran-data.table
914s   r-cran-mockr r-cran-formattable r-cran-generics r-cran-pkgdown
914s   r-cran-zeallot r-cran-mime r-cran-remotes r-cran-renv r-cran-jsonlite
914s   r-cran-runit libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl
914s   x11-utils x11-xserver-utils
914s The following NEW packages will be installed:
914s   autopkgtest-satdep build-essential cpp cpp-13 cpp-13-arm-linux-gnueabihf
914s   cpp-arm-linux-gnueabihf dctrl-tools fontconfig fontconfig-config
914s   fonts-dejavu-core fonts-dejavu-mono fonts-glyphicons-halflings fonts-mathjax
914s   g++ g++-13 g++-13-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-13
914s   gcc-13-arm-linux-gnueabihf gcc-13-base gcc-arm-linux-gnueabihf gfortran
914s   gfortran-13 gfortran-13-arm-linux-gnueabihf gfortran-arm-linux-gnueabihf
914s   icu-devtools libasan8 libatomic1 libblas-dev libblas3 libbz2-dev
914s   libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libdatrie1
914s   libdeflate-dev libdeflate0 libfontconfig1 libfreetype6 libgcc-13-dev
914s   libgfortran-13-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b
914s   libice6 libicu-dev libisl23 libjbig0 libjpeg-dev libjpeg-turbo8
914s   libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-bootstrap libjs-highlight.js
914s   libjs-jquery libjs-jquery-datatables libjs-mathjax liblapack-dev liblapack3
914s   liblerc4 liblzma-dev libmpc3 libncurses-dev libpango-1.0-0
914s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre2-16-0
914s   libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3
914s   libpng-dev libreadline-dev libsharpyuv0 libsm6 libstdc++-13-dev libtcl8.6
914s   libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libubsan1 libwebp7
914s   libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64
914s   linux-libc-dev node-normalize.css pkg-r-autopkgtest pkgconf pkgconf-bin
914s   r-base-core r-base-dev r-cran-base64enc r-cran-cli r-cran-colorspace
914s   r-cran-commonmark r-cran-evaluate r-cran-fansi r-cran-farver r-cran-ggplot2
914s   r-cran-glue r-cran-gtable r-cran-highr r-cran-isoband r-cran-knitr
914s   r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-magrittr
914s   r-cran-markdown r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-mgcv
914s   r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-r6
914s   r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8
914s   r-cran-vctrs r-cran-viridislite r-cran-withr r-cran-xfun r-cran-yaml
914s   rpcsvc-proto unzip x11-common xdg-utils zip zlib1g-dev
914s 0 upgraded, 148 newly installed, 0 to remove and 0 not upgraded.
914s Need to get 152 MB/152 MB of archives.
914s After this operation, 402 MB of additional disk space will be used.
914s Get:1 /tmp/autopkgtest.nMUE6C/2-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [752 B]
914s Get:2 http://ftpmaster.internal/ubuntu oracular/main armhf libc-dev-bin armhf 2.39-0ubuntu8.1 [19.1 kB]
914s Get:3 http://ftpmaster.internal/ubuntu oracular/main armhf linux-libc-dev armhf 6.8.0-31.31 [1557 kB]
915s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf libcrypt-dev armhf 1:4.4.36-4build1 [120 kB]
915s Get:5 http://ftpmaster.internal/ubuntu oracular/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB]
915s Get:6 http://ftpmaster.internal/ubuntu oracular/main armhf libc6-dev armhf 2.39-0ubuntu8.1 [1351 kB]
915s Get:7 http://ftpmaster.internal/ubuntu oracular/main armhf gcc-13-base armhf 13.2.0-23ubuntu4 [48.9 kB]
915s Get:8 http://ftpmaster.internal/ubuntu oracular/main armhf libisl23 armhf 0.26-3build1 [544 kB]
915s Get:9 http://ftpmaster.internal/ubuntu oracular/main armhf libmpc3 armhf 1.3.1-1build1 [46.7 kB]
915s Get:10 http://ftpmaster.internal/ubuntu oracular/main armhf cpp-13-arm-linux-gnueabihf armhf 13.2.0-23ubuntu4 [8759 kB]
916s Get:11 http://ftpmaster.internal/ubuntu oracular/main armhf cpp-13 armhf 13.2.0-23ubuntu4 [1034 B]
916s Get:12 http://ftpmaster.internal/ubuntu oracular/main armhf cpp-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu1 [5320 B]
916s Get:13 http://ftpmaster.internal/ubuntu oracular/main armhf cpp armhf 4:13.2.0-7ubuntu1 [22.4 kB]
916s Get:14 http://ftpmaster.internal/ubuntu oracular/main armhf libcc1-0 armhf 14.1.0-1ubuntu1 [43.3 kB]
916s Get:15 http://ftpmaster.internal/ubuntu oracular/main armhf libgomp1 armhf 14.1.0-1ubuntu1 [125 kB]
916s Get:16 http://ftpmaster.internal/ubuntu oracular/main armhf libatomic1 armhf 14.1.0-1ubuntu1 [7816 B]
916s Get:17 http://ftpmaster.internal/ubuntu oracular/main armhf libasan8 armhf 14.1.0-1ubuntu1 [2913 kB]
916s Get:18 http://ftpmaster.internal/ubuntu oracular/main armhf libubsan1 armhf 14.1.0-1ubuntu1 [1154 kB]
916s Get:19 http://ftpmaster.internal/ubuntu oracular/main armhf libgcc-13-dev armhf 13.2.0-23ubuntu4 [899 kB]
916s Get:20 http://ftpmaster.internal/ubuntu oracular/main armhf gcc-13-arm-linux-gnueabihf armhf 13.2.0-23ubuntu4 [16.9 MB]
917s Get:21 http://ftpmaster.internal/ubuntu oracular/main armhf gcc-13 armhf 13.2.0-23ubuntu4 [453 kB]
917s Get:22 http://ftpmaster.internal/ubuntu oracular/main armhf gcc-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu1 [1220 B]
917s Get:23 http://ftpmaster.internal/ubuntu oracular/main armhf gcc armhf 4:13.2.0-7ubuntu1 [5022 B]
917s Get:24 http://ftpmaster.internal/ubuntu oracular/main armhf libstdc++-13-dev armhf 13.2.0-23ubuntu4 [2456 kB]
917s Get:25 http://ftpmaster.internal/ubuntu oracular/main armhf g++-13-arm-linux-gnueabihf armhf 13.2.0-23ubuntu4 [9941 kB]
918s Get:26 http://ftpmaster.internal/ubuntu oracular/main armhf g++-13 armhf 13.2.0-23ubuntu4 [14.5 kB]
918s Get:27 http://ftpmaster.internal/ubuntu oracular/main armhf g++-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu1 [966 B]
918s Get:28 http://ftpmaster.internal/ubuntu oracular/main armhf g++ armhf 4:13.2.0-7ubuntu1 [1090 B]
918s Get:29 http://ftpmaster.internal/ubuntu oracular/main armhf build-essential armhf 12.10ubuntu1 [4928 B]
918s Get:30 http://ftpmaster.internal/ubuntu oracular/main armhf dctrl-tools armhf 2.24-3build3 [94.7 kB]
918s Get:31 http://ftpmaster.internal/ubuntu oracular/main armhf libfreetype6 armhf 2.13.2+dfsg-1build3 [331 kB]
918s Get:32 http://ftpmaster.internal/ubuntu oracular/main armhf fonts-dejavu-mono all 2.37-8 [502 kB]
918s Get:33 http://ftpmaster.internal/ubuntu oracular/main armhf fonts-dejavu-core all 2.37-8 [835 kB]
918s Get:34 http://ftpmaster.internal/ubuntu oracular/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB]
918s Get:35 http://ftpmaster.internal/ubuntu oracular/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB]
918s Get:36 http://ftpmaster.internal/ubuntu oracular/main armhf fontconfig armhf 2.15.0-1.1ubuntu2 [189 kB]
918s Get:37 http://ftpmaster.internal/ubuntu oracular/universe armhf fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB]
918s Get:38 http://ftpmaster.internal/ubuntu oracular/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
918s Get:39 http://ftpmaster.internal/ubuntu oracular/main armhf libgfortran5 armhf 14.1.0-1ubuntu1 [311 kB]
918s Get:40 http://ftpmaster.internal/ubuntu oracular/main armhf libgfortran-13-dev armhf 13.2.0-23ubuntu4 [359 kB]
918s Get:41 http://ftpmaster.internal/ubuntu oracular/main armhf gfortran-13-arm-linux-gnueabihf armhf 13.2.0-23ubuntu4 [9182 kB]
918s Get:42 http://ftpmaster.internal/ubuntu oracular/main armhf gfortran-13 armhf 13.2.0-23ubuntu4 [11.7 kB]
918s Get:43 http://ftpmaster.internal/ubuntu oracular/main armhf gfortran-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu1 [1024 B]
918s Get:44 http://ftpmaster.internal/ubuntu oracular/main armhf gfortran armhf 4:13.2.0-7ubuntu1 [1166 B]
918s Get:45 http://ftpmaster.internal/ubuntu oracular/main armhf icu-devtools armhf 74.2-1ubuntu3 [201 kB]
918s Get:46 http://ftpmaster.internal/ubuntu oracular/main armhf libblas3 armhf 3.12.0-3build1 [123 kB]
918s Get:47 http://ftpmaster.internal/ubuntu oracular/main armhf libblas-dev armhf 3.12.0-3build1 [132 kB]
918s Get:48 http://ftpmaster.internal/ubuntu oracular/main armhf libbz2-dev armhf 1.0.8-5.1 [30.5 kB]
918s Get:49 http://ftpmaster.internal/ubuntu oracular/main armhf libpixman-1-0 armhf 0.42.2-1build1 [193 kB]
918s Get:50 http://ftpmaster.internal/ubuntu oracular/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB]
918s Get:51 http://ftpmaster.internal/ubuntu oracular/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B]
918s Get:52 http://ftpmaster.internal/ubuntu oracular/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB]
918s Get:53 http://ftpmaster.internal/ubuntu oracular/main armhf libcairo2 armhf 1.18.0-3build1 [482 kB]
918s Get:54 http://ftpmaster.internal/ubuntu oracular/main armhf libdatrie1 armhf 0.2.13-3build1 [15.7 kB]
918s Get:55 http://ftpmaster.internal/ubuntu oracular/main armhf libdeflate0 armhf 1.20-1 [38.3 kB]
918s Get:56 http://ftpmaster.internal/ubuntu oracular/main armhf libdeflate-dev armhf 1.20-1 [44.6 kB]
918s Get:57 http://ftpmaster.internal/ubuntu oracular/main armhf libgraphite2-3 armhf 1.3.14-2build1 [64.6 kB]
918s Get:58 http://ftpmaster.internal/ubuntu oracular/main armhf libharfbuzz0b armhf 8.3.0-2build2 [446 kB]
918s Get:59 http://ftpmaster.internal/ubuntu oracular/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB]
918s Get:60 http://ftpmaster.internal/ubuntu oracular/main armhf libice6 armhf 2:1.0.10-1build3 [35.4 kB]
918s Get:61 http://ftpmaster.internal/ubuntu oracular/main armhf libicu-dev armhf 74.2-1ubuntu3 [11.6 MB]
919s Get:62 http://ftpmaster.internal/ubuntu oracular/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu2 [125 kB]
919s Get:63 http://ftpmaster.internal/ubuntu oracular/main armhf libjpeg-turbo8-dev armhf 2.1.5-2ubuntu2 [262 kB]
919s Get:64 http://ftpmaster.internal/ubuntu oracular/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B]
919s Get:65 http://ftpmaster.internal/ubuntu oracular/main armhf libjpeg8-dev armhf 8c-2ubuntu11 [1484 B]
919s Get:66 http://ftpmaster.internal/ubuntu oracular/main armhf libjpeg-dev armhf 8c-2ubuntu11 [1482 B]
919s Get:67 http://ftpmaster.internal/ubuntu oracular/universe armhf libjs-bootstrap all 3.4.1+dfsg-3 [129 kB]
919s Get:68 http://ftpmaster.internal/ubuntu oracular/universe armhf libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB]
919s Get:69 http://ftpmaster.internal/ubuntu oracular/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
919s Get:70 http://ftpmaster.internal/ubuntu oracular/universe armhf libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB]
919s Get:71 http://ftpmaster.internal/ubuntu oracular/main armhf liblapack3 armhf 3.12.0-3build1 [2085 kB]
919s Get:72 http://ftpmaster.internal/ubuntu oracular/main armhf liblapack-dev armhf 3.12.0-3build1 [2177 kB]
919s Get:73 http://ftpmaster.internal/ubuntu oracular/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu2 [151 kB]
919s Get:74 http://ftpmaster.internal/ubuntu oracular/main armhf libncurses-dev armhf 6.4+20240113-1ubuntu2 [501 kB]
919s Get:75 http://ftpmaster.internal/ubuntu oracular/main armhf libthai-data all 0.1.29-2build1 [158 kB]
919s Get:76 http://ftpmaster.internal/ubuntu oracular/main armhf libthai0 armhf 0.1.29-2build1 [15.2 kB]
919s Get:77 http://ftpmaster.internal/ubuntu oracular/main armhf libpango-1.0-0 armhf 1.52.2+ds-1 [209 kB]
919s Get:78 http://ftpmaster.internal/ubuntu oracular/main armhf libpangoft2-1.0-0 armhf 1.52.2+ds-1 [36.4 kB]
919s Get:79 http://ftpmaster.internal/ubuntu oracular/main armhf libpangocairo-1.0-0 armhf 1.52.2+ds-1 [24.9 kB]
919s Get:80 http://ftpmaster.internal/ubuntu oracular/main armhf libpaper1 armhf 1.1.29build1 [12.6 kB]
919s Get:81 http://ftpmaster.internal/ubuntu oracular/main armhf libpaper-utils armhf 1.1.29build1 [8184 B]
919s Get:82 http://ftpmaster.internal/ubuntu oracular/main armhf libpcre2-16-0 armhf 10.42-4ubuntu2 [180 kB]
919s Get:83 http://ftpmaster.internal/ubuntu oracular/main armhf libpcre2-32-0 armhf 10.42-4ubuntu2 [171 kB]
919s Get:84 http://ftpmaster.internal/ubuntu oracular/main armhf libpcre2-posix3 armhf 10.42-4ubuntu2 [6088 B]
919s Get:85 http://ftpmaster.internal/ubuntu oracular/main armhf libpcre2-dev armhf 10.42-4ubuntu2 [664 kB]
919s Get:86 http://ftpmaster.internal/ubuntu oracular/main armhf libpkgconf3 armhf 1.8.1-2build1 [26.3 kB]
919s Get:87 http://ftpmaster.internal/ubuntu oracular/main armhf zlib1g-dev armhf 1:1.3.dfsg-3.1ubuntu2 [880 kB]
919s Get:88 http://ftpmaster.internal/ubuntu oracular/main armhf libpng-dev armhf 1.6.43-5build1 [248 kB]
919s Get:89 http://ftpmaster.internal/ubuntu oracular/main armhf libreadline-dev armhf 8.2-4build1 [153 kB]
919s Get:90 http://ftpmaster.internal/ubuntu oracular/main armhf libsharpyuv0 armhf 1.4.0-0.1 [16.3 kB]
919s Get:91 http://ftpmaster.internal/ubuntu oracular/main armhf libsm6 armhf 2:1.2.3-1build3 [14.1 kB]
919s Get:92 http://ftpmaster.internal/ubuntu oracular/main armhf libtcl8.6 armhf 8.6.14+dfsg-1build1 [903 kB]
919s Get:93 http://ftpmaster.internal/ubuntu oracular/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB]
919s Get:94 http://ftpmaster.internal/ubuntu oracular/main armhf libwebp7 armhf 1.4.0-0.1 [184 kB]
919s Get:95 http://ftpmaster.internal/ubuntu oracular/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu2 [178 kB]
919s Get:96 http://ftpmaster.internal/ubuntu oracular/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB]
919s Get:97 http://ftpmaster.internal/ubuntu oracular/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B]
919s Get:98 http://ftpmaster.internal/ubuntu oracular/main armhf libtk8.6 armhf 8.6.14-1build1 [681 kB]
919s Get:99 http://ftpmaster.internal/ubuntu oracular/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB]
919s Get:100 http://ftpmaster.internal/ubuntu oracular/universe armhf node-normalize.css all 8.0.1-5 [10.8 kB]
919s Get:101 http://ftpmaster.internal/ubuntu oracular/main armhf zip armhf 3.0-13build1 [163 kB]
919s Get:102 http://ftpmaster.internal/ubuntu oracular/main armhf unzip armhf 6.0-28ubuntu4 [163 kB]
919s Get:103 http://ftpmaster.internal/ubuntu oracular/main armhf xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB]
920s Get:104 http://ftpmaster.internal/ubuntu oracular/universe armhf r-base-core armhf 4.4.0-2 [28.1 MB]
921s Get:105 http://ftpmaster.internal/ubuntu oracular/main armhf liblzma-dev armhf 5.6.1+really5.4.5-1 [165 kB]
921s Get:106 http://ftpmaster.internal/ubuntu oracular/main armhf pkgconf-bin armhf 1.8.1-2build1 [20.7 kB]
921s Get:107 http://ftpmaster.internal/ubuntu oracular/main armhf pkgconf armhf 1.8.1-2build1 [16.8 kB]
921s Get:108 http://ftpmaster.internal/ubuntu oracular/main armhf libtirpc-dev armhf 1.3.4+ds-1.3 [184 kB]
921s Get:109 http://ftpmaster.internal/ubuntu oracular/universe armhf r-base-dev all 4.4.0-2 [4340 B]
921s Get:110 http://ftpmaster.internal/ubuntu oracular/universe armhf pkg-r-autopkgtest all 20231212ubuntu1 [6448 B]
921s Get:111 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-base64enc armhf 0.1-3-3 [27.3 kB]
921s Get:112 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-cli armhf 3.6.2-1 [1363 kB]
921s Get:113 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-colorspace armhf 2.1-0+dfsg-1 [1538 kB]
921s Get:114 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-commonmark armhf 1.9.1-1 [110 kB]
921s Get:115 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-evaluate all 0.23-1 [90.2 kB]
921s Get:116 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-fansi armhf 1.0.5-1 [611 kB]
921s Get:117 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-farver armhf 2.1.1-2 [1353 kB]
921s Get:118 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-glue armhf 1.7.0-1 [153 kB]
921s Get:119 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-rlang armhf 1.1.3-1 [1658 kB]
921s Get:120 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
921s Get:121 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-gtable all 0.3.4+dfsg-1 [191 kB]
921s Get:122 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-isoband armhf 0.2.7-1 [1477 kB]
921s Get:123 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-mass armhf 7.3-60.0.1-1 [1118 kB]
921s Get:124 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-lattice armhf 0.22-6-1 [1363 kB]
921s Get:125 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-nlme armhf 3.1.164-1build1 [2248 kB]
921s Get:126 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-matrix armhf 1.6-5-1 [3762 kB]
921s Get:127 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-mgcv armhf 1.9-1-1 [3205 kB]
921s Get:128 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-labeling all 0.4.3-1 [62.1 kB]
921s Get:129 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-munsell all 0.5.0-2build1 [208 kB]
921s Get:130 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-r6 all 2.5.1-1 [99.0 kB]
921s Get:131 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB]
921s Get:132 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-viridislite all 0.4.2-2 [1088 kB]
921s Get:133 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-scales all 1.3.0-1 [603 kB]
921s Get:134 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-magrittr armhf 2.0.3-1 [154 kB]
921s Get:135 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-utf8 armhf 1.2.4-1 [136 kB]
921s Get:136 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-vctrs armhf 0.6.5-1 [1310 kB]
922s Get:137 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-pillar all 1.9.0+dfsg-1 [464 kB]
922s Get:138 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB]
922s Get:139 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-tibble armhf 3.2.1+dfsg-2 [415 kB]
922s Get:140 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-withr all 2.5.0-1 [225 kB]
922s Get:141 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB]
922s Get:142 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-xfun armhf 0.44+dfsg-1 [517 kB]
922s Get:143 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-highr all 0.10+dfsg-2 [38.5 kB]
922s Get:144 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-yaml armhf 2.3.8-2 [100 kB]
922s Get:145 http://ftpmaster.internal/ubuntu oracular/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
922s Get:146 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-knitr all 1.46+dfsg-1 [911 kB]
922s Get:147 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-markdown all 1.12+dfsg-2 [179 kB]
922s Get:148 http://ftpmaster.internal/ubuntu oracular/universe armhf r-cran-matrixstats armhf 1.2.0-1 [478 kB]
923s Preconfiguring packages ...
924s Fetched 152 MB in 8s (18.8 MB/s)
924s Selecting previously unselected package libc-dev-bin.
924s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
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(Reading database ... 58565 files and directories currently installed.)
924s Preparing to unpack .../000-libc-dev-bin_2.39-0ubuntu8.1_armhf.deb ...
924s Unpacking libc-dev-bin (2.39-0ubuntu8.1) ...
924s Selecting previously unselected package linux-libc-dev:armhf.
924s Preparing to unpack .../001-linux-libc-dev_6.8.0-31.31_armhf.deb ...
924s Unpacking linux-libc-dev:armhf (6.8.0-31.31) ...
924s Selecting previously unselected package libcrypt-dev:armhf.
924s Preparing to unpack .../002-libcrypt-dev_1%3a4.4.36-4build1_armhf.deb ...
924s Unpacking libcrypt-dev:armhf (1:4.4.36-4build1) ...
924s Selecting previously unselected package rpcsvc-proto.
924s Preparing to unpack .../003-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ...
924s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ...
924s Selecting previously unselected package libc6-dev:armhf.
924s Preparing to unpack .../004-libc6-dev_2.39-0ubuntu8.1_armhf.deb ...
924s Unpacking libc6-dev:armhf (2.39-0ubuntu8.1) ...
925s Selecting previously unselected package gcc-13-base:armhf.
925s Preparing to unpack .../005-gcc-13-base_13.2.0-23ubuntu4_armhf.deb ...
925s Unpacking gcc-13-base:armhf (13.2.0-23ubuntu4) ...
925s Selecting previously unselected package libisl23:armhf.
925s Preparing to unpack .../006-libisl23_0.26-3build1_armhf.deb ...
925s Unpacking libisl23:armhf (0.26-3build1) ...
925s Selecting previously unselected package libmpc3:armhf.
925s Preparing to unpack .../007-libmpc3_1.3.1-1build1_armhf.deb ...
925s Unpacking libmpc3:armhf (1.3.1-1build1) ...
925s Selecting previously unselected package cpp-13-arm-linux-gnueabihf.
925s Preparing to unpack .../008-cpp-13-arm-linux-gnueabihf_13.2.0-23ubuntu4_armhf.deb ...
925s Unpacking cpp-13-arm-linux-gnueabihf (13.2.0-23ubuntu4) ...
925s Selecting previously unselected package cpp-13.
925s Preparing to unpack .../009-cpp-13_13.2.0-23ubuntu4_armhf.deb ...
925s Unpacking cpp-13 (13.2.0-23ubuntu4) ...
925s Selecting previously unselected package cpp-arm-linux-gnueabihf.
925s Preparing to unpack .../010-cpp-arm-linux-gnueabihf_4%3a13.2.0-7ubuntu1_armhf.deb ...
925s Unpacking cpp-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ...
925s Selecting previously unselected package cpp.
925s Preparing to unpack .../011-cpp_4%3a13.2.0-7ubuntu1_armhf.deb ...
925s Unpacking cpp (4:13.2.0-7ubuntu1) ...
925s Selecting previously unselected package libcc1-0:armhf.
925s Preparing to unpack .../012-libcc1-0_14.1.0-1ubuntu1_armhf.deb ...
925s Unpacking libcc1-0:armhf (14.1.0-1ubuntu1) ...
925s Selecting previously unselected package libgomp1:armhf.
925s Preparing to unpack .../013-libgomp1_14.1.0-1ubuntu1_armhf.deb ...
925s Unpacking libgomp1:armhf (14.1.0-1ubuntu1) ...
926s Selecting previously unselected package libatomic1:armhf.
926s Preparing to unpack .../014-libatomic1_14.1.0-1ubuntu1_armhf.deb ...
926s Unpacking libatomic1:armhf (14.1.0-1ubuntu1) ...
926s Selecting previously unselected package libasan8:armhf.
926s Preparing to unpack .../015-libasan8_14.1.0-1ubuntu1_armhf.deb ...
926s Unpacking libasan8:armhf (14.1.0-1ubuntu1) ...
926s Selecting previously unselected package libubsan1:armhf.
926s Preparing to unpack .../016-libubsan1_14.1.0-1ubuntu1_armhf.deb ...
926s Unpacking libubsan1:armhf (14.1.0-1ubuntu1) ...
926s Selecting previously unselected package libgcc-13-dev:armhf.
926s Preparing to unpack .../017-libgcc-13-dev_13.2.0-23ubuntu4_armhf.deb ...
926s Unpacking libgcc-13-dev:armhf (13.2.0-23ubuntu4) ...
926s Selecting previously unselected package gcc-13-arm-linux-gnueabihf.
926s Preparing to unpack .../018-gcc-13-arm-linux-gnueabihf_13.2.0-23ubuntu4_armhf.deb ...
926s Unpacking gcc-13-arm-linux-gnueabihf (13.2.0-23ubuntu4) ...
927s Selecting previously unselected package gcc-13.
927s Preparing to unpack .../019-gcc-13_13.2.0-23ubuntu4_armhf.deb ...
927s Unpacking gcc-13 (13.2.0-23ubuntu4) ...
927s Selecting previously unselected package gcc-arm-linux-gnueabihf.
927s Preparing to unpack .../020-gcc-arm-linux-gnueabihf_4%3a13.2.0-7ubuntu1_armhf.deb ...
927s Unpacking gcc-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ...
927s Selecting previously unselected package gcc.
927s Preparing to unpack .../021-gcc_4%3a13.2.0-7ubuntu1_armhf.deb ...
927s Unpacking gcc (4:13.2.0-7ubuntu1) ...
927s Selecting previously unselected package libstdc++-13-dev:armhf.
927s Preparing to unpack .../022-libstdc++-13-dev_13.2.0-23ubuntu4_armhf.deb ...
927s Unpacking libstdc++-13-dev:armhf (13.2.0-23ubuntu4) ...
927s Selecting previously unselected package g++-13-arm-linux-gnueabihf.
927s Preparing to unpack .../023-g++-13-arm-linux-gnueabihf_13.2.0-23ubuntu4_armhf.deb ...
927s Unpacking g++-13-arm-linux-gnueabihf (13.2.0-23ubuntu4) ...
928s Selecting previously unselected package g++-13.
928s Preparing to unpack .../024-g++-13_13.2.0-23ubuntu4_armhf.deb ...
928s Unpacking g++-13 (13.2.0-23ubuntu4) ...
928s Selecting previously unselected package g++-arm-linux-gnueabihf.
928s Preparing to unpack .../025-g++-arm-linux-gnueabihf_4%3a13.2.0-7ubuntu1_armhf.deb ...
928s Unpacking g++-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ...
928s Selecting previously unselected package g++.
928s Preparing to unpack .../026-g++_4%3a13.2.0-7ubuntu1_armhf.deb ...
928s Unpacking g++ (4:13.2.0-7ubuntu1) ...
928s Selecting previously unselected package build-essential.
928s Preparing to unpack .../027-build-essential_12.10ubuntu1_armhf.deb ...
928s Unpacking build-essential (12.10ubuntu1) ...
928s Selecting previously unselected package dctrl-tools.
928s Preparing to unpack .../028-dctrl-tools_2.24-3build3_armhf.deb ...
928s Unpacking dctrl-tools (2.24-3build3) ...
928s Selecting previously unselected package libfreetype6:armhf.
928s Preparing to unpack .../029-libfreetype6_2.13.2+dfsg-1build3_armhf.deb ...
928s Unpacking libfreetype6:armhf (2.13.2+dfsg-1build3) ...
928s Selecting previously unselected package fonts-dejavu-mono.
928s Preparing to unpack .../030-fonts-dejavu-mono_2.37-8_all.deb ...
928s Unpacking fonts-dejavu-mono (2.37-8) ...
928s Selecting previously unselected package fonts-dejavu-core.
928s Preparing to unpack .../031-fonts-dejavu-core_2.37-8_all.deb ...
928s Unpacking fonts-dejavu-core (2.37-8) ...
928s Selecting previously unselected package fontconfig-config.
928s Preparing to unpack .../032-fontconfig-config_2.15.0-1.1ubuntu2_armhf.deb ...
929s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
929s Selecting previously unselected package libfontconfig1:armhf.
929s Preparing to unpack .../033-libfontconfig1_2.15.0-1.1ubuntu2_armhf.deb ...
929s Unpacking libfontconfig1:armhf (2.15.0-1.1ubuntu2) ...
929s Selecting previously unselected package fontconfig.
929s Preparing to unpack .../034-fontconfig_2.15.0-1.1ubuntu2_armhf.deb ...
929s Unpacking fontconfig (2.15.0-1.1ubuntu2) ...
929s Selecting previously unselected package fonts-glyphicons-halflings.
929s Preparing to unpack .../035-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ...
929s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ...
929s Selecting previously unselected package fonts-mathjax.
929s Preparing to unpack .../036-fonts-mathjax_2.7.9+dfsg-1_all.deb ...
929s Unpacking fonts-mathjax (2.7.9+dfsg-1) ...
929s Selecting previously unselected package libgfortran5:armhf.
929s Preparing to unpack .../037-libgfortran5_14.1.0-1ubuntu1_armhf.deb ...
929s Unpacking libgfortran5:armhf (14.1.0-1ubuntu1) ...
929s Selecting previously unselected package libgfortran-13-dev:armhf.
929s Preparing to unpack .../038-libgfortran-13-dev_13.2.0-23ubuntu4_armhf.deb ...
929s Unpacking libgfortran-13-dev:armhf (13.2.0-23ubuntu4) ...
930s Selecting previously unselected package gfortran-13-arm-linux-gnueabihf.
930s Preparing to unpack .../039-gfortran-13-arm-linux-gnueabihf_13.2.0-23ubuntu4_armhf.deb ...
930s Unpacking gfortran-13-arm-linux-gnueabihf (13.2.0-23ubuntu4) ...
930s Selecting previously unselected package gfortran-13.
930s Preparing to unpack .../040-gfortran-13_13.2.0-23ubuntu4_armhf.deb ...
930s Unpacking gfortran-13 (13.2.0-23ubuntu4) ...
930s Selecting previously unselected package gfortran-arm-linux-gnueabihf.
930s Preparing to unpack .../041-gfortran-arm-linux-gnueabihf_4%3a13.2.0-7ubuntu1_armhf.deb ...
930s Unpacking gfortran-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ...
930s Selecting previously unselected package gfortran.
930s Preparing to unpack .../042-gfortran_4%3a13.2.0-7ubuntu1_armhf.deb ...
930s Unpacking gfortran (4:13.2.0-7ubuntu1) ...
930s Selecting previously unselected package icu-devtools.
930s Preparing to unpack .../043-icu-devtools_74.2-1ubuntu3_armhf.deb ...
930s Unpacking icu-devtools (74.2-1ubuntu3) ...
930s Selecting previously unselected package libblas3:armhf.
930s Preparing to unpack .../044-libblas3_3.12.0-3build1_armhf.deb ...
930s Unpacking libblas3:armhf (3.12.0-3build1) ...
930s Selecting previously unselected package libblas-dev:armhf.
930s Preparing to unpack .../045-libblas-dev_3.12.0-3build1_armhf.deb ...
930s Unpacking libblas-dev:armhf (3.12.0-3build1) ...
930s Selecting previously unselected package libbz2-dev:armhf.
930s Preparing to unpack .../046-libbz2-dev_1.0.8-5.1_armhf.deb ...
930s Unpacking libbz2-dev:armhf (1.0.8-5.1) ...
930s Selecting previously unselected package libpixman-1-0:armhf.
930s Preparing to unpack .../047-libpixman-1-0_0.42.2-1build1_armhf.deb ...
930s Unpacking libpixman-1-0:armhf (0.42.2-1build1) ...
930s Selecting previously unselected package libxcb-render0:armhf.
931s Preparing to unpack .../048-libxcb-render0_1.17.0-2_armhf.deb ...
931s Unpacking libxcb-render0:armhf (1.17.0-2) ...
931s Selecting previously unselected package libxcb-shm0:armhf.
931s Preparing to unpack .../049-libxcb-shm0_1.17.0-2_armhf.deb ...
931s Unpacking libxcb-shm0:armhf (1.17.0-2) ...
931s Selecting previously unselected package libxrender1:armhf.
931s Preparing to unpack .../050-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ...
931s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ...
931s Selecting previously unselected package libcairo2:armhf.
931s Preparing to unpack .../051-libcairo2_1.18.0-3build1_armhf.deb ...
931s Unpacking libcairo2:armhf (1.18.0-3build1) ...
931s Selecting previously unselected package libdatrie1:armhf.
931s Preparing to unpack .../052-libdatrie1_0.2.13-3build1_armhf.deb ...
931s Unpacking libdatrie1:armhf (0.2.13-3build1) ...
931s Selecting previously unselected package libdeflate0:armhf.
931s Preparing to unpack .../053-libdeflate0_1.20-1_armhf.deb ...
931s Unpacking libdeflate0:armhf (1.20-1) ...
931s Selecting previously unselected package libdeflate-dev:armhf.
931s Preparing to unpack .../054-libdeflate-dev_1.20-1_armhf.deb ...
931s Unpacking libdeflate-dev:armhf (1.20-1) ...
931s Selecting previously unselected package libgraphite2-3:armhf.
931s Preparing to unpack .../055-libgraphite2-3_1.3.14-2build1_armhf.deb ...
931s Unpacking libgraphite2-3:armhf (1.3.14-2build1) ...
931s Selecting previously unselected package libharfbuzz0b:armhf.
931s Preparing to unpack .../056-libharfbuzz0b_8.3.0-2build2_armhf.deb ...
931s Unpacking libharfbuzz0b:armhf (8.3.0-2build2) ...
931s Selecting previously unselected package x11-common.
931s Preparing to unpack .../057-x11-common_1%3a7.7+23ubuntu3_all.deb ...
931s Unpacking x11-common (1:7.7+23ubuntu3) ...
931s Selecting previously unselected package libice6:armhf.
931s Preparing to unpack .../058-libice6_2%3a1.0.10-1build3_armhf.deb ...
931s Unpacking libice6:armhf (2:1.0.10-1build3) ...
931s Selecting previously unselected package libicu-dev:armhf.
931s Preparing to unpack .../059-libicu-dev_74.2-1ubuntu3_armhf.deb ...
931s Unpacking libicu-dev:armhf (74.2-1ubuntu3) ...
932s Selecting previously unselected package libjpeg-turbo8:armhf.
932s Preparing to unpack .../060-libjpeg-turbo8_2.1.5-2ubuntu2_armhf.deb ...
932s Unpacking libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ...
932s Selecting previously unselected package libjpeg-turbo8-dev:armhf.
932s Preparing to unpack .../061-libjpeg-turbo8-dev_2.1.5-2ubuntu2_armhf.deb ...
932s Unpacking libjpeg-turbo8-dev:armhf (2.1.5-2ubuntu2) ...
932s Selecting previously unselected package libjpeg8:armhf.
932s Preparing to unpack .../062-libjpeg8_8c-2ubuntu11_armhf.deb ...
932s Unpacking libjpeg8:armhf (8c-2ubuntu11) ...
932s Selecting previously unselected package libjpeg8-dev:armhf.
932s Preparing to unpack .../063-libjpeg8-dev_8c-2ubuntu11_armhf.deb ...
932s Unpacking libjpeg8-dev:armhf (8c-2ubuntu11) ...
932s Selecting previously unselected package libjpeg-dev:armhf.
932s Preparing to unpack .../064-libjpeg-dev_8c-2ubuntu11_armhf.deb ...
932s Unpacking libjpeg-dev:armhf (8c-2ubuntu11) ...
932s Selecting previously unselected package libjs-bootstrap.
932s Preparing to unpack .../065-libjs-bootstrap_3.4.1+dfsg-3_all.deb ...
932s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ...
932s Selecting previously unselected package libjs-highlight.js.
932s Preparing to unpack .../066-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ...
932s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ...
932s Selecting previously unselected package libjs-jquery.
932s Preparing to unpack .../067-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
932s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
932s Selecting previously unselected package libjs-jquery-datatables.
933s Preparing to unpack .../068-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ...
933s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ...
933s Selecting previously unselected package liblapack3:armhf.
933s Preparing to unpack .../069-liblapack3_3.12.0-3build1_armhf.deb ...
933s Unpacking liblapack3:armhf (3.12.0-3build1) ...
933s Selecting previously unselected package liblapack-dev:armhf.
933s Preparing to unpack .../070-liblapack-dev_3.12.0-3build1_armhf.deb ...
933s Unpacking liblapack-dev:armhf (3.12.0-3build1) ...
933s Selecting previously unselected package liblerc4:armhf.
933s Preparing to unpack .../071-liblerc4_4.0.0+ds-4ubuntu2_armhf.deb ...
933s Unpacking liblerc4:armhf (4.0.0+ds-4ubuntu2) ...
933s Selecting previously unselected package libncurses-dev:armhf.
933s Preparing to unpack .../072-libncurses-dev_6.4+20240113-1ubuntu2_armhf.deb ...
933s Unpacking libncurses-dev:armhf (6.4+20240113-1ubuntu2) ...
933s Selecting previously unselected package libthai-data.
933s Preparing to unpack .../073-libthai-data_0.1.29-2build1_all.deb ...
933s Unpacking libthai-data (0.1.29-2build1) ...
933s Selecting previously unselected package libthai0:armhf.
933s Preparing to unpack .../074-libthai0_0.1.29-2build1_armhf.deb ...
933s Unpacking libthai0:armhf (0.1.29-2build1) ...
933s Selecting previously unselected package libpango-1.0-0:armhf.
933s Preparing to unpack .../075-libpango-1.0-0_1.52.2+ds-1_armhf.deb ...
933s Unpacking libpango-1.0-0:armhf (1.52.2+ds-1) ...
933s Selecting previously unselected package libpangoft2-1.0-0:armhf.
933s Preparing to unpack .../076-libpangoft2-1.0-0_1.52.2+ds-1_armhf.deb ...
933s Unpacking libpangoft2-1.0-0:armhf (1.52.2+ds-1) ...
933s Selecting previously unselected package libpangocairo-1.0-0:armhf.
933s Preparing to unpack .../077-libpangocairo-1.0-0_1.52.2+ds-1_armhf.deb ...
933s Unpacking libpangocairo-1.0-0:armhf (1.52.2+ds-1) ...
933s Selecting previously unselected package libpaper1:armhf.
933s Preparing to unpack .../078-libpaper1_1.1.29build1_armhf.deb ...
933s Unpacking libpaper1:armhf (1.1.29build1) ...
934s Selecting previously unselected package libpaper-utils.
934s Preparing to unpack .../079-libpaper-utils_1.1.29build1_armhf.deb ...
934s Unpacking libpaper-utils (1.1.29build1) ...
934s Selecting previously unselected package libpcre2-16-0:armhf.
934s Preparing to unpack .../080-libpcre2-16-0_10.42-4ubuntu2_armhf.deb ...
934s Unpacking libpcre2-16-0:armhf (10.42-4ubuntu2) ...
934s Selecting previously unselected package libpcre2-32-0:armhf.
934s Preparing to unpack .../081-libpcre2-32-0_10.42-4ubuntu2_armhf.deb ...
934s Unpacking libpcre2-32-0:armhf (10.42-4ubuntu2) ...
934s Selecting previously unselected package libpcre2-posix3:armhf.
934s Preparing to unpack .../082-libpcre2-posix3_10.42-4ubuntu2_armhf.deb ...
934s Unpacking libpcre2-posix3:armhf (10.42-4ubuntu2) ...
934s Selecting previously unselected package libpcre2-dev:armhf.
934s Preparing to unpack .../083-libpcre2-dev_10.42-4ubuntu2_armhf.deb ...
934s Unpacking libpcre2-dev:armhf (10.42-4ubuntu2) ...
934s Selecting previously unselected package libpkgconf3:armhf.
934s Preparing to unpack .../084-libpkgconf3_1.8.1-2build1_armhf.deb ...
934s Unpacking libpkgconf3:armhf (1.8.1-2build1) ...
934s Selecting previously unselected package zlib1g-dev:armhf.
934s Preparing to unpack .../085-zlib1g-dev_1%3a1.3.dfsg-3.1ubuntu2_armhf.deb ...
934s Unpacking zlib1g-dev:armhf (1:1.3.dfsg-3.1ubuntu2) ...
934s Selecting previously unselected package libpng-dev:armhf.
934s Preparing to unpack .../086-libpng-dev_1.6.43-5build1_armhf.deb ...
934s Unpacking libpng-dev:armhf (1.6.43-5build1) ...
934s Selecting previously unselected package libreadline-dev:armhf.
934s Preparing to unpack .../087-libreadline-dev_8.2-4build1_armhf.deb ...
934s Unpacking libreadline-dev:armhf (8.2-4build1) ...
934s Selecting previously unselected package libsharpyuv0:armhf.
934s Preparing to unpack .../088-libsharpyuv0_1.4.0-0.1_armhf.deb ...
934s Unpacking libsharpyuv0:armhf (1.4.0-0.1) ...
934s Selecting previously unselected package libsm6:armhf.
934s Preparing to unpack .../089-libsm6_2%3a1.2.3-1build3_armhf.deb ...
934s Unpacking libsm6:armhf (2:1.2.3-1build3) ...
934s Selecting previously unselected package libtcl8.6:armhf.
934s Preparing to unpack .../090-libtcl8.6_8.6.14+dfsg-1build1_armhf.deb ...
934s Unpacking libtcl8.6:armhf (8.6.14+dfsg-1build1) ...
935s Selecting previously unselected package libjbig0:armhf.
935s Preparing to unpack .../091-libjbig0_2.1-6.1ubuntu2_armhf.deb ...
935s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ...
935s Selecting previously unselected package libwebp7:armhf.
935s Preparing to unpack .../092-libwebp7_1.4.0-0.1_armhf.deb ...
935s Unpacking libwebp7:armhf (1.4.0-0.1) ...
935s Selecting previously unselected package libtiff6:armhf.
935s Preparing to unpack .../093-libtiff6_4.5.1+git230720-4ubuntu2_armhf.deb ...
935s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu2) ...
935s Selecting previously unselected package libxft2:armhf.
935s Preparing to unpack .../094-libxft2_2.3.6-1build1_armhf.deb ...
935s Unpacking libxft2:armhf (2.3.6-1build1) ...
935s Selecting previously unselected package libxss1:armhf.
935s Preparing to unpack .../095-libxss1_1%3a1.2.3-1build3_armhf.deb ...
935s Unpacking libxss1:armhf (1:1.2.3-1build3) ...
935s Selecting previously unselected package libtk8.6:armhf.
935s Preparing to unpack .../096-libtk8.6_8.6.14-1build1_armhf.deb ...
935s Unpacking libtk8.6:armhf (8.6.14-1build1) ...
935s Selecting previously unselected package libxt6t64:armhf.
935s Preparing to unpack .../097-libxt6t64_1%3a1.2.1-1.2build1_armhf.deb ...
935s Unpacking libxt6t64:armhf (1:1.2.1-1.2build1) ...
935s Selecting previously unselected package node-normalize.css.
935s Preparing to unpack .../098-node-normalize.css_8.0.1-5_all.deb ...
935s Unpacking node-normalize.css (8.0.1-5) ...
935s Selecting previously unselected package zip.
935s Preparing to unpack .../099-zip_3.0-13build1_armhf.deb ...
935s Unpacking zip (3.0-13build1) ...
935s Selecting previously unselected package unzip.
935s Preparing to unpack .../100-unzip_6.0-28ubuntu4_armhf.deb ...
935s Unpacking unzip (6.0-28ubuntu4) ...
935s Selecting previously unselected package xdg-utils.
935s Preparing to unpack .../101-xdg-utils_1.1.3-4.1ubuntu3_all.deb ...
935s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ...
936s Selecting previously unselected package r-base-core.
936s Preparing to unpack .../102-r-base-core_4.4.0-2_armhf.deb ...
936s Unpacking r-base-core (4.4.0-2) ...
937s Selecting previously unselected package liblzma-dev:armhf.
937s Preparing to unpack .../103-liblzma-dev_5.6.1+really5.4.5-1_armhf.deb ...
937s Unpacking liblzma-dev:armhf (5.6.1+really5.4.5-1) ...
937s Selecting previously unselected package pkgconf-bin.
937s Preparing to unpack .../104-pkgconf-bin_1.8.1-2build1_armhf.deb ...
937s Unpacking pkgconf-bin (1.8.1-2build1) ...
937s Selecting previously unselected package pkgconf:armhf.
937s Preparing to unpack .../105-pkgconf_1.8.1-2build1_armhf.deb ...
937s Unpacking pkgconf:armhf (1.8.1-2build1) ...
937s Selecting previously unselected package libtirpc-dev:armhf.
937s Preparing to unpack .../106-libtirpc-dev_1.3.4+ds-1.3_armhf.deb ...
937s Unpacking libtirpc-dev:armhf (1.3.4+ds-1.3) ...
937s Selecting previously unselected package r-base-dev.
937s Preparing to unpack .../107-r-base-dev_4.4.0-2_all.deb ...
937s Unpacking r-base-dev (4.4.0-2) ...
937s Selecting previously unselected package pkg-r-autopkgtest.
937s Preparing to unpack .../108-pkg-r-autopkgtest_20231212ubuntu1_all.deb ...
937s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ...
937s Selecting previously unselected package r-cran-base64enc.
937s Preparing to unpack .../109-r-cran-base64enc_0.1-3-3_armhf.deb ...
937s Unpacking r-cran-base64enc (0.1-3-3) ...
937s Selecting previously unselected package r-cran-cli.
937s Preparing to unpack .../110-r-cran-cli_3.6.2-1_armhf.deb ...
937s Unpacking r-cran-cli (3.6.2-1) ...
937s Selecting previously unselected package r-cran-colorspace.
937s Preparing to unpack .../111-r-cran-colorspace_2.1-0+dfsg-1_armhf.deb ...
937s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ...
937s Selecting previously unselected package r-cran-commonmark.
937s Preparing to unpack .../112-r-cran-commonmark_1.9.1-1_armhf.deb ...
937s Unpacking r-cran-commonmark (1.9.1-1) ...
938s Selecting previously unselected package r-cran-evaluate.
938s Preparing to unpack .../113-r-cran-evaluate_0.23-1_all.deb ...
938s Unpacking r-cran-evaluate (0.23-1) ...
938s Selecting previously unselected package r-cran-fansi.
938s Preparing to unpack .../114-r-cran-fansi_1.0.5-1_armhf.deb ...
938s Unpacking r-cran-fansi (1.0.5-1) ...
938s Selecting previously unselected package r-cran-farver.
938s Preparing to unpack .../115-r-cran-farver_2.1.1-2_armhf.deb ...
938s Unpacking r-cran-farver (2.1.1-2) ...
938s Selecting previously unselected package r-cran-glue.
938s Preparing to unpack .../116-r-cran-glue_1.7.0-1_armhf.deb ...
938s Unpacking r-cran-glue (1.7.0-1) ...
938s Selecting previously unselected package r-cran-rlang.
938s Preparing to unpack .../117-r-cran-rlang_1.1.3-1_armhf.deb ...
938s Unpacking r-cran-rlang (1.1.3-1) ...
938s Selecting previously unselected package r-cran-lifecycle.
938s Preparing to unpack .../118-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ...
938s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ...
938s Selecting previously unselected package r-cran-gtable.
938s Preparing to unpack .../119-r-cran-gtable_0.3.4+dfsg-1_all.deb ...
938s Unpacking r-cran-gtable (0.3.4+dfsg-1) ...
938s Selecting previously unselected package r-cran-isoband.
938s Preparing to unpack .../120-r-cran-isoband_0.2.7-1_armhf.deb ...
938s Unpacking r-cran-isoband (0.2.7-1) ...
938s Selecting previously unselected package r-cran-mass.
938s Preparing to unpack .../121-r-cran-mass_7.3-60.0.1-1_armhf.deb ...
938s Unpacking r-cran-mass (7.3-60.0.1-1) ...
938s Selecting previously unselected package r-cran-lattice.
938s Preparing to unpack .../122-r-cran-lattice_0.22-6-1_armhf.deb ...
938s Unpacking r-cran-lattice (0.22-6-1) ...
939s Selecting previously unselected package r-cran-nlme.
939s Preparing to unpack .../123-r-cran-nlme_3.1.164-1build1_armhf.deb ...
939s Unpacking r-cran-nlme (3.1.164-1build1) ...
939s Selecting previously unselected package r-cran-matrix.
939s Preparing to unpack .../124-r-cran-matrix_1.6-5-1_armhf.deb ...
939s Unpacking r-cran-matrix (1.6-5-1) ...
939s Selecting previously unselected package r-cran-mgcv.
939s Preparing to unpack .../125-r-cran-mgcv_1.9-1-1_armhf.deb ...
939s Unpacking r-cran-mgcv (1.9-1-1) ...
939s Selecting previously unselected package r-cran-labeling.
939s Preparing to unpack .../126-r-cran-labeling_0.4.3-1_all.deb ...
939s Unpacking r-cran-labeling (0.4.3-1) ...
939s Selecting previously unselected package r-cran-munsell.
939s Preparing to unpack .../127-r-cran-munsell_0.5.0-2build1_all.deb ...
939s Unpacking r-cran-munsell (0.5.0-2build1) ...
939s Selecting previously unselected package r-cran-r6.
939s Preparing to unpack .../128-r-cran-r6_2.5.1-1_all.deb ...
939s Unpacking r-cran-r6 (2.5.1-1) ...
939s Selecting previously unselected package r-cran-rcolorbrewer.
939s Preparing to unpack .../129-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ...
939s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ...
939s Selecting previously unselected package r-cran-viridislite.
939s Preparing to unpack .../130-r-cran-viridislite_0.4.2-2_all.deb ...
939s Unpacking r-cran-viridislite (0.4.2-2) ...
939s Selecting previously unselected package r-cran-scales.
939s Preparing to unpack .../131-r-cran-scales_1.3.0-1_all.deb ...
939s Unpacking r-cran-scales (1.3.0-1) ...
939s Selecting previously unselected package r-cran-magrittr.
940s Preparing to unpack .../132-r-cran-magrittr_2.0.3-1_armhf.deb ...
940s Unpacking r-cran-magrittr (2.0.3-1) ...
940s Selecting previously unselected package r-cran-utf8.
940s Preparing to unpack .../133-r-cran-utf8_1.2.4-1_armhf.deb ...
940s Unpacking r-cran-utf8 (1.2.4-1) ...
940s Selecting previously unselected package r-cran-vctrs.
940s Preparing to unpack .../134-r-cran-vctrs_0.6.5-1_armhf.deb ...
940s Unpacking r-cran-vctrs (0.6.5-1) ...
940s Selecting previously unselected package r-cran-pillar.
940s Preparing to unpack .../135-r-cran-pillar_1.9.0+dfsg-1_all.deb ...
940s Unpacking r-cran-pillar (1.9.0+dfsg-1) ...
940s Selecting previously unselected package r-cran-pkgconfig.
940s Preparing to unpack .../136-r-cran-pkgconfig_2.0.3-2build1_all.deb ...
940s Unpacking r-cran-pkgconfig (2.0.3-2build1) ...
940s Selecting previously unselected package r-cran-tibble.
940s Preparing to unpack .../137-r-cran-tibble_3.2.1+dfsg-2_armhf.deb ...
940s Unpacking r-cran-tibble (3.2.1+dfsg-2) ...
940s Selecting previously unselected package r-cran-withr.
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940s Unpacking r-cran-withr (2.5.0-1) ...
940s Selecting previously unselected package r-cran-ggplot2.
940s Preparing to unpack .../139-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ...
940s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ...
941s Selecting previously unselected package r-cran-xfun.
941s Preparing to unpack .../140-r-cran-xfun_0.44+dfsg-1_armhf.deb ...
941s Unpacking r-cran-xfun (0.44+dfsg-1) ...
941s Selecting previously unselected package r-cran-highr.
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941s Selecting previously unselected package r-cran-yaml.
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941s Selecting previously unselected package libjs-mathjax.
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943s Selecting previously unselected package r-cran-knitr.
943s Preparing to unpack .../144-r-cran-knitr_1.46+dfsg-1_all.deb ...
943s Unpacking r-cran-knitr (1.46+dfsg-1) ...
943s Selecting previously unselected package r-cran-markdown.
943s Preparing to unpack .../145-r-cran-markdown_1.12+dfsg-2_all.deb ...
943s Unpacking r-cran-markdown (1.12+dfsg-2) ...
943s Selecting previously unselected package r-cran-matrixstats.
943s Preparing to unpack .../146-r-cran-matrixstats_1.2.0-1_armhf.deb ...
943s Unpacking r-cran-matrixstats (1.2.0-1) ...
943s Selecting previously unselected package autopkgtest-satdep.
943s Preparing to unpack .../147-2-autopkgtest-satdep.deb ...
943s Unpacking autopkgtest-satdep (0) ...
943s Setting up libgraphite2-3:armhf (1.3.14-2build1) ...
943s Setting up libpixman-1-0:armhf (0.42.2-1build1) ...
943s Setting up libsharpyuv0:armhf (1.4.0-0.1) ...
943s Setting up libpaper1:armhf (1.1.29build1) ...
944s 
944s Creating config file /etc/papersize with new version
944s Setting up fonts-mathjax (2.7.9+dfsg-1) ...
944s Setting up liblerc4:armhf (4.0.0+ds-4ubuntu2) ...
944s Setting up libjs-mathjax (2.7.9+dfsg-1) ...
944s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ...
944s Setting up libdatrie1:armhf (0.2.13-3build1) ...
944s Setting up libxcb-render0:armhf (1.17.0-2) ...
944s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ...
944s Setting up unzip (6.0-28ubuntu4) ...
944s Setting up x11-common (1:7.7+23ubuntu3) ...
945s Setting up libdeflate0:armhf (1.20-1) ...
945s Setting up linux-libc-dev:armhf (6.8.0-31.31) ...
945s Setting up libxcb-shm0:armhf (1.17.0-2) ...
945s Setting up libpaper-utils (1.1.29build1) ...
945s Setting up libgomp1:armhf (14.1.0-1ubuntu1) ...
945s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ...
945s Setting up libpcre2-16-0:armhf (10.42-4ubuntu2) ...
945s Setting up zip (3.0-13build1) ...
945s Setting up libpcre2-32-0:armhf (10.42-4ubuntu2) ...
945s Setting up libblas3:armhf (3.12.0-3build1) ...
945s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
945s Setting up libtirpc-dev:armhf (1.3.4+ds-1.3) ...
945s Setting up libpkgconf3:armhf (1.8.1-2build1) ...
945s Setting up rpcsvc-proto (1.4.2-0ubuntu7) ...
945s Setting up gcc-13-base:armhf (13.2.0-23ubuntu4) ...
945s Setting up libfreetype6:armhf (2.13.2+dfsg-1build3) ...
945s Setting up fonts-dejavu-mono (2.37-8) ...
945s Setting up libmpc3:armhf (1.3.1-1build1) ...
945s Setting up libatomic1:armhf (14.1.0-1ubuntu1) ...
945s Setting up libtcl8.6:armhf (8.6.14+dfsg-1build1) ...
945s Setting up icu-devtools (74.2-1ubuntu3) ...
945s Setting up fonts-dejavu-core (2.37-8) ...
945s Setting up pkgconf-bin (1.8.1-2build1) ...
945s Setting up libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ...
945s Setting up libgfortran5:armhf (14.1.0-1ubuntu1) ...
945s Setting up libwebp7:armhf (1.4.0-0.1) ...
945s Setting up liblzma-dev:armhf (5.6.1+really5.4.5-1) ...
945s Setting up libubsan1:armhf (14.1.0-1ubuntu1) ...
945s Setting up libpcre2-posix3:armhf (10.42-4ubuntu2) ...
945s Setting up libjs-highlight.js (9.18.5+dfsg1-2) ...
945s Setting up libcrypt-dev:armhf (1:4.4.36-4build1) ...
945s Setting up libasan8:armhf (14.1.0-1ubuntu1) ...
945s Setting up libharfbuzz0b:armhf (8.3.0-2build2) ...
945s Setting up libthai-data (0.1.29-2build1) ...
945s Setting up libxss1:armhf (1:1.2.3-1build3) ...
945s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
945s Setting up libisl23:armhf (0.26-3build1) ...
945s Setting up libc-dev-bin (2.39-0ubuntu8.1) ...
945s Setting up libdeflate-dev:armhf (1.20-1) ...
945s Setting up node-normalize.css (8.0.1-5) ...
945s Setting up xdg-utils (1.1.3-4.1ubuntu3) ...
945s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
945s Setting up libcc1-0:armhf (14.1.0-1ubuntu1) ...
945s Setting up libblas-dev:armhf (3.12.0-3build1) ...
945s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
945s Setting up dctrl-tools (2.24-3build3) ...
945s Setting up libjs-bootstrap (3.4.1+dfsg-3) ...
945s Setting up libjpeg8:armhf (8c-2ubuntu11) ...
945s Setting up libice6:armhf (2:1.0.10-1build3) ...
945s Setting up liblapack3:armhf (3.12.0-3build1) ...
945s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
945s Setting up cpp-13-arm-linux-gnueabihf (13.2.0-23ubuntu4) ...
945s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
945s Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ...
945s Setting up pkgconf:armhf (1.8.1-2build1) ...
945s Setting up libthai0:armhf (0.1.29-2build1) ...
945s Setting up liblapack-dev:armhf (3.12.0-3build1) ...
945s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
945s Setting up libgcc-13-dev:armhf (13.2.0-23ubuntu4) ...
945s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu2) ...
945s Setting up libc6-dev:armhf (2.39-0ubuntu8.1) ...
945s Setting up libfontconfig1:armhf (2.15.0-1.1ubuntu2) ...
945s Setting up libgfortran-13-dev:armhf (13.2.0-23ubuntu4) ...
945s Setting up libsm6:armhf (2:1.2.3-1build3) ...
945s Setting up libicu-dev:armhf (74.2-1ubuntu3) ...
945s Setting up cpp-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ...
945s Setting up libstdc++-13-dev:armhf (13.2.0-23ubuntu4) ...
945s Setting up libbz2-dev:armhf (1.0.8-5.1) ...
945s Setting up fontconfig (2.15.0-1.1ubuntu2) ...
947s Regenerating fonts cache... done.
948s Setting up libjpeg-turbo8-dev:armhf (2.1.5-2ubuntu2) ...
948s Setting up libxft2:armhf (2.3.6-1build1) ...
948s Setting up libncurses-dev:armhf (6.4+20240113-1ubuntu2) ...
948s Setting up libpcre2-dev:armhf (10.42-4ubuntu2) ...
948s Setting up cpp-13 (13.2.0-23ubuntu4) ...
948s Setting up libtk8.6:armhf (8.6.14-1build1) ...
948s Setting up libpango-1.0-0:armhf (1.52.2+ds-1) ...
948s Setting up libreadline-dev:armhf (8.2-4build1) ...
948s Setting up libcairo2:armhf (1.18.0-3build1) ...
948s Setting up gcc-13-arm-linux-gnueabihf (13.2.0-23ubuntu4) ...
948s Setting up libxt6t64:armhf (1:1.2.1-1.2build1) ...
948s Setting up gcc-13 (13.2.0-23ubuntu4) ...
948s Setting up zlib1g-dev:armhf (1:1.3.dfsg-3.1ubuntu2) ...
948s Setting up cpp (4:13.2.0-7ubuntu1) ...
948s Setting up libpangoft2-1.0-0:armhf (1.52.2+ds-1) ...
948s Setting up libjpeg8-dev:armhf (8c-2ubuntu11) ...
948s Setting up libpangocairo-1.0-0:armhf (1.52.2+ds-1) ...
948s Setting up gcc-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ...
948s Setting up g++-13-arm-linux-gnueabihf (13.2.0-23ubuntu4) ...
948s Setting up gfortran-13-arm-linux-gnueabihf (13.2.0-23ubuntu4) ...
948s Setting up g++-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ...
948s Setting up g++-13 (13.2.0-23ubuntu4) ...
948s Setting up libpng-dev:armhf (1.6.43-5build1) ...
948s Setting up libjpeg-dev:armhf (8c-2ubuntu11) ...
948s Setting up gcc (4:13.2.0-7ubuntu1) ...
948s Setting up gfortran-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ...
948s Setting up gfortran-13 (13.2.0-23ubuntu4) ...
948s Setting up r-base-core (4.4.0-2) ...
948s 
948s Creating config file /etc/R/Renviron with new version
948s Setting up r-cran-labeling (0.4.3-1) ...
948s Setting up r-cran-lattice (0.22-6-1) ...
948s Setting up r-cran-nlme (3.1.164-1build1) ...
948s Setting up r-cran-farver (2.1.1-2) ...
948s Setting up g++ (4:13.2.0-7ubuntu1) ...
948s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
948s Setting up r-cran-viridislite (0.4.2-2) ...
948s Setting up build-essential (12.10ubuntu1) ...
948s Setting up r-cran-commonmark (1.9.1-1) ...
948s Setting up r-cran-r6 (2.5.1-1) ...
948s Setting up r-cran-magrittr (2.0.3-1) ...
948s Setting up r-cran-rlang (1.1.3-1) ...
948s Setting up r-cran-matrixstats (1.2.0-1) ...
948s Setting up r-cran-xfun (0.44+dfsg-1) ...
948s Setting up r-cran-withr (2.5.0-1) ...
948s Setting up r-cran-base64enc (0.1-3-3) ...
948s Setting up r-cran-yaml (2.3.8-2) ...
948s Setting up r-cran-evaluate (0.23-1) ...
948s Setting up r-cran-highr (0.10+dfsg-2) ...
948s Setting up r-cran-fansi (1.0.5-1) ...
948s Setting up r-cran-mass (7.3-60.0.1-1) ...
948s Setting up r-cran-glue (1.7.0-1) ...
948s Setting up r-cran-cli (3.6.2-1) ...
948s Setting up gfortran (4:13.2.0-7ubuntu1) ...
948s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
948s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist
948s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
948s update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist
948s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
948s Setting up r-cran-pkgconfig (2.0.3-2build1) ...
948s Setting up r-cran-utf8 (1.2.4-1) ...
948s Setting up r-cran-colorspace (2.1-0+dfsg-1) ...
948s Setting up r-cran-markdown (1.12+dfsg-2) ...
948s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ...
948s Setting up r-cran-isoband (0.2.7-1) ...
948s Setting up r-cran-gtable (0.3.4+dfsg-1) ...
948s Setting up r-cran-matrix (1.6-5-1) ...
948s Setting up r-cran-knitr (1.46+dfsg-1) ...
948s Setting up r-cran-mgcv (1.9-1-1) ...
948s Setting up r-cran-vctrs (0.6.5-1) ...
948s Setting up r-cran-pillar (1.9.0+dfsg-1) ...
948s Setting up r-base-dev (4.4.0-2) ...
948s Setting up r-cran-munsell (0.5.0-2build1) ...
948s Setting up r-cran-tibble (3.2.1+dfsg-2) ...
948s Setting up r-cran-scales (1.3.0-1) ...
948s Setting up pkg-r-autopkgtest (20231212ubuntu1) ...
948s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ...
948s Setting up autopkgtest-satdep (0) ...
948s Processing triggers for man-db (2.12.1-1) ...
950s Processing triggers for install-info (7.1-3build2) ...
950s Processing triggers for libc-bin (2.39-0ubuntu8.1) ...
985s (Reading database ... 72695 files and directories currently installed.)
985s Removing autopkgtest-satdep (0) ...
998s autopkgtest [08:38:30]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
998s autopkgtest [08:38:30]: test pkg-r-autopkgtest: [-----------------------
1001s Test: Try to load the R library matrixStats
1001s 
1001s R version 4.4.0 (2024-04-24) -- "Puppy Cup"
1001s Copyright (C) 2024 The R Foundation for Statistical Computing
1001s Platform: arm-unknown-linux-gnueabihf (32-bit)
1001s 
1001s R is free software and comes with ABSOLUTELY NO WARRANTY.
1001s You are welcome to redistribute it under certain conditions.
1001s Type 'license()' or 'licence()' for distribution details.
1001s 
1001s R is a collaborative project with many contributors.
1001s Type 'contributors()' for more information and
1001s 'citation()' on how to cite R or R packages in publications.
1001s 
1001s Type 'demo()' for some demos, 'help()' for on-line help, or
1001s 'help.start()' for an HTML browser interface to help.
1001s Type 'q()' to quit R.
1001s 
1001s > library('matrixStats')
1001s > 
1001s > 
1001s Other tests are currently unsupported!
1001s They will be progressively added.
1002s autopkgtest [08:38:34]: test pkg-r-autopkgtest: -----------------------]
1006s autopkgtest [08:38:38]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
1006s pkg-r-autopkgtest    PASS
1010s autopkgtest [08:38:42]: @@@@@@@@@@@@@@@@@@@@ summary
1010s run-unit-test        PASS
1010s pkg-r-autopkgtest    PASS