0s autopkgtest [05:26:29]: starting date and time: 2026-02-10 05:26:29+0000
  0s autopkgtest [05:26:29]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op
  0s autopkgtest [05:26:29]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.alncvhkh/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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-ggplot2/4.0.2+dfsg-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-10.secgroup --name adt-resolute-amd64-r-cran-matrixstats-20260210-052629-juju-7f2275-prod-proposed-migration-environment-2-bcb2911b-cc5a-4553-b510-6a8e48ee2fa6 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/
  4s Creating nova instance adt-resolute-amd64-r-cran-matrixstats-20260210-052629-juju-7f2275-prod-proposed-migration-environment-2-bcb2911b-cc5a-4553-b510-6a8e48ee2fa6 from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)...
 74s autopkgtest [05:27:43]: testbed dpkg architecture: amd64
 74s autopkgtest [05:27:43]: testbed apt version: 3.1.14
 74s autopkgtest [05:27:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 74s autopkgtest [05:27:43]: testbed release detected to be: None
 75s autopkgtest [05:27:44]: updating testbed package index (apt update)
 75s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB]
 75s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
 75s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
 75s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
 75s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [31.1 kB]
 75s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1727 kB]
 76s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [178 kB]
 76s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [219 kB]
 76s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [266 kB]
 76s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6184 B]
 76s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B]
 76s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1787 kB]
 76s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [792 kB]
 76s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [32.5 kB]
 76s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [5020 B]
 76s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [26.4 kB]
 76s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [996 B]
 77s Fetched 5197 kB in 1s (4917 kB/s)
 77s Reading package lists...
 78s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease
 78s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
 78s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
 78s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
 79s Reading package lists...
 79s Reading package lists...
 79s Building dependency tree...
 79s Reading state information...
 79s Calculating upgrade...
 79s The following package was automatically installed and is no longer required:
 79s   libpython3.13
 79s Use 'sudo apt autoremove' to remove it.
 79s The following NEW packages will be installed:
 79s   gcc-16-base libpython3.14 libpython3.14-minimal libpython3.14-stdlib
 79s   linux-headers-6.19.0-3 linux-headers-6.19.0-3-generic
 79s   linux-image-6.19.0-3-generic linux-modules-6.19.0-3-generic
 79s   linux-tools-6.19.0-3 linux-tools-6.19.0-3-generic
 79s The following packages will be upgraded:
 79s   3cpio amd64-microcode apt bpftool busybox-initramfs busybox-static
 79s   cryptsetup-bin dash dbus dbus-bin dbus-daemon dbus-session-bus-common
 79s   dbus-system-bus-common dbus-user-session debianutils dmsetup dracut-install
 79s   ethtool findutils gir1.2-girepository-3.0 gir1.2-glib-2.0 hwdata iproute2
 79s   iptables less libapt-pkg7.0 libatomic1 libattr1 libbpf1 libbrotli1 libbsd0
 79s   libcryptsetup12 libdbus-1-3 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common
 79s   libdrm2 libevent-core-2.1-7t64 libgcc-s1 libgdbm-compat4t64 libgdbm6t64
 79s   libgirepository-2.0-0 libglib2.0-0t64 libglib2.0-data libgpm2 libgudev-1.0-0
 79s   libidn2-0 libip4tc2 libip6tc2 libjansson4 libkeyutils1 liblsof0
 79s   libmaxminddb0 libnetfilter-conntrack3 libnpth0t64 libonig5 libpcap0.8t64
 79s   libpci3 libsensors-config libsensors5 libstdc++6 libusb-1.0-0 libwrap0
 79s   libxau6 libxkbcommon0 libxtables12 linux-generic linux-headers-generic
 79s   linux-headers-virtual linux-image-generic linux-image-virtual linux-perf
 79s   linux-tools-common linux-virtual lsof man-db mawk patch pciutils pnp.ids
 79s   pollinate python3-linkify-it python3-markdown-it python3-referencing sed
 79s   shared-mime-info tar tcpdump ubuntu-kernel-accessories ubuntu-standard wget
 79s 91 upgraded, 10 newly installed, 0 to remove and 0 not upgraded.
 79s Need to get 237 MB of archives.
 79s After this operation, 339 MB of additional disk space will be used.
 79s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 debianutils amd64 5.23.2build1 [93.3 kB]
 79s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 dash amd64 0.5.12-12ubuntu3 [96.0 kB]
 79s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB]
 79s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB]
 79s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB]
 79s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB]
 79s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-16-base amd64 16-20260208-1ubuntu1 [59.7 kB]
 79s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1 amd64 16-20260208-1ubuntu1 [80.3 kB]
 79s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libbsd0 amd64 0.12.2-2build2 [42.3 kB]
 79s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB]
 79s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6 amd64 16-20260208-1ubuntu1 [844 kB]
 79s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB]
 79s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB]
 80s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-system-bus-common all 1.16.2-2ubuntu3 [55.8 kB]
 80s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-session-bus-common all 1.16.2-2ubuntu3 [54.4 kB]
 80s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-user-session amd64 1.16.2-2ubuntu3 [9696 B]
 80s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-daemon amd64 1.16.2-2ubuntu3 [119 kB]
 80s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-bin amd64 1.16.2-2ubuntu3 [40.1 kB]
 80s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus amd64 1.16.2-2ubuntu3 [24.2 kB]
 80s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libdbus-1-3 amd64 1.16.2-2ubuntu3 [185 kB]
 80s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB]
 80s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB]
 80s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 ethtool amd64 1:6.15-3build1 [318 kB]
 80s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-3.0 amd64 2.87.2-2 [25.2 kB]
 80s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-2.0-0 amd64 2.87.2-2 [76.1 kB]
 80s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1 amd64 16-20260208-1ubuntu1 [11.4 kB]
 80s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-glib-2.0 amd64 2.87.2-2 [182 kB]
 80s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-0t64 amd64 2.87.2-2 [1613 kB]
 80s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libbpf1 amd64 1:1.6.2-1build1 [184 kB]
 80s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 iptables amd64 1.8.11-2ubuntu3 [381 kB]
 80s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libip4tc2 amd64 1.8.11-2ubuntu3 [24.2 kB]
 80s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libip6tc2 amd64 1.8.11-2ubuntu3 [24.4 kB]
 80s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libnetfilter-conntrack3 amd64 1.1.1-1 [47.5 kB]
 80s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libxtables12 amd64 1.8.11-2ubuntu3 [36.6 kB]
 80s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 iproute2 amd64 6.18.0-1ubuntu1 [1178 kB]
 80s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB]
 80s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libcryptsetup12 amd64 2:2.8.0-1ubuntu3 [283 kB]
 80s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-data all 2.87.2-2 [58.2 kB]
 80s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libidn2-0 amd64 2.3.8-4build1 [67.6 kB]
 80s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB]
 80s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB]
 80s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB]
 80s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 shared-mime-info amd64 2.4-5build3 [476 kB]
 80s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB]
 80s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B]
 80s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB]
 80s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm6t64 amd64 1.26-1build1 [36.5 kB]
 80s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB]
 80s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libjansson4 amd64 2.14-2build4 [33.2 kB]
 80s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 lsof amd64 4.99.4+dfsg-2build2 [239 kB]
 80s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsof0 amd64 4.99.4+dfsg-2build2 [56.5 kB]
 80s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB]
 80s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcap0.8t64 amd64 1.10.5-2ubuntu3 [154 kB]
 80s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 pciutils amd64 1:3.14.0-1build2 [95.5 kB]
 80s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libpci3 amd64 1:3.14.0-1build2 [38.1 kB]
 80s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B]
 80s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB]
 80s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libusb-1.0-0 amd64 2:1.0.29-2build1 [56.9 kB]
 80s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxau6 amd64 1:1.0.11-1build2 [7502 B]
 80s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxkbcommon0 amd64 1.13.1-1 [159 kB]
 80s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 man-db amd64 2.13.1-1build1 [1392 kB]
 80s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 tcpdump amd64 4.99.5-2ubuntu3 [477 kB]
 80s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 wget amd64 1.25.0-2ubuntu4 [353 kB]
 80s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-standard amd64 1.564 [13.3 kB]
 80s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 3cpio amd64 0.14.0-1ubuntu1 [285 kB]
 80s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 bpftool amd64 7.7.0+6.19.0-3.3 [1229 kB]
 80s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB]
 80s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 cryptsetup-bin amd64 2:2.8.0-1ubuntu3 [228 kB]
 80s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 dracut-install amd64 109-11ubuntu1 [45.8 kB]
 80s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 hwdata all 0.394-1build1 [1566 B]
 80s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 pnp.ids all 0.394-1build1 [29.6 kB]
 80s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libbrotli1 amd64 1.2.0-3 [343 kB]
 80s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB]
 80s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10build2 [93.1 kB]
 80s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm-compat4t64 amd64 1.26-1build1 [6796 B]
 80s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libgudev-1.0-0 amd64 1:238-7build1 [15.9 kB]
 80s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B]
 80s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libonig5 amd64 6.9.10-1build1 [174 kB]
 80s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB]
 81s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB]
 81s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14 amd64 3.14.2-1 [2568 kB]
 81s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 libwrap0 amd64 7.6.q-36build2 [48.5 kB]
 81s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-modules-6.19.0-3-generic amd64 6.19.0-3.3 [171 MB]
 87s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-6.19.0-3-generic amd64 6.19.0-3.3+1 [16.8 MB]
 87s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB]
 87s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-generic amd64 6.19.0-3.3 [1698 B]
 87s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-generic amd64 6.19.0-3.3 [12.2 kB]
 87s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-virtual amd64 6.19.0-3.3 [1700 B]
 87s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-virtual amd64 6.19.0-3.3 [12.1 kB]
 87s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-virtual amd64 6.19.0-3.3 [1646 B]
 87s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3 all 6.19.0-3.3 [14.9 MB]
 87s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3-generic amd64 6.19.0-3.3 [4330 kB]
 88s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-generic amd64 6.19.0-3.3 [12.0 kB]
 88s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-perf amd64 6.19.0-3.3 [4480 kB]
 88s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-common all 6.19.0-3.3 [345 kB]
 88s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3 amd64 6.19.0-3.3 [1455 kB]
 88s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3-generic amd64 6.19.0-3.3 [1612 B]
 88s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB]
 88s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB]
 88s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB]
 88s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-kernel-accessories amd64 1.564 [13.1 kB]
 88s dpkg-preconfigure: unable to re-open stdin: No such file or directory
 88s Fetched 237 MB in 9s (27.5 MB/s)
 88s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 88s Preparing to unpack .../debianutils_5.23.2build1_amd64.deb ...
 88s Unpacking debianutils (5.23.2build1) over (5.23.2) ...
 88s Setting up debianutils (5.23.2build1) ...
 88s (Reading database ... 
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 88s Preparing to unpack .../dash_0.5.12-12ubuntu3_amd64.deb ...
 88s Unpacking dash (0.5.12-12ubuntu3) over (0.5.12-12ubuntu2) ...
 88s Setting up dash (0.5.12-12ubuntu3) ...
 88s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 88s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ...
 88s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ...
 88s Setting up findutils (4.10.0-3build2) ...
 88s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 88s Preparing to unpack .../sed_4.9-2build3_amd64.deb ...
 88s Unpacking sed (4.9-2build3) over (4.9-2build2) ...
 88s Setting up sed (4.9-2build3) ...
 89s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 89s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ...
 89s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ...
 89s Setting up tar (1.35+dfsg-3.1build2) ...
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 96s Setting up linux-headers-6.19.0-3 (6.19.0-3.3) ...
 96s Setting up libidn2-0:amd64 (2.3.8-4build1) ...
 96s Setting up amd64-microcode (3.20251202.1ubuntu1) ...
 96s amd64-microcode: microcode will be updated at next boot
 96s Setting up man-db (2.13.1-1build1) ...
 96s Updating database of manual pages ...
 98s man-db.service is a disabled or a static unit not running, not starting it.
 98s Setting up libjansson4:amd64 (2.14-2build4) ...
 98s Setting up libglib2.0-data (2.87.2-2) ...
 98s Setting up pollinate (4.33-4ubuntu5) ...
108s Setting up busybox-static (1:1.37.0-7ubuntu1) ...
108s Setting up libwrap0:amd64 (7.6.q-36build2) ...
108s Setting up linux-image-6.19.0-3-generic (6.19.0-3.3+1) ...
109s I: /boot/vmlinuz is now a symlink to vmlinuz-6.19.0-3-generic
109s I: /boot/initrd.img is now a symlink to initrd.img-6.19.0-3-generic
109s Setting up libdbus-1-3:amd64 (1.16.2-2ubuntu3) ...
109s Setting up libatomic1:amd64 (16-20260208-1ubuntu1) ...
109s Setting up patch (2.8-2build1) ...
109s Setting up libsensors5:amd64 (1:3.6.2-2build1) ...
109s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ...
109s Setting up libxtables12:amd64 (1.8.11-2ubuntu3) ...
109s Setting up lsof (4.99.4+dfsg-2build2) ...
109s Setting up libpci3:amd64 (1:3.14.0-1build2) ...
109s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ...
109s Setting up dracut-install (109-11ubuntu1) ...
109s Setting up dmsetup (2:1.02.205-2ubuntu3) ...
109s Setting up libnetfilter-conntrack3:amd64 (1.1.1-1) ...
109s Setting up pnp.ids (0.394-1build1) ...
109s Setting up dbus-session-bus-common (1.16.2-2ubuntu3) ...
109s Setting up python3-linkify-it (2.0.3-1ubuntu3) ...
109s Setting up libpcap0.8t64:amd64 (1.10.5-2ubuntu3) ...
109s Setting up libcryptsetup12:amd64 (2:2.8.0-1ubuntu3) ...
109s Setting up mawk (1.3.4.20260129-1) ...
109s Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build2) ...
109s Setting up libusb-1.0-0:amd64 (2:1.0.29-2build1) ...
109s Setting up linux-image-virtual (6.19.0-3.3) ...
109s Setting up dbus-system-bus-common (1.16.2-2ubuntu3) ...
109s Setting up libbsd0:amd64 (0.12.2-2build2) ...
109s Setting up libdrm-common (2.4.131-1) ...
109s Setting up libstdc++6:amd64 (16-20260208-1ubuntu1) ...
109s Setting up dbus-bin (1.16.2-2ubuntu3) ...
109s Setting up libonig5:amd64 (6.9.10-1build1) ...
109s Setting up libbpf1:amd64 (1:1.6.2-1build1) ...
109s Setting up ethtool (1:6.15-3build1) ...
109s Setting up python3-referencing (0.36.2-1ubuntu2) ...
110s Setting up libxkbcommon0:amd64 (1.13.1-1) ...
110s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ...
110s Setting up linux-headers-6.19.0-3-generic (6.19.0-3.3) ...
110s Setting up tcpdump (4.99.5-2ubuntu3) ...
110s Setting up linux-image-generic (6.19.0-3.3) ...
110s Setting up wget (1.25.0-2ubuntu4) ...
110s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ...
110s Setting up iptables (1.8.11-2ubuntu3) ...
110s Setting up iproute2 (6.18.0-1ubuntu1) ...
110s Setting up linux-headers-generic (6.19.0-3.3) ...
110s Setting up dbus-daemon (1.16.2-2ubuntu3) ...
110s Setting up hwdata (0.394-1build1) ...
110s Setting up dbus-user-session (1.16.2-2ubuntu3) ...
110s Setting up libglib2.0-0t64:amd64 (2.87.2-2) ...
110s No schema files found: doing nothing.
110s Setting up dbus (1.16.2-2ubuntu3) ...
110s A reboot is required to replace the running dbus-daemon.
110s Please reboot the system when convenient.
110s Setting up shared-mime-info (2.4-5build3) ...
111s Setting up gir1.2-glib-2.0:amd64 (2.87.2-2) ...
111s Setting up pciutils (1:3.14.0-1build2) ...
111s Setting up python3-markdown-it (3.0.0-3build1) ...
111s Setting up libdrm2:amd64 (2.4.131-1) ...
111s Setting up libpython3.14:amd64 (3.14.2-1) ...
111s Setting up libapt-pkg7.0:amd64 (3.1.15) ...
111s Setting up linux-tools-common (6.19.0-3.3) ...
111s Setting up libgudev-1.0-0:amd64 (1:238-7build1) ...
111s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ...
111s Setting up apt (3.1.15) ...
111s Setting up linux-headers-virtual (6.19.0-3.3) ...
111s Setting up linux-generic (6.19.0-3.3) ...
111s Setting up libgirepository-2.0-0:amd64 (2.87.2-2) ...
111s Setting up linux-tools-6.19.0-3 (6.19.0-3.3) ...
111s Setting up ubuntu-standard (1.564) ...
111s Setting up gir1.2-girepository-3.0:amd64 (2.87.2-2) ...
111s Setting up linux-virtual (6.19.0-3.3) ...
111s Setting up linux-perf (6.19.0-3.3) ...
111s Setting up linux-tools-6.19.0-3-generic (6.19.0-3.3) ...
111s Processing triggers for debianutils (5.23.2build1) ...
111s Processing triggers for install-info (7.2-5) ...
111s Processing triggers for initramfs-tools (0.150ubuntu7) ...
111s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic
116s Processing triggers for libc-bin (2.42-2ubuntu4) ...
116s Processing triggers for linux-image-6.19.0-3-generic (6.19.0-3.3+1) ...
116s /etc/kernel/postinst.d/initramfs-tools:
116s update-initramfs: Generating /boot/initrd.img-6.19.0-3-generic
120s /etc/kernel/postinst.d/zz-update-grub:
120s Sourcing file `/etc/default/grub'
120s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
120s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg'
120s Generating grub configuration file ...
120s Found linux image: /boot/vmlinuz-6.19.0-3-generic
120s Found initrd image: /boot/initrd.img-6.19.0-3-generic
120s Found linux image: /boot/vmlinuz-6.18.0-9-generic
120s Found initrd image: /boot/initrd.img-6.18.0-9-generic
120s Warning: os-prober will not be executed to detect other bootable partitions.
120s Systems on them will not be added to the GRUB boot configuration.
120s Check GRUB_DISABLE_OS_PROBER documentation entry.
120s Adding boot menu entry for UEFI Firmware Settings ...
120s done
120s autopkgtest [05:28:29]: upgrading testbed (apt dist-upgrade and autopurge)
121s Reading package lists...
121s Building dependency tree...
121s Reading state information...
121s Calculating upgrade...
121s The following package was automatically installed and is no longer required:
121s   libpython3.13
121s Use 'sudo apt autoremove' to remove it.
121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
122s Reading package lists...
122s Building dependency tree...
122s Reading state information...
122s Solving dependencies...
122s The following packages will be REMOVED:
122s   libpython3.13*
122s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded.
122s After this operation, 7599 kB disk space will be freed.
122s (Reading database ... 
(Reading database ... 5%
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(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
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(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 125273 files and directories currently installed.)
122s Removing libpython3.13:amd64 (3.13.11-1) ...
122s Processing triggers for libc-bin (2.42-2ubuntu4) ...
122s autopkgtest [05:28:31]: rebooting testbed after setup commands that affected boot
150s autopkgtest [05:28:59]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 20:01:24 UTC 2026
152s autopkgtest [05:29:01]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-matrixstats
153s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-matrixstats 1.5.0-1 (dsc) [2228 B]
153s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-matrixstats 1.5.0-1 (tar) [212 kB]
153s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-matrixstats 1.5.0-1 (diff) [4864 B]
153s gpgv: Signature made Sat Jan 18 11:46:01 2025 UTC
153s gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
153s gpgv: Can't check signature: No public key
153s dpkg-source: warning: cannot verify inline signature for ./r-cran-matrixstats_1.5.0-1.dsc: no acceptable signature found
153s autopkgtest [05:29:02]: testing package r-cran-matrixstats version 1.5.0-1
154s autopkgtest [05:29:03]: build not needed
155s autopkgtest [05:29:04]: test run-unit-test: preparing testbed
155s Reading package lists...
156s Building dependency tree...
156s Reading state information...
156s Solving dependencies...
156s The following NEW packages will be installed:
156s   fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
156s   fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1
156s   libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3
156s   libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap
156s   libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax
156s   liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
156s   libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6
156s   libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0
156s   libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css r-base-core
156s   r-cran-base64enc r-cran-cli r-cran-commonmark r-cran-digest r-cran-evaluate
156s   r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-highr
156s   r-cran-isoband r-cran-knitr r-cran-labeling r-cran-lifecycle r-cran-markdown
156s   r-cran-matrixstats r-cran-microbenchmark r-cran-r.cache r-cran-r.devices
156s   r-cran-r.methodss3 r-cran-r.oo r-cran-r.rsp r-cran-r.utils r-cran-r6
156s   r-cran-rcolorbrewer r-cran-rlang r-cran-s7 r-cran-scales r-cran-vctrs
156s   r-cran-viridislite r-cran-withr r-cran-xfun r-cran-yaml tcl tcl8.6 unzip
156s   x11-common xdg-utils zip
156s 0 upgraded, 87 newly installed, 0 to remove and 0 not upgraded.
156s Need to get 71.9 MB of archives.
156s After this operation, 171 MB of additional disk space will be used.
156s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB]
156s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB]
156s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB]
156s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB]
156s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.17.1-3ubuntu1 [180 kB]
156s Get:6 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB]
156s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB]
156s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB]
156s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB]
156s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2ubuntu1 [16.2 kB]
156s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2ubuntu1 [5808 B]
156s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB]
156s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB]
156s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB]
156s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2build1 [51.6 kB]
156s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 16-20260208-1ubuntu1 [957 kB]
156s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 16-20260208-1ubuntu1 [162 kB]
156s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB]
156s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.2-1 [519 kB]
156s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB]
156s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1build1 [44.0 kB]
156s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu3 [156 kB]
156s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu12 [2142 B]
156s Get:24 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB]
156s Get:25 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-highlight.js all 10.7.3+dfsg-2 [144 kB]
156s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB]
156s Get:27 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB]
156s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB]
157s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB]
157s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.30-1 [155 kB]
157s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.30-1 [19.2 kB]
157s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.57.0-1 [241 kB]
157s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.57.0-1 [53.3 kB]
157s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.57.0-1 [29.0 kB]
157s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3build1 [17.3 kB]
157s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3build1 [15.6 kB]
157s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB]
157s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1build1 [16.9 kB]
157s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1build1 [1003 kB]
157s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB]
157s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB]
157s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB]
157s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build2 [45.1 kB]
157s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build4 [7084 B]
157s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB]
157s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB]
157s Get:47 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-normalize.css all 8.0.1-5.1 [10.4 kB]
157s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu3 [175 kB]
157s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-29ubuntu1 [180 kB]
157s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB]
157s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.2-1ubuntu2 [28.8 MB]
158s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-base64enc amd64 0.1-3-3build1 [28.5 kB]
158s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB]
158s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-commonmark amd64 1.9.5-1 [138 kB]
158s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-digest amd64 0.6.39-1 [203 kB]
158s Get:56 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-evaluate all 1.0.5-1 [117 kB]
158s Get:57 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB]
158s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB]
158s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rlang amd64 1.1.5-3 [1721 kB]
158s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB]
158s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB]
158s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB]
158s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-s7 amd64 0.2.0-1 [328 kB]
158s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB]
158s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB]
158s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB]
158s Get:67 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-viridislite all 0.4.3-1 [1088 kB]
158s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-scales all 1.4.0-1 [725 kB]
159s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB]
159s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB]
159s Get:71 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB]
159s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xfun amd64 0.55+dfsg-1 [587 kB]
159s Get:73 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB]
159s Get:74 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB]
159s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB]
159s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-knitr all 1.51+dfsg-1 [847 kB]
159s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-markdown all 1.13-1 [162 kB]
159s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrixstats amd64 1.5.0-1 [542 kB]
159s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-microbenchmark amd64 1.5.0-1 [67.4 kB]
159s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r.methodss3 all 1.8.2-1 [84.0 kB]
160s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r.oo all 1.27.1-1 [978 kB]
160s Get:82 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r.utils all 2.13.0-1 [1423 kB]
160s Get:83 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r.cache all 0.17.0-1 [117 kB]
160s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r.devices all 2.17.3+ds-1 [400 kB]
160s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 tcl8.6 amd64 8.6.17+dfsg-1build1 [14.9 kB]
160s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 tcl amd64 8.6.16build1 [4200 B]
160s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r.rsp all 0.46.0+ds-1 [1412 kB]
160s Preconfiguring packages ...
160s Fetched 71.9 MB in 4s (17.9 MB/s)
160s Selecting previously unselected package fonts-dejavu-mono.
160s (Reading database ... 
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(Reading database ... 30%
(Reading database ... 35%
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162s Setting up libgraphite2-3:amd64 (1.3.14-11ubuntu1) ...
162s Setting up libpixman-1-0:amd64 (0.46.4-1) ...
162s Setting up libsharpyuv0:amd64 (1.5.0-0.1build1) ...
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162s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu2) ...
162s Setting up libjs-mathjax (2.7.9+dfsg-1build1) ...
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162s Setting up libdatrie1:amd64 (0.2.14-1) ...
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162s Setting up x11-common (1:7.7+24ubuntu1) ...
162s Setting up libdeflate0:amd64 (1.23-2build1) ...
162s Setting up libxcb-shm0:amd64 (1.17.0-2ubuntu1) ...
162s Setting up libgomp1:amd64 (16-20260208-1ubuntu1) ...
162s Setting up libjbig0:amd64 (2.1-6.1ubuntu3) ...
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162s Setting up libtcl8.6:amd64 (8.6.17+dfsg-1build1) ...
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162s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu3) ...
162s Setting up libgfortran5:amd64 (16-20260208-1ubuntu1) ...
162s Setting up libwebp7:amd64 (1.5.0-0.1build1) ...
162s Setting up libjs-highlight.js (10.7.3+dfsg-2) ...
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162s Setting up tcl8.6 (8.6.17+dfsg-1build1) ...
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163s Setting up fontconfig (2.17.1-3ubuntu1) ...
165s Regenerating fonts cache... done.
165s Setting up libxft2:amd64 (2.3.6-1build2) ...
165s Setting up libtk8.6:amd64 (8.6.17-1) ...
165s Setting up libpango-1.0-0:amd64 (1.57.0-1) ...
165s Setting up libcairo2:amd64 (1.18.4-3) ...
165s Setting up libxt6t64:amd64 (1:1.2.1-1.3) ...
165s Setting up libpangoft2-1.0-0:amd64 (1.57.0-1) ...
165s Setting up libpangocairo-1.0-0:amd64 (1.57.0-1) ...
165s Setting up r-base-core (4.5.2-1ubuntu2) ...
165s Creating config file /etc/R/Renviron with new version
165s Setting up r-cran-labeling (0.4.3-1) ...
165s Setting up r-cran-farver (2.1.2-1) ...
165s Setting up r-cran-viridislite (0.4.3-1) ...
165s Setting up r-cran-commonmark (1.9.5-1) ...
165s Setting up r-cran-r6 (2.6.1-1) ...
165s Setting up r-cran-microbenchmark (1.5.0-1) ...
165s Setting up r-cran-rlang (1.1.5-3) ...
165s Setting up r-cran-matrixstats (1.5.0-1) ...
165s Setting up r-cran-xfun (0.55+dfsg-1) ...
165s Setting up r-cran-withr (3.0.2+dfsg-1) ...
165s Setting up r-cran-base64enc (0.1-3-3build1) ...
165s Setting up r-cran-digest (0.6.39-1) ...
165s Setting up r-cran-yaml (2.3.10-1) ...
165s Setting up r-cran-evaluate (1.0.5-1) ...
165s Setting up r-cran-highr (0.11+dfsg-1) ...
165s Setting up r-cran-glue (1.8.0-1) ...
165s Setting up r-cran-cli (3.6.4-1) ...
165s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ...
165s Setting up r-cran-r.methodss3 (1.8.2-1) ...
165s Setting up r-cran-markdown (1.13-1) ...
165s Setting up r-cran-s7 (0.2.0-1) ...
165s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ...
165s Setting up r-cran-isoband (0.2.7-1) ...
165s Setting up r-cran-scales (1.4.0-1) ...
165s Setting up r-cran-gtable (0.3.6+dfsg-1) ...
165s Setting up r-cran-knitr (1.51+dfsg-1) ...
165s Setting up r-cran-vctrs (0.6.5-1) ...
165s Setting up r-cran-ggplot2 (4.0.2+dfsg-1) ...
165s Setting up r-cran-r.oo (1.27.1-1) ...
165s Setting up r-cran-r.utils (2.13.0-1) ...
165s Setting up r-cran-r.devices (2.17.3+ds-1) ...
165s Setting up r-cran-r.cache (0.17.0-1) ...
165s Setting up r-cran-r.rsp (0.46.0+ds-1) ...
165s Processing triggers for libc-bin (2.42-2ubuntu4) ...
165s Processing triggers for man-db (2.13.1-1build1) ...
166s Processing triggers for install-info (7.2-5) ...
166s autopkgtest [05:29:15]: test run-unit-test: [-----------------------
167s 
167s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
167s Copyright (C) 2025 The R Foundation for Statistical Computing
167s Platform: x86_64-pc-linux-gnu
167s 
167s R is free software and comes with ABSOLUTELY NO WARRANTY.
167s You are welcome to redistribute it under certain conditions.
167s Type 'license()' or 'licence()' for distribution details.
167s 
167s R is a collaborative project with many contributors.
167s Type 'contributors()' for more information and
167s 'citation()' on how to cite R or R packages in publications.
167s 
167s Type 'demo()' for some demos, 'help()' for on-line help, or
167s 'help.start()' for an HTML browser interface to help.
167s Type 'q()' to quit R.
167s 
167s > library("matrixStats")
167s > 
167s > allocArray_R <- function(nrow, ncol, value = NA) {
167s +   array(data = value, dim = dim)
167s + }
167s > 
167s > values <- list(
167s +   -1L, 0L, +1L, NA_integer_, .Machine$integer.max,
167s +   -1, 0, +1, NA_real_, NaN, -Inf, +Inf,
167s +   .Machine$double.xmin, .Machine$double.xmax,
167s +   .Machine$double.eps, .Machine$double.neg.eps,
167s +   FALSE, TRUE, NA
167s + )
167s > 
167s > dim <- c(2L, 4L, 3L)
167s > for (value in values) {
167s +   x0 <- allocArray_R(dim, value = value)
167s +   x <- allocArray(dim, value = value)
167s +   if (!identical(x, x0)) {
167s +     str(list(dim = dim, value = value, x = x, x0 = x0))
167s +     stopifnot(identical(x, x0))
167s +   }
167s + }
167s > 
167s 
167s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
167s Copyright (C) 2025 The R Foundation for Statistical Computing
167s Platform: x86_64-pc-linux-gnu
167s 
167s R is free software and comes with ABSOLUTELY NO WARRANTY.
167s You are welcome to redistribute it under certain conditions.
167s Type 'license()' or 'licence()' for distribution details.
167s 
167s R is a collaborative project with many contributors.
167s Type 'contributors()' for more information and
167s 'citation()' on how to cite R or R packages in publications.
167s 
167s Type 'demo()' for some demos, 'help()' for on-line help, or
167s 'help.start()' for an HTML browser interface to help.
167s Type 'q()' to quit R.
167s 
167s > library("matrixStats")
167s > 
167s > allocMatrix_R <- function(nrow, ncol, value = NA) {
167s +   matrix(data = value, nrow = nrow, ncol = ncol)
167s + }
167s > 
167s > values <- list(
167s +   -1L, 0L, +1L, NA_integer_, .Machine$integer.max,
167s +   -1, 0, +1, NA_real_, NaN, -Inf, +Inf,
167s +   .Machine$double.xmin, .Machine$double.xmax,
167s +   .Machine$double.eps, .Machine$double.neg.eps,
167s +   FALSE, TRUE, NA
167s + )
167s > 
167s > nrow <- 2L
167s > ncol <- 3L
167s > for (value in values) {
167s +   x0 <- allocMatrix_R(nrow, ncol, value = value)
167s +   x <- allocMatrix(nrow, ncol, value = value)
167s +   if (!identical(x, x0)) {
167s +     str(list(nrow = nrow, ncol = ncol, value = value, x = x, x0 = x0))
167s +     stopifnot(identical(x, x0))
167s +   }
167s + }
167s > 
167s 
167s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
167s Copyright (C) 2025 The R Foundation for Statistical Computing
167s Platform: x86_64-pc-linux-gnu
167s 
167s R is free software and comes with ABSOLUTELY NO WARRANTY.
167s You are welcome to redistribute it under certain conditions.
167s Type 'license()' or 'licence()' for distribution details.
167s 
167s R is a collaborative project with many contributors.
167s Type 'contributors()' for more information and
167s 'citation()' on how to cite R or R packages in publications.
167s 
167s Type 'demo()' for some demos, 'help()' for on-line help, or
167s 'help.start()' for an HTML browser interface to help.
167s Type 'q()' to quit R.
167s 
167s > library("matrixStats")
167s > 
167s > allocVector_R <- function(length, value = NA) {
167s +   x <- vector(mode = typeof(value), length = length)
167s +   if (!is.finite(value) || value != 0) x[] <- value
167s +   x
167s + }
167s > 
167s > values <- list(
167s +   -1L, 0L, +1L, NA_integer_, .Machine$integer.max,
167s +   -1, 0, +1, NA_real_, NaN, -Inf, +Inf,
167s +   .Machine$double.xmin, .Machine$double.xmax,
167s +   .Machine$double.eps, .Machine$double.neg.eps,
167s +   FALSE, TRUE, NA
167s + )
167s > 
167s > n <- 10L
167s > for (value in values) {
167s +   x0 <- allocVector_R(n, value = value)
167s +   x <- allocVector(n, value = value)
167s +   if (!identical(x, x0)) {
167s +     str(list(n = n, value = value, x = x, x0 = x0))
167s +     stopifnot(identical(x, x0))
167s +   }
167s + }
167s > 
167s 
167s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
167s Copyright (C) 2025 The R Foundation for Statistical Computing
167s Platform: x86_64-pc-linux-gnu
167s 
167s R is free software and comes with ABSOLUTELY NO WARRANTY.
167s You are welcome to redistribute it under certain conditions.
167s Type 'license()' or 'licence()' for distribution details.
167s 
167s R is a collaborative project with many contributors.
167s Type 'contributors()' for more information and
167s 'citation()' on how to cite R or R packages in publications.
167s 
167s Type 'demo()' for some demos, 'help()' for on-line help, or
167s 'help.start()' for an HTML browser interface to help.
167s Type 'q()' to quit R.
167s 
167s > library("matrixStats")
167s > 
167s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
167s > # Setup
167s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
167s > data <- data.frame(
167s +   logical   = c(TRUE, FALSE, TRUE),
167s +   integer   = 1:3,
167s +   double    = seq(from = 1.0, to = 3.0, by = 1.0),
167s +   complex   = seq(from = 1.0, to = 3.0, by = 1.0) + 1.0i,
167s +   character = letters[1:3],
167s +   stringsAsFactors = FALSE
167s + )
167s > 
167s > modes <- names(data)
167s > 
167s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
167s > # Special cases
167s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
167s > cat("NULL...\n")
167s NULL...
167s > stopifnot(identical(anyMissing(NULL), FALSE))
167s > cat("NULL...done\n")
167s NULL...done
167s > 
167s > cat("raw...\n")
167s raw...
167s > stopifnot(identical(anyMissing(as.raw(0:2)), FALSE))
167s > cat("raw...done\n")
167s raw...done
167s > 
167s > cat("list(NULL)...\n")
167s list(NULL)...
167s > stopifnot(identical(anyMissing(list(NULL)), FALSE))
167s > cat("list(NULL)...done\n")
167s list(NULL)...done
167s > 
167s > 
167s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
167s > # Scalars, vectors, and matrices of various modes
167s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
167s > for (mode in modes) {
167s +   cat(sprintf("Mode: %s...\n", mode))
167s +   values <- data[[mode]]
167s + 
167s +   # Scalars
167s +   cat(" scalar\n")
167s +   x <- values[1L]
167s +   print(x)
167s +   stopifnot(identical(anyMissing(x), FALSE))
167s +   is.na(x) <- TRUE
167s +   print(x)
167s +   stopifnot(identical(anyMissing(x), TRUE))
167s + 
167s +   # Vectors
167s +   cat(" vector\n")
167s +   x <- values
167s +   print(x)
167s +   stopifnot(identical(anyMissing(x), FALSE))
167s +   is.na(x)[2L] <- TRUE
167s +   print(x)
167s +   stopifnot(identical(anyMissing(x), TRUE))
167s + 
167s +   # Matrices
167s +   cat(" matrix\n")
167s +   x <- matrix(c(values, values), ncol = 2L)
167s +   print(x)
167s +   stopifnot(identical(anyMissing(x), FALSE))
167s +   is.na(x)[2L] <- TRUE
167s +   print(x)
167s +   stopifnot(identical(anyMissing(x), TRUE))
167s + 
167s +   cat(sprintf("Mode: %s...done\n", mode))
167s + } # for (mode ...)
167s Mode: logical...
167s  scalar
167s [1] TRUE
167s [1] NA
167s  vector
167s [1]  TRUE FALSE  TRUE
167s [1] TRUE   NA TRUE
167s  matrix
167s       [,1]  [,2]
167s [1,]  TRUE  TRUE
167s [2,] FALSE FALSE
167s [3,]  TRUE  TRUE
167s      [,1]  [,2]
167s [1,] TRUE  TRUE
167s [2,]   NA FALSE
167s [3,] TRUE  TRUE
167s Mode: logical...done
167s Mode: integer...
167s  scalar
167s [1] 1
167s [1] NA
167s  vector
167s [1] 1 2 3
167s [1]  1 NA  3
167s  matrix
167s      [,1] [,2]
167s [1,]    1    1
167s [2,]    2    2
167s [3,]    3    3
167s      [,1] [,2]
167s [1,]    1    1
167s [2,]   NA    2
167s [3,]    3    3
167s Mode: integer...done
167s Mode: double...
167s  scalar
167s [1] 1
167s [1] NA
167s  vector
167s [1] 1 2 3
167s [1]  1 NA  3
167s  matrix
167s      [,1] [,2]
167s [1,]    1    1
167s [2,]    2    2
167s [3,]    3    3
167s      [,1] [,2]
167s [1,]    1    1
167s [2,]   NA    2
167s [3,]    3    3
167s Mode: double...done
167s Mode: complex...
167s  scalar
167s [1] 1+1i
167s [1] NA
167s  vector
167s [1] 1+1i 2+1i 3+1i
167s [1] 1+1i   NA 3+1i
167s  matrix
167s      [,1] [,2]
167s [1,] 1+1i 1+1i
167s [2,] 2+1i 2+1i
167s [3,] 3+1i 3+1i
167s      [,1] [,2]
167s [1,] 1+1i 1+1i
167s [2,]   NA 2+1i
167s [3,] 3+1i 3+1i
167s Mode: complex...done
167s Mode: character...
167s  scalar
167s [1] "a"
167s [1] NA
167s  vector
167s [1] "a" "b" "c"
167s [1] "a" NA  "c"
167s  matrix
167s      [,1] [,2]
167s [1,] "a"  "a" 
167s [2,] "b"  "b" 
167s [3,] "c"  "c" 
167s      [,1] [,2]
167s [1,] "a"  "a" 
167s [2,] NA   "b" 
167s [3,] "c"  "c" 
167s Mode: character...done
167s > 
167s > 
167s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
167s > # Data frames
167s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
167s > cat("data.frame...\n")
167s data.frame...
167s > x <- data
167s > stopifnot(identical(anyMissing(x), FALSE))
167s > for (mode in modes) {
167s +   x <- data
167s +   is.na(x[[mode]])[2L] <- TRUE
167s +   print(x)
167s +   stopifnot(identical(anyMissing(x), TRUE))
167s + } # for (mode ...)
167s   logical integer double complex character
167s 1    TRUE       1      1    1+1i         a
167s 2      NA       2      2    2+1i         b
167s 3    TRUE       3      3    3+1i         c
167s   logical integer double complex character
167s 1    TRUE       1      1    1+1i         a
167s 2   FALSE      NA      2    2+1i         b
167s 3    TRUE       3      3    3+1i         c
167s   logical integer double complex character
167s 1    TRUE       1      1    1+1i         a
167s 2   FALSE       2     NA    2+1i         b
167s 3    TRUE       3      3    3+1i         c
167s   logical integer double complex character
167s 1    TRUE       1      1    1+1i         a
167s 2   FALSE       2      2      NA         b
167s 3    TRUE       3      3    3+1i         c
167s   logical integer double complex character
167s 1    TRUE       1      1    1+1i         a
167s 2   FALSE       2      2    2+1i      <NA>
167s 3    TRUE       3      3    3+1i         c
167s > cat("data.frame...done\n")
167s data.frame...done
167s > 
167s > 
167s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
167s > # Lists
167s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
167s > cat("list...\n")
167s list...
167s > x <- as.list(data)
167s > stopifnot(identical(anyMissing(x), FALSE))
167s > for (mode in modes) {
167s +   x <- as.list(data)
167s +   is.na(x[[mode]])[2L] <- TRUE
167s +   print(x)
167s +   stopifnot(identical(anyMissing(x), TRUE))
167s + } # for (mode ...)
167s $logical
167s [1] TRUE   NA TRUE
167s 
167s $integer
167s [1] 1 2 3
167s 
167s $double
167s [1] 1 2 3
167s 
167s $complex
167s [1] 1+1i 2+1i 3+1i
167s 
167s $character
167s [1] "a" "b" "c"
167s 
167s $logical
167s [1]  TRUE FALSE  TRUE
167s 
167s $integer
167s [1]  1 NA  3
167s 
167s $double
167s [1] 1 2 3
167s 
167s $complex
167s [1] 1+1i 2+1i 3+1i
167s 
167s $character
167s [1] "a" "b" "c"
167s 
167s $logical
167s [1]  TRUE FALSE  TRUE
167s 
167s $integer
167s [1] 1 2 3
167s 
167s $double
167s [1]  1 NA  3
167s 
167s $complex
167s [1] 1+1i 2+1i 3+1i
167s 
167s $character
167s [1] "a" "b" "c"
167s 
167s $logical
167s [1]  TRUE FALSE  TRUE
167s 
167s $integer
167s [1] 1 2 3
167s 
167s $double
167s [1] 1 2 3
167s 
167s $complex
167s [1] 1+1i   NA 3+1i
167s 
167s $character
167s [1] "a" "b" "c"
167s 
167s $logical
167s [1]  TRUE FALSE  TRUE
167s 
167s $integer
167s [1] 1 2 3
167s 
167s $double
167s [1] 1 2 3
167s 
167s $complex
167s [1] 1+1i 2+1i 3+1i
167s 
167s $character
167s [1] "a" NA  "c"
167s 
167s > cat("list...done\n")
167s list...done
167s > 
167s 
167s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
167s Copyright (C) 2025 The R Foundation for Statistical Computing
167s Platform: x86_64-pc-linux-gnu
167s 
167s R is free software and comes with ABSOLUTELY NO WARRANTY.
167s You are welcome to redistribute it under certain conditions.
167s Type 'license()' or 'licence()' for distribution details.
167s 
167s R is a collaborative project with many contributors.
167s Type 'contributors()' for more information and
167s 'citation()' on how to cite R or R packages in publications.
167s 
167s Type 'demo()' for some demos, 'help()' for on-line help, or
167s 'help.start()' for an HTML browser interface to help.
167s Type 'q()' to quit R.
167s 
167s > library("matrixStats")
167s > 
167s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
167s > # Subsetted tests
167s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
167s > source("utils/validateIndicesFramework.R")
167s > x <- runif(4, min = -3, max = 3)
167s > x[2] <- NA
167s > for (mode in c("integer", "numeric")) {
167s +   storage.mode(x) <- mode
167s +   for (idxs in index_cases) {
167s +     validateIndicesTestVector(x, idxs,
167s +                               ftest = anyMissing, fsure = function(x, ...) {
167s +         anyValue(x, value = NA)
167s +     })
167s +   }
167s + }
167s > 
167s 
167s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
167s Copyright (C) 2025 The R Foundation for Statistical Computing
167s Platform: x86_64-pc-linux-gnu
167s 
167s R is free software and comes with ABSOLUTELY NO WARRANTY.
167s You are welcome to redistribute it under certain conditions.
167s Type 'license()' or 'licence()' for distribution details.
167s 
167s R is a collaborative project with many contributors.
167s Type 'contributors()' for more information and
167s 'citation()' on how to cite R or R packages in publications.
167s 
167s Type 'demo()' for some demos, 'help()' for on-line help, or
167s 'help.start()' for an HTML browser interface to help.
167s Type 'q()' to quit R.
167s 
167s Loading required namespace: base64enc
167s > ## Don't test with valgrind
167s > if (Sys.getenv("_R_CHECK_USE_VALGRIND_") == "") {
167s + 
167s + ## 3. Make sure all suggested packages are installed / can be loaded
167s + pkgs <- c("base64enc", "ggplot2", "knitr", "markdown", "microbenchmark",
167s +           "R.devices", "R.rsp")
167s + if (all(unlist(lapply(pkgs, FUN = requireNamespace)))) {
167s +   html <- matrixStats:::benchmark("binCounts")
167s +   print(html)
167s + }
167s + 
167s + rm(list = "pkgs")
167s + 
167s + }
167s Loading required namespace: ggplot2
168s Loading required namespace: knitr
168s Loading required namespace: markdown
168s Loading required namespace: microbenchmark
168s Loading required namespace: R.devices
168s Loading required namespace: R.rsp
168s integer: unsorted
170s integer: sorted
171s double: unsorted
173s double: sorted
174s RspFileProduct:
174s Pathname: /tmp/autopkgtest.gRqc2u/autopkgtest_tmp/reports/binCounts.html
174s File size: 71.45 kB (73163 bytes)
174s Content type: text/html
174s Metadata 'author': 'Henrik Bengtsson'
174s Metadata 'title': 'binCounts() benchmarks'
174s Metadata 'date': '2014-05-25'
174s Has processor: FALSE
174s > 
174s Warning message:
174s In par(parT) : argument 1 does not name a graphical parameter
174s 
174s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
174s Copyright (C) 2025 The R Foundation for Statistical Computing
174s Platform: x86_64-pc-linux-gnu
174s 
174s R is free software and comes with ABSOLUTELY NO WARRANTY.
174s You are welcome to redistribute it under certain conditions.
174s Type 'license()' or 'licence()' for distribution details.
174s 
174s R is a collaborative project with many contributors.
174s Type 'contributors()' for more information and
174s 'citation()' on how to cite R or R packages in publications.
174s 
174s Type 'demo()' for some demos, 'help()' for on-line help, or
174s 'help.start()' for an HTML browser interface to help.
174s Type 'q()' to quit R.
174s 
174s > library("matrixStats")
174s > library("stats")
174s > 
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > # Local functions
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > binCounts_hist <- function(x, bx, right = FALSE, ...) {
174s +   n0 <- graphics::hist(x, breaks = bx, right = right,
174s +                        include.lowest = TRUE, plot = FALSE)$counts
174s + }
174s > 
174s > 
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > # Non-sorted and sorted positions
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > nx <- 1000L  # Number of data points
174s > nb <- 200L   # Number of bins
174s > 
174s > # Uniformely distributed bins
174s > bx <- seq(from = 0, to = 1, length.out = nb + 1L)
174s > bx <- c(-1, bx, 2)
174s > 
174s > # Sample data points
174s > set.seed(0xBEEF)
174s > x <- runif(nx, min = 0, max = 1)
174s > 
174s > for (kk in 1:2) {
174s +   n0 <- binCounts_hist(x, bx = bx)
174s +   n1 <- binCounts(x, bx = bx)
174s +   # Sanity check
174s +   stopifnot(identical(n1, n0))
174s + 
174s +   # Check reversed
174s +   n1r <- rev(binCounts(-x, bx = rev(-bx), right = TRUE))
174s +   stopifnot(identical(n1r, n1))
174s + 
174s +   # Retry with a sorted vector
174s +   x <- sort(x)
174s + } # for (kk in 1:2)
174s > 
174s > 
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > # Missing values
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > x <- 1:40
174s > x[20] <- NA_integer_
174s > nx <- length(x)
174s > 
174s > # Bins
174s > bx <- c(0.5, 50.5, 100.5, 150.5, 200.5)
174s > 
174s > y_smooth0 <- binCounts_hist(x, bx = bx)
174s > y_smooth <- binCounts(x, bx = bx)
174s > # Sanity check
174s > stopifnot(all.equal(y_smooth, y_smooth0))
174s > 
174s > 
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > # Border cases
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > x <- 1:10
174s > bx <- min(x) - c(10, 1)
174s > y_smooth <- binCounts(x, bx = bx)
174s > stopifnot(all.equal(y_smooth, 0L))
174s > bx <- range(x)
174s > y_smooth <- binCounts(x, bx = bx)
174s > stopifnot(all.equal(y_smooth, length(x) - 1L))
174s > bx <- max(x) + c(1, 10)
174s > y_smooth <- binCounts(x, bx = bx)
174s > stopifnot(all.equal(y_smooth, 0L))
174s > 
174s > # Every second empty
174s > x <- 1:10
174s > bx <- rep(x, each = 2L)
174s > y_smooth <- binCounts(x, bx = bx)
174s > stopifnot(all.equal(y_smooth, rep(c(0L, 1L), length.out = length(bx) - 1L)))
174s > ## NOTE: binCounts_hist() does not give the same last bin count
174s > 
174s > 
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > # Exception handling
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > # Zero bin boundaries (invalid bin definition)
174s > bx <- double(0L)
174s > res <- try(y_smooth <- binCounts(1:10, bx = bx), silent = TRUE)
174s > stopifnot(inherits(res, "try-error"))
174s > 
174s > # One bin boundary (invalid bin definition)
174s > bx <- double(1L)
174s > res <- try(y_smooth <- binCounts(1:10, bx = bx), silent = TRUE)
174s > stopifnot(inherits(res, "try-error"))
174s > 
174s 
174s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
174s Copyright (C) 2025 The R Foundation for Statistical Computing
174s Platform: x86_64-pc-linux-gnu
174s 
174s R is free software and comes with ABSOLUTELY NO WARRANTY.
174s You are welcome to redistribute it under certain conditions.
174s Type 'license()' or 'licence()' for distribution details.
174s 
174s R is a collaborative project with many contributors.
174s Type 'contributors()' for more information and
174s 'citation()' on how to cite R or R packages in publications.
174s 
174s Type 'demo()' for some demos, 'help()' for on-line help, or
174s 'help.start()' for an HTML browser interface to help.
174s Type 'q()' to quit R.
174s 
174s > library("matrixStats")
174s > 
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > # Local functions
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > binCounts_hist <- function(x, bx, right = FALSE, ...) {
174s +   n0 <- graphics::hist(x, breaks = bx, right = right,
174s +                        include.lowest = TRUE, plot = FALSE)$counts
174s + }
174s > 
174s > 
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > # Subsetted tests
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > source("utils/validateIndicesFramework.R")
174s > x <- runif(6, min = -6, max = 6)
174s > storage.mode(x) <- "integer"
174s > bx <- c(-6, 0, 3, 4, 10)
174s > for (idxs in index_cases) {
174s +   validateIndicesTestVector(x, idxs,
174s +                             ftest = binCounts, fsure = binCounts_hist,
174s +                             bx = bx, right = FALSE)
174s +   validateIndicesTestVector(x, idxs,
174s +                             ftest = binCounts, fsure = binCounts_hist,
174s +                             bx = bx, right = TRUE)
174s + }
174s > 
174s 
174s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
174s Copyright (C) 2025 The R Foundation for Statistical Computing
174s Platform: x86_64-pc-linux-gnu
174s 
174s R is free software and comes with ABSOLUTELY NO WARRANTY.
174s You are welcome to redistribute it under certain conditions.
174s Type 'license()' or 'licence()' for distribution details.
174s 
174s R is a collaborative project with many contributors.
174s Type 'contributors()' for more information and
174s 'citation()' on how to cite R or R packages in publications.
174s 
174s Type 'demo()' for some demos, 'help()' for on-line help, or
174s 'help.start()' for an HTML browser interface to help.
174s Type 'q()' to quit R.
174s 
174s > library("matrixStats")
174s > library("stats")
174s > 
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > # Naive R implementation of binMeans()
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > binMeans0 <- function(y, x, bx, na.rm = TRUE, count = TRUE, right = FALSE) {
174s +   n_smooth <- length(bx) - 1L
174s +   res <- double(n_smooth)
174s +   counts <- rep(NaN, times = n_smooth)
174s + 
174s +   if (na.rm) {
174s +     keep <- !is.na(x) & !is.na(y)
174s +     x <- x[keep]
174s +     y <- y[keep]
174s +   }
174s + 
174s +   # For each bin...
174s +   for (kk in seq_len(n_smooth)) {
174s +     if (right) {
174s +       idxs <- which(bx[kk] <  x & x <= bx[kk + 1L])
174s +     } else {
174s +       idxs <- which(bx[kk] <= x & x <  bx[kk + 1L])
174s +     }
174s +     y_kk <- y[idxs]
174s +     res[kk] <- mean(y_kk)
174s +     counts[kk] <- length(idxs)
174s +   } # for (kk ...)
174s + 
174s +   if (count) attr(res, "count") <- counts
174s +   res
174s + }
174s > 
174s > 
174s > 
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > # Case #1
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > x <- 1:100
174s > nx <- length(x)
174s > y <- double(nx)
174s > y[1:25] <- 5
174s > y[51:75] <- -5
174s > y <- y + rnorm(nx)
174s > 
174s > # Bins
174s > bx <- c(0.5, 25.5, 50.5, 75.5, 100.5)
174s > 
174s > y_smooth0 <- binMeans0(y, x = x, bx = bx)
174s > y_smooth <- binMeans(y, x = x, bx = bx)
174s > n_smooth <- binCounts(x, bx = bx)
174s > # Sanity check
174s > stopifnot(all.equal(y_smooth, y_smooth0))
174s > stopifnot(all.equal(attr(y_smooth, "count"), n_smooth))
174s > 
174s > y_smooth0r <- rev(binMeans0(y, x = -x, bx = rev(-bx),
174s +                             count = FALSE, right = TRUE))
174s > y_smoothr <- rev(binMeans(y, x = -x, bx = rev(-bx),
174s +                           count = FALSE, right = TRUE))
174s > # Sanity check
174s > stopifnot(all.equal(y_smooth0r, y_smooth0, check.attributes = FALSE))
174s > stopifnot(all.equal(y_smoothr, y_smooth0r))
174s > 
174s > 
174s > # Integer input
174s > y <- as.integer(y)
174s > y_smooth0 <- binMeans0(y, x = x, bx = bx)
174s > y_smooth <- binMeans(y, x = x, bx = bx)
174s > n_smooth <- binCounts(x, bx = bx)
174s > # Sanity check
174s > stopifnot(is.integer(y),
174s +           all.equal(y_smooth, y_smooth0),
174s +           all.equal(attr(y_smooth, "count"), n_smooth))
174s > 
174s > # Logical input
174s > y <- as.logical(y)
174s > y_smooth0 <- binMeans0(y, x = x, bx = bx)
174s > y_smooth <- binMeans(y, x = x, bx = bx)
174s > n_smooth <- binCounts(x, bx = bx)
174s > # Sanity check
174s > stopifnot(is.logical(y),
174s +           all.equal(y_smooth, y_smooth0),
174s +           all.equal(attr(y_smooth, "count"), n_smooth))
174s > 
174s > 
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > # Case #2
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > nx <- 1e3
174s > x <- runif(nx)
174s > y <- runif(nx)
174s > 
174s > nb <- 10
174s > bx <- do.call(seq, c(as.list(range(x)), length.out = nb))
174s > bx1 <- c(bx[-1], bx[nb] + 1)
174s > 
174s > y_smooth0 <- binMeans0(y, x = x, bx = bx1)
174s > y_smooth <- binMeans(y, x = x, bx = bx1)
174s > n_smooth <- binCounts(x, bx = bx1)
174s > y_smoothr <- rev(binMeans(y, x = -x, bx = rev(-bx1), right = TRUE))
174s > 
174s > # Sanity check
174s > stopifnot(all.equal(y_smooth, y_smooth0))
174s > stopifnot(all.equal(attr(y_smooth, "count"), n_smooth))
174s > stopifnot(all.equal(y_smoothr, y_smooth, check.attributes = FALSE))
174s > 
174s > 
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > # Empty bins
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > x <- c(6:8, 16:19)
174s > nx <- length(x)
174s > y <- runif(nx)
174s > bx <- c(0, 5, 10, 15, 20, 25)
174s > y_smooth0 <- binMeans0(y, x = x, bx = bx)
174s > y_smooth <- binMeans(y, x = x, bx = bx)
174s > n_smooth <- binCounts(x, bx = bx)
174s > stopifnot(all.equal(attr(y_smooth, "count"), n_smooth))
174s > stopifnot(all.equal(y_smooth, y_smooth0))
174s > 
174s > 
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > # Missing values
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > x <- 1:100
174s > x[50] <- NA_integer_
174s > nx <- length(x)
174s > y <- double(nx)
174s > y[1:25] <- 5
174s > y[51:75] <- -5
174s > y[82:92] <- NA_real_
174s > y <- y + rnorm(nx)
174s > 
174s > # Bins
174s > bx <- c(0.5, 25.5, 75.5, 82.5, 100.5)
174s > 
174s > y_smooth0 <- binMeans0(y, x = x, bx = bx)
174s > y_smooth <- binMeans(y, x = x, bx = bx)
174s > # Sanity check
174s > stopifnot(all.equal(y_smooth, y_smooth0))
174s > 
174s > 
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > # Exception handling
174s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174s > # Zero bin boundaries (invalid bin definition)
174s > bx <- double(0L)
174s > res <- try(y_smooth <- binMeans(x = 1:5, y = 1:5, bx = bx), silent = TRUE)
174s > stopifnot(inherits(res, "try-error"))
174s > 
174s > # One bin boundary (invalid bin definition)
174s > bx <- double(1L)
174s > res <- try(y_smooth <- binMeans(x = 1:5, y = 1:5, bx = bx), silent = TRUE)
174s > stopifnot(inherits(res, "try-error"))
174s > 
174s 
174s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
174s Copyright (C) 2025 The R Foundation for Statistical Computing
174s Platform: x86_64-pc-linux-gnu
174s 
174s R is free software and comes with ABSOLUTELY NO WARRANTY.
174s You are welcome to redistribute it under certain conditions.
174s Type 'license()' or 'licence()' for distribution details.
174s 
174s R is a collaborative project with many contributors.
174s Type 'contributors()' for more information and
174s 'citation()' on how to cite R or R packages in publications.
174s 
174s Type 'demo()' for some demos, 'help()' for on-line help, or
174s 'help.start()' for an HTML browser interface to help.
174s Type 'q()' to quit R.
174s 
175s > library("matrixStats")
175s > 
175s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
175s > # Naive R implementation of binMeans()
175s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
175s > binMeans0 <- function(y, x, bx, na.rm = TRUE, count = TRUE, right = FALSE) {
175s +   n_smooth <- length(bx) - 1L
175s +   res <- double(n_smooth)
175s +   counts <- rep(NaN, times = n_smooth)
175s + 
175s +   if (na.rm) {
175s +     keep <- !is.na(x) & !is.na(y)
175s +     x <- x[keep]
175s +     y <- y[keep]
175s +   }
175s + 
175s +   # For each bin...
175s +   for (kk in seq_len(n_smooth)) {
175s +     if (right) {
175s +       idxs <- which(bx[kk] <  x & x <= bx[kk + 1L])
175s +     } else {
175s +       idxs <- which(bx[kk] <= x & x <  bx[kk + 1L])
175s +     }
175s +     y_kk <- y[idxs]
175s +     res[kk] <- mean(y_kk)
175s +     counts[kk] <- length(idxs)
175s +   } # for (kk ...)
175s + 
175s +   if (count) attr(res, "count") <- counts
175s +   res
175s + }
175s > 
175s > 
175s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
175s > # Subsetted tests
175s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
175s > source("utils/validateIndicesFramework.R")
175s > y <- runif(6, min = -6, max = 6)
175s > x <- runif(6, min = -6, max = 6)
175s > storage.mode(x) <- "integer"
175s > bx <- c(-6, 0, 3, 4, 10)
175s > for (idxs in index_cases) {
175s +   for (na.rm in c(TRUE, FALSE)) {
175s +     validateIndicesTestVector_w(y, x, idxs,
175s +                                 ftest = binMeans, fsure = binMeans0,
175s +                                 bx = bx, na.rm = na.rm,
175s +                                 count = TRUE, right = FALSE)
175s +     validateIndicesTestVector_w(y, x, idxs,
175s +                                 ftest = binMeans, fsure = binMeans0,
175s +                                 bx = bx, na.rm = na.rm,
175s +                                 count = TRUE, right = TRUE)
175s +   }
175s + }
175s > 
175s 
175s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
175s Copyright (C) 2025 The R Foundation for Statistical Computing
175s Platform: x86_64-pc-linux-gnu
175s 
175s R is free software and comes with ABSOLUTELY NO WARRANTY.
175s You are welcome to redistribute it under certain conditions.
175s Type 'license()' or 'licence()' for distribution details.
175s 
175s R is a collaborative project with many contributors.
175s Type 'contributors()' for more information and
175s 'citation()' on how to cite R or R packages in publications.
175s 
175s Type 'demo()' for some demos, 'help()' for on-line help, or
175s 'help.start()' for an HTML browser interface to help.
175s Type 'q()' to quit R.
175s 
175s > library("matrixStats")
175s > 
175s > count_R <- function(x, value = TRUE, na.rm = FALSE, ...) {
175s +   if (is.na(value)) {
175s +     counts <- sum(is.na(x))
175s +   } else {
175s +     counts <- sum(x == value, na.rm = na.rm)
175s +   }
175s +   as.integer(counts)
175s + }
175s > 
175s > 
175s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
175s > # Data type: integer and numeric
175s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
175s > for (mode in c("integer", "double")) {
175s +   x <- runif(20 * 5, min = -3, max = 3)
175s +   x[sample.int(length(x), size = 7)] <- 0
175s +   storage.mode(x) <- mode
175s + 
175s +   for (na.rm in c(FALSE, TRUE)) {
175s +     # Count zeros
175s +     n0 <- count_R(x, value = 0, na.rm = na.rm)
175s +     n1 <- count(x, value = 0, na.rm = na.rm)
175s +     stopifnot(identical(n1, n0))
175s +     all <- allValue(x, value = 0, na.rm = na.rm)
175s +     any <- anyValue(x, value = 0, na.rm = na.rm)
175s + 
175s +     # Count NAs
175s +     n0 <- count_R(x, value = NA, na.rm = na.rm)
175s +     n1 <- count(x, value = NA, na.rm = na.rm)
175s +     stopifnot(identical(n1, n0))
175s +     all <- allValue(x, value = NA, na.rm = na.rm)
175s +     any <- anyValue(x, value = NA, na.rm = na.rm)
175s + 
175s +     if (mode == "integer") {
175s +       ux <- unique(as.vector(x))
175s +       n0 <- n1 <- integer(length(x))
175s +       for (value in ux) {
175s +         n0 <- n0 + count_R(x, value = value, na.rm = na.rm)
175s +         n1 <- n1 + count(x, value = value, na.rm = na.rm)
175s +         stopifnot(identical(n1, n0))
175s +       }
175s +       stopifnot(all(n0 == ncol(x)))
175s +     } # if (mode == "integer")
175s + 
175s +   } # for (na.rm ...)
175s + } # for (mode ...)
175s > 
175s > # All NAs
175s > na_list <- list(NA_integer_, NA_real_, NaN)
175s > for (na_value in na_list) {
175s +   x <- rep(na_value, times = 10L)
175s +   for (na.rm in c(FALSE, TRUE)) {
175s +     n0 <- count_R(x, na.rm = na.rm)
175s +     n1 <- count(x, na.rm = na.rm)
175s +     stopifnot(identical(n1, n0))
175s + 
175s +     # Count NAs
175s +     n0 <- count_R(x, value = NA, na.rm = na.rm)
175s +     n1 <- count(x, value = NA, na.rm = na.rm)
175s +     stopifnot(identical(n1, n0))
175s +     any <- anyValue(x, value = NA, na.rm = na.rm)
175s +     all <- allValue(x, value = NA, na.rm = na.rm)
175s +     stopifnot(any)
175s +     stopifnot(all)
175s +   }
175s + } # for (na_value ...)
175s > 
175s > 
175s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
175s > # Data type: logical
175s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
175s > x <- logical(length = 10L)
175s > x[3:7] <- TRUE
175s > 
175s > # Row/column counts
175s > for (na.rm in c(FALSE, TRUE)) {
175s +   n0 <- count_R(x, na.rm = na.rm)
175s +   n1 <- count(x, na.rm = na.rm)
175s +   stopifnot(identical(n1, n0))
175s + 
175s +   n_true <- count(x, value = TRUE, na.rm = na.rm)
175s +   n_false <- count(x, value = FALSE, na.rm = na.rm)
175s +   stopifnot(n_true + n_false == ncol(x))
175s + 
175s +   # Count NAs
175s +   n0 <- count_R(x, value = NA, na.rm = na.rm)
175s +   n1 <- count(x, value = NA, na.rm = na.rm)
175s +   stopifnot(identical(n1, n0))
175s + }
175s > 
175s 
175s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
175s Copyright (C) 2025 The R Foundation for Statistical Computing
175s Platform: x86_64-pc-linux-gnu
175s 
175s R is free software and comes with ABSOLUTELY NO WARRANTY.
175s You are welcome to redistribute it under certain conditions.
175s Type 'license()' or 'licence()' for distribution details.
175s 
175s R is a collaborative project with many contributors.
175s Type 'contributors()' for more information and
175s 'citation()' on how to cite R or R packages in publications.
175s 
175s Type 'demo()' for some demos, 'help()' for on-line help, or
175s 'help.start()' for an HTML browser interface to help.
175s Type 'q()' to quit R.
175s 
175s > library("matrixStats")
175s > 
175s > count_R <- function(x, value = TRUE, na.rm = FALSE, ...) {
175s +   if (is.na(value)) {
175s +     counts <- sum(is.na(x))
175s +   } else {
175s +     counts <- sum(x == value, na.rm = na.rm)
175s +   }
175s +   as.integer(counts)
175s + }
175s > 
175s > 
175s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
175s > # Subsetted tests
175s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
175s > source("utils/validateIndicesFramework.R")
175s > x <- runif(6, min = -3, max = 3)
175s > storage.mode(x) <- "integer"
175s > for (idxs in index_cases) {
175s +   validateIndicesTestVector(x, idxs,
175s +                             ftest = count, fsure = count_R,
175s +                             value = 0, na.rm = TRUE)
175s +   validateIndicesTestVector(x, idxs,
175s +                             ftest = count, fsure = count_R,
175s +                             value = 0, na.rm = FALSE)
175s +   validateIndicesTestVector(x, idxs,
175s +                             ftest = count, fsure = count_R,
175s +                             value = NA_integer_)
175s + }
175s > 
175s 
175s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
175s Copyright (C) 2025 The R Foundation for Statistical Computing
175s Platform: x86_64-pc-linux-gnu
175s 
175s R is free software and comes with ABSOLUTELY NO WARRANTY.
175s You are welcome to redistribute it under certain conditions.
175s Type 'license()' or 'licence()' for distribution details.
175s 
175s R is a collaborative project with many contributors.
175s Type 'contributors()' for more information and
175s 'citation()' on how to cite R or R packages in publications.
175s 
175s Type 'demo()' for some demos, 'help()' for on-line help, or
175s 'help.start()' for an HTML browser interface to help.
175s Type 'q()' to quit R.
175s 
175s > library("matrixStats")
175s > 
175s > diff2_R <- function(..., useNames = TRUE){
175s +   res <- diff(...)
175s +   if (!useNames) names(res) <- NULL
175s +   res
175s + }
175s > 
175s > set.seed(0x42)
175s > 
175s > for (mode in c("integer", "double")) {
175s +   x <- rnorm(10, sd = 5)
175s +   storage.mode(x) <- mode
175s +   str(x)
175s + 
175s +   for (has_na in c(FALSE, TRUE)) {
175s +     for (setNames in c(TRUE, FALSE)) {
175s +       for (useNames in c(TRUE, FALSE)) {
175s +         if (has_na) {
175s +           x[sample(1:10, size = 3)] <- NA
175s +         }
175s +         if (setNames) {
175s +           names(x) <- LETTERS[1:10]
175s +         }
175s +         for (l in 1:3) {
175s +           for (d in 1:4) {
175s +             cat(sprintf("%s: NAs = %s, lag = %d, differences = %d, setNames = %d, useNames = %d\n",
175s +                         mode, has_na, l, d, setNames, useNames))
175s +             y0 <- diff2_R(x, lag = l, differences = d, useNames = useNames)
175s +             str(y0)
175s +             y1 <- diff2(x, lag = l, differences = d, useNames = useNames)
175s +             str(y1)
175s +             stopifnot(identical(y1, y0))
175s +           }
175s +         }  
175s +       }
175s +     }
175s +   } # for (has_na ...)
175s + }
175s  int [1:10] 11 1 2 0 -1 -3 -3 6 0 0
175s integer: NAs = FALSE, lag = 1, differences = 1, setNames = 1, useNames = 1
175s  Named int [1:9] -10 1 -2 -1 -2 0 9 -6 0
175s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
175s  Named int [1:9] -10 1 -2 -1 -2 0 9 -6 0
175s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
175s integer: NAs = FALSE, lag = 1, differences = 2, setNames = 1, useNames = 1
175s  Named int [1:8] 11 -3 1 -1 2 9 -15 6
175s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
175s  Named int [1:8] 11 -3 1 -1 2 9 -15 6
175s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
175s integer: NAs = FALSE, lag = 1, differences = 3, setNames = 1, useNames = 1
175s  Named int [1:7] -14 4 -2 3 7 -24 21
175s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
175s  Named int [1:7] -14 4 -2 3 7 -24 21
175s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
175s integer: NAs = FALSE, lag = 1, differences = 4, setNames = 1, useNames = 1
175s  Named int [1:6] 18 -6 5 4 -31 45
175s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
175s  Named int [1:6] 18 -6 5 4 -31 45
175s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
175s integer: NAs = FALSE, lag = 2, differences = 1, setNames = 1, useNames = 1
175s  Named int [1:8] -9 -1 -3 -3 -2 9 3 -6
175s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
175s  Named int [1:8] -9 -1 -3 -3 -2 9 3 -6
175s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
175s integer: NAs = FALSE, lag = 2, differences = 2, setNames = 1, useNames = 1
175s  Named int [1:6] 6 -2 1 12 5 -15
175s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
175s  Named int [1:6] 6 -2 1 12 5 -15
175s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
175s integer: NAs = FALSE, lag = 2, differences = 3, setNames = 1, useNames = 1
175s  Named int [1:4] -5 14 4 -27
175s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
175s  Named int [1:4] -5 14 4 -27
175s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
175s integer: NAs = FALSE, lag = 2, differences = 4, setNames = 1, useNames = 1
175s  Named int [1:2] 9 -41
175s  - attr(*, "names")= chr [1:2] "I" "J"
175s  Named int [1:2] 9 -41
175s  - attr(*, "names")= chr [1:2] "I" "J"
175s integer: NAs = FALSE, lag = 3, differences = 1, setNames = 1, useNames = 1
175s  Named int [1:7] -11 -2 -5 -3 7 3 3
175s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
175s  Named int [1:7] -11 -2 -5 -3 7 3 3
175s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
175s integer: NAs = FALSE, lag = 3, differences = 2, setNames = 1, useNames = 1
175s  Named int [1:4] 8 9 8 6
175s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
175s  Named int [1:4] 8 9 8 6
175s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
175s integer: NAs = FALSE, lag = 3, differences = 3, setNames = 1, useNames = 1
175s  Named int -2
175s  - attr(*, "names")= chr "J"
175s  Named int -2
175s  - attr(*, "names")= chr "J"
175s integer: NAs = FALSE, lag = 3, differences = 4, setNames = 1, useNames = 1
175s  Named int(0) 
175s  - attr(*, "names")= chr(0) 
175s  Named int(0) 
175s  - attr(*, "names")= chr(0) 
175s integer: NAs = FALSE, lag = 1, differences = 1, setNames = 1, useNames = 0
175s  int [1:9] -10 1 -2 -1 -2 0 9 -6 0
175s  int [1:9] -10 1 -2 -1 -2 0 9 -6 0
175s integer: NAs = FALSE, lag = 1, differences = 2, setNames = 1, useNames = 0
175s  int [1:8] 11 -3 1 -1 2 9 -15 6
175s  int [1:8] 11 -3 1 -1 2 9 -15 6
175s integer: NAs = FALSE, lag = 1, differences = 3, setNames = 1, useNames = 0
175s  int [1:7] -14 4 -2 3 7 -24 21
175s  int [1:7] -14 4 -2 3 7 -24 21
175s integer: NAs = FALSE, lag = 1, differences = 4, setNames = 1, useNames = 0
175s  int [1:6] 18 -6 5 4 -31 45
175s  int [1:6] 18 -6 5 4 -31 45
175s integer: NAs = FALSE, lag = 2, differences = 1, setNames = 1, useNames = 0
175s  int [1:8] -9 -1 -3 -3 -2 9 3 -6
175s  int [1:8] -9 -1 -3 -3 -2 9 3 -6
175s integer: NAs = FALSE, lag = 2, differences = 2, setNames = 1, useNames = 0
175s  int [1:6] 6 -2 1 12 5 -15
175s  int [1:6] 6 -2 1 12 5 -15
175s integer: NAs = FALSE, lag = 2, differences = 3, setNames = 1, useNames = 0
175s  int [1:4] -5 14 4 -27
175s  int [1:4] -5 14 4 -27
175s integer: NAs = FALSE, lag = 2, differences = 4, setNames = 1, useNames = 0
175s  int [1:2] 9 -41
175s  int [1:2] 9 -41
175s integer: NAs = FALSE, lag = 3, differences = 1, setNames = 1, useNames = 0
175s  int [1:7] -11 -2 -5 -3 7 3 3
175s  int [1:7] -11 -2 -5 -3 7 3 3
175s integer: NAs = FALSE, lag = 3, differences = 2, setNames = 1, useNames = 0
175s  int [1:4] 8 9 8 6
175s  int [1:4] 8 9 8 6
175s integer: NAs = FALSE, lag = 3, differences = 3, setNames = 1, useNames = 0
175s  int -2
175s  int -2
175s integer: NAs = FALSE, lag = 3, differences = 4, setNames = 1, useNames = 0
175s  int(0) 
175s  int(0) 
175s integer: NAs = FALSE, lag = 1, differences = 1, setNames = 0, useNames = 1
175s  Named int [1:9] -10 1 -2 -1 -2 0 9 -6 0
175s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
175s  Named int [1:9] -10 1 -2 -1 -2 0 9 -6 0
175s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
175s integer: NAs = FALSE, lag = 1, differences = 2, setNames = 0, useNames = 1
175s  Named int [1:8] 11 -3 1 -1 2 9 -15 6
175s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
175s  Named int [1:8] 11 -3 1 -1 2 9 -15 6
175s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
175s integer: NAs = FALSE, lag = 1, differences = 3, setNames = 0, useNames = 1
175s  Named int [1:7] -14 4 -2 3 7 -24 21
175s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
175s  Named int [1:7] -14 4 -2 3 7 -24 21
175s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
175s integer: NAs = FALSE, lag = 1, differences = 4, setNames = 0, useNames = 1
175s  Named int [1:6] 18 -6 5 4 -31 45
175s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
175s  Named int [1:6] 18 -6 5 4 -31 45
175s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
175s integer: NAs = FALSE, lag = 2, differences = 1, setNames = 0, useNames = 1
175s  Named int [1:8] -9 -1 -3 -3 -2 9 3 -6
175s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
175s  Named int [1:8] -9 -1 -3 -3 -2 9 3 -6
175s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
175s integer: NAs = FALSE, lag = 2, differences = 2, setNames = 0, useNames = 1
175s  Named int [1:6] 6 -2 1 12 5 -15
175s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
175s  Named int [1:6] 6 -2 1 12 5 -15
175s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
175s integer: NAs = FALSE, lag = 2, differences = 3, setNames = 0, useNames = 1
175s  Named int [1:4] -5 14 4 -27
175s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
175s  Named int [1:4] -5 14 4 -27
175s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
175s integer: NAs = FALSE, lag = 2, differences = 4, setNames = 0, useNames = 1
175s  Named int [1:2] 9 -41
175s  - attr(*, "names")= chr [1:2] "I" "J"
175s  Named int [1:2] 9 -41
175s  - attr(*, "names")= chr [1:2] "I" "J"
175s integer: NAs = FALSE, lag = 3, differences = 1, setNames = 0, useNames = 1
175s  Named int [1:7] -11 -2 -5 -3 7 3 3
175s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
175s  Named int [1:7] -11 -2 -5 -3 7 3 3
175s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
175s integer: NAs = FALSE, lag = 3, differences = 2, setNames = 0, useNames = 1
175s  Named int [1:4] 8 9 8 6
175s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
175s  Named int [1:4] 8 9 8 6
175s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
175s integer: NAs = FALSE, lag = 3, differences = 3, setNames = 0, useNames = 1
175s  Named int -2
175s  - attr(*, "names")= chr "J"
175s  Named int -2
175s  - attr(*, "names")= chr "J"
175s integer: NAs = FALSE, lag = 3, differences = 4, setNames = 0, useNames = 1
175s  Named int(0) 
175s  - attr(*, "names")= chr(0) 
175s  Named int(0) 
175s  - attr(*, "names")= chr(0) 
175s integer: NAs = FALSE, lag = 1, differences = 1, setNames = 0, useNames = 0
175s  int [1:9] -10 1 -2 -1 -2 0 9 -6 0
175s  int [1:9] -10 1 -2 -1 -2 0 9 -6 0
175s integer: NAs = FALSE, lag = 1, differences = 2, setNames = 0, useNames = 0
175s  int [1:8] 11 -3 1 -1 2 9 -15 6
175s  int [1:8] 11 -3 1 -1 2 9 -15 6
175s integer: NAs = FALSE, lag = 1, differences = 3, setNames = 0, useNames = 0
175s  int [1:7] -14 4 -2 3 7 -24 21
175s  int [1:7] -14 4 -2 3 7 -24 21
175s integer: NAs = FALSE, lag = 1, differences = 4, setNames = 0, useNames = 0
175s  int [1:6] 18 -6 5 4 -31 45
175s  int [1:6] 18 -6 5 4 -31 45
175s integer: NAs = FALSE, lag = 2, differences = 1, setNames = 0, useNames = 0
175s  int [1:8] -9 -1 -3 -3 -2 9 3 -6
175s  int [1:8] -9 -1 -3 -3 -2 9 3 -6
175s integer: NAs = FALSE, lag = 2, differences = 2, setNames = 0, useNames = 0
175s  int [1:6] 6 -2 1 12 5 -15
175s  int [1:6] 6 -2 1 12 5 -15
175s integer: NAs = FALSE, lag = 2, differences = 3, setNames = 0, useNames = 0
175s  int [1:4] -5 14 4 -27
175s  int [1:4] -5 14 4 -27
175s integer: NAs = FALSE, lag = 2, differences = 4, setNames = 0, useNames = 0
175s  int [1:2] 9 -41
175s  int [1:2] 9 -41
175s integer: NAs = FALSE, lag = 3, differences = 1, setNames = 0, useNames = 0
175s  int [1:7] -11 -2 -5 -3 7 3 3
175s  int [1:7] -11 -2 -5 -3 7 3 3
175s integer: NAs = FALSE, lag = 3, differences = 2, setNames = 0, useNames = 0
175s  int [1:4] 8 9 8 6
175s  int [1:4] 8 9 8 6
175s integer: NAs = FALSE, lag = 3, differences = 3, setNames = 0, useNames = 0
175s  int -2
175s  int -2
175s integer: NAs = FALSE, lag = 3, differences = 4, setNames = 0, useNames = 0
175s  int(0) 
175s  int(0) 
175s integer: NAs = TRUE, lag = 1, differences = 1, setNames = 1, useNames = 1
175s  Named int [1:9] NA NA NA NA NA 0 9 -6 0
175s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
175s  Named int [1:9] NA NA NA NA NA 0 9 -6 0
175s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
175s integer: NAs = TRUE, lag = 1, differences = 2, setNames = 1, useNames = 1
175s  Named int [1:8] NA NA NA NA NA 9 -15 6
175s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
175s  Named int [1:8] NA NA NA NA NA 9 -15 6
175s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
175s integer: NAs = TRUE, lag = 1, differences = 3, setNames = 1, useNames = 1
175s  Named int [1:7] NA NA NA NA NA -24 21
175s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
175s  Named int [1:7] NA NA NA NA NA -24 21
175s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
175s integer: NAs = TRUE, lag = 1, differences = 4, setNames = 1, useNames = 1
175s  Named int [1:6] NA NA NA NA NA 45
175s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
175s  Named int [1:6] NA NA NA NA NA 45
175s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
175s integer: NAs = TRUE, lag = 2, differences = 1, setNames = 1, useNames = 1
175s  Named int [1:8] -9 NA NA NA NA 9 3 -6
175s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
175s  Named int [1:8] -9 NA NA NA NA 9 3 -6
175s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
175s integer: NAs = TRUE, lag = 2, differences = 2, setNames = 1, useNames = 1
175s  Named int [1:6] NA NA NA NA NA -15
175s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
175s  Named int [1:6] NA NA NA NA NA -15
175s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
175s integer: NAs = TRUE, lag = 2, differences = 3, setNames = 1, useNames = 1
175s  Named int [1:4] NA NA NA NA
175s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
175s  Named int [1:4] NA NA NA NA
175s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
175s integer: NAs = TRUE, lag = 2, differences = 4, setNames = 1, useNames = 1
175s  Named int [1:2] NA NA
175s  - attr(*, "names")= chr [1:2] "I" "J"
175s  Named int [1:2] NA NA
175s  - attr(*, "names")= chr [1:2] "I" "J"
175s integer: NAs = TRUE, lag = 3, differences = 1, setNames = 1, useNames = 1
175s  Named int [1:7] NA NA -5 NA NA 3 3
175s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
175s  Named int [1:7] NA NA -5 NA NA 3 3
175s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
175s integer: NAs = TRUE, lag = 3, differences = 2, setNames = 1, useNames = 1
175s  Named int [1:4] NA NA 8 NA
175s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
175s  Named int [1:4] NA NA 8 NA
175s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
175s integer: NAs = TRUE, lag = 3, differences = 3, setNames = 1, useNames = 1
175s  Named int NA
175s  - attr(*, "names")= chr "J"
175s  Named int NA
175s  - attr(*, "names")= chr "J"
175s integer: NAs = TRUE, lag = 3, differences = 4, setNames = 1, useNames = 1
175s  Named int(0) 
175s  - attr(*, "names")= chr(0) 
175s  Named int(0) 
175s  - attr(*, "names")= chr(0) 
175s integer: NAs = TRUE, lag = 1, differences = 1, setNames = 1, useNames = 0
175s  int [1:9] NA NA NA NA NA 0 9 NA NA
175s  int [1:9] NA NA NA NA NA 0 9 NA NA
175s integer: NAs = TRUE, lag = 1, differences = 2, setNames = 1, useNames = 0
175s  int [1:8] NA NA NA NA NA 9 NA NA
175s  int [1:8] NA NA NA NA NA 9 NA NA
175s integer: NAs = TRUE, lag = 1, differences = 3, setNames = 1, useNames = 0
175s  int [1:7] NA NA NA NA NA NA NA
175s  int [1:7] NA NA NA NA NA NA NA
175s integer: NAs = TRUE, lag = 1, differences = 4, setNames = 1, useNames = 0
175s  int [1:6] NA NA NA NA NA NA
175s  int [1:6] NA NA NA NA NA NA
175s integer: NAs = TRUE, lag = 2, differences = 1, setNames = 1, useNames = 0
175s  int [1:8] NA NA NA NA NA 9 NA -6
175s  int [1:8] NA NA NA NA NA 9 NA -6
175s integer: NAs = TRUE, lag = 2, differences = 2, setNames = 1, useNames = 0
175s  int [1:6] NA NA NA NA NA -15
175s  int [1:6] NA NA NA NA NA -15
175s integer: NAs = TRUE, lag = 2, differences = 3, setNames = 1, useNames = 0
175s  int [1:4] NA NA NA NA
175s  int [1:4] NA NA NA NA
175s integer: NAs = TRUE, lag = 2, differences = 4, setNames = 1, useNames = 0
175s  int [1:2] NA NA
175s  int [1:2] NA NA
175s integer: NAs = TRUE, lag = 3, differences = 1, setNames = 1, useNames = 0
175s  int [1:7] NA NA NA NA NA NA 3
175s  int [1:7] NA NA NA NA NA NA 3
175s integer: NAs = TRUE, lag = 3, differences = 2, setNames = 1, useNames = 0
175s  int [1:4] NA NA NA NA
175s  int [1:4] NA NA NA NA
175s integer: NAs = TRUE, lag = 3, differences = 3, setNames = 1, useNames = 0
175s  int NA
175s  int NA
175s integer: NAs = TRUE, lag = 3, differences = 4, setNames = 1, useNames = 0
175s  int(0) 
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175s  Named int [1:9] NA NA NA NA NA NA NA NA NA
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175s  Named int [1:9] NA NA NA NA NA NA NA NA NA
175s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
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175s  Named int [1:8] NA NA NA NA NA NA NA NA
175s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
175s  Named int [1:8] NA NA NA NA NA NA NA NA
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175s integer: NAs = TRUE, lag = 1, differences = 3, setNames = 0, useNames = 1
175s  Named int [1:7] NA NA NA NA NA NA NA
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175s  int [1:9] NA NA NA NA NA NA NA NA NA
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175s double: NAs = FALSE, lag = 1, differences = 3, setNames = 1, useNames = 1
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175s double: NAs = FALSE, lag = 3, differences = 2, setNames = 1, useNames = 1
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175s  num [1:7] 4.55 -29.39 32.42 -13.29 14.97 ...
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175s  num [1:6] -33.9 61.8 -45.7 28.3 -37 ...
175s double: NAs = FALSE, lag = 2, differences = 1, setNames = 1, useNames = 0
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175s  num [1:8] -2.26 9.5 -3.58 -13.63 -4.54 ...
175s double: NAs = FALSE, lag = 2, differences = 2, setNames = 1, useNames = 0
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175s  num [1:6] -1.33 -23.13 -0.96 19.86 14.44 ...
175s double: NAs = FALSE, lag = 2, differences = 3, setNames = 1, useNames = 0
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175s  num [1:4] 0.368 42.988 15.396 -29.313
175s double: NAs = FALSE, lag = 2, differences = 4, setNames = 1, useNames = 0
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175s  num [1:4] -23.52 7.92 11.38 23.27
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175s  num [1:4] -23.52 7.92 11.38 23.27
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175s double: NAs = TRUE, lag = 3, differences = 2, setNames = 1, useNames = 1
175s  Named num [1:4] -23.5 NA NA 23.3
175s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
175s  Named num [1:4] -23.5 NA NA 23.3
175s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
175s double: NAs = TRUE, lag = 3, differences = 3, setNames = 1, useNames = 1
175s  Named num 46.8
175s  - attr(*, "names")= chr "J"
175s  Named num 46.8
175s  - attr(*, "names")= chr "J"
175s double: NAs = TRUE, lag = 3, differences = 4, setNames = 1, useNames = 1
175s  Named num(0) 
175s  - attr(*, "names")= chr(0) 
175s  Named num(0) 
175s  - attr(*, "names")= chr(0) 
175s double: NAs = TRUE, lag = 1, differences = 1, setNames = 1, useNames = 0
175s  num [1:9] NA 0.673 8.826 NA NA ...
175s  num [1:9] NA 0.673 8.826 NA NA ...
175s double: NAs = TRUE, lag = 1, differences = 2, setNames = 1, useNames = 0
175s  num [1:8] NA 8.15 NA NA NA ...
175s  num [1:8] NA 8.15 NA NA NA ...
175s double: NAs = TRUE, lag = 1, differences = 3, setNames = 1, useNames = 0
175s  num [1:7] NA NA NA NA NA NA NA
175s  num [1:7] NA NA NA NA NA NA NA
175s double: NAs = TRUE, lag = 1, differences = 4, setNames = 1, useNames = 0
175s  num [1:6] NA NA NA NA NA NA
175s  num [1:6] NA NA NA NA NA NA
175s double: NAs = TRUE, lag = 2, differences = 1, setNames = 1, useNames = 0
175s  num [1:8] NA 9.5 NA NA NA ...
175s  num [1:8] NA 9.5 NA NA NA ...
175s double: NAs = TRUE, lag = 2, differences = 2, setNames = 1, useNames = 0
175s  num [1:6] NA NA NA NA NA NA
175s  num [1:6] NA NA NA NA NA NA
175s double: NAs = TRUE, lag = 2, differences = 3, setNames = 1, useNames = 0
175s  num [1:4] NA NA NA NA
175s  num [1:4] NA NA NA NA
175s double: NAs = TRUE, lag = 2, differences = 4, setNames = 1, useNames = 0
175s  num [1:2] NA NA
175s  num [1:2] NA NA
175s double: NAs = TRUE, lag = 3, differences = 1, setNames = 1, useNames = 0
175s  num [1:7] NA NA NA NA NA NA NA
175s  num [1:7] NA NA NA NA NA NA NA
175s double: NAs = TRUE, lag = 3, differences = 2, setNames = 1, useNames = 0
175s  num [1:4] NA NA NA NA
175s  num [1:4] NA NA NA NA
175s double: NAs = TRUE, lag = 3, differences = 3, setNames = 1, useNames = 0
175s  num NA
175s  num NA
175s double: NAs = TRUE, lag = 3, differences = 4, setNames = 1, useNames = 0
175s  num(0) 
175s  num(0) 
175s double: NAs = TRUE, lag = 1, differences = 1, setNames = 0, useNames = 1
175s  Named num [1:9] NA 0.673 8.826 NA NA ...
175s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
175s  Named num [1:9] NA 0.673 8.826 NA NA ...
175s  - attr(*, "names")= chr [1:9] "B" "C" "D" "E" ...
175s double: NAs = TRUE, lag = 1, differences = 2, setNames = 0, useNames = 1
175s  Named num [1:8] NA 8.15 NA NA NA ...
175s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
175s  Named num [1:8] NA 8.15 NA NA NA ...
175s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
175s double: NAs = TRUE, lag = 1, differences = 3, setNames = 0, useNames = 1
175s  Named num [1:7] NA NA NA NA NA NA NA
175s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
175s  Named num [1:7] NA NA NA NA NA NA NA
175s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
175s double: NAs = TRUE, lag = 1, differences = 4, setNames = 0, useNames = 1
175s  Named num [1:6] NA NA NA NA NA NA
175s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
175s  Named num [1:6] NA NA NA NA NA NA
175s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
175s double: NAs = TRUE, lag = 2, differences = 1, setNames = 0, useNames = 1
175s  Named num [1:8] NA 9.5 NA NA NA ...
175s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
175s  Named num [1:8] NA 9.5 NA NA NA ...
175s  - attr(*, "names")= chr [1:8] "C" "D" "E" "F" ...
175s double: NAs = TRUE, lag = 2, differences = 2, setNames = 0, useNames = 1
175s  Named num [1:6] NA NA NA NA NA NA
175s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
175s  Named num [1:6] NA NA NA NA NA NA
175s  - attr(*, "names")= chr [1:6] "E" "F" "G" "H" ...
175s double: NAs = TRUE, lag = 2, differences = 3, setNames = 0, useNames = 1
175s  Named num [1:4] NA NA NA NA
175s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
175s  Named num [1:4] NA NA NA NA
175s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
175s double: NAs = TRUE, lag = 2, differences = 4, setNames = 0, useNames = 1
175s  Named num [1:2] NA NA
175s  - attr(*, "names")= chr [1:2] "I" "J"
175s  Named num [1:2] NA NA
175s  - attr(*, "names")= chr [1:2] "I" "J"
175s double: NAs = TRUE, lag = 3, differences = 1, setNames = 0, useNames = 1
175s  Named num [1:7] NA NA NA NA NA NA NA
175s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
175s  Named num [1:7] NA NA NA NA NA NA NA
175s  - attr(*, "names")= chr [1:7] "D" "E" "F" "G" ...
175s double: NAs = TRUE, lag = 3, differences = 2, setNames = 0, useNames = 1
175s  Named num [1:4] NA NA NA NA
175s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
175s  Named num [1:4] NA NA NA NA
175s  - attr(*, "names")= chr [1:4] "G" "H" "I" "J"
175s double: NAs = TRUE, lag = 3, differences = 3, setNames = 0, useNames = 1
175s  Named num NA
175s  - attr(*, "names")= chr "J"
175s  Named num NA
175s  - attr(*, "names")= chr "J"
175s double: NAs = TRUE, lag = 3, differences = 4, setNames = 0, useNames = 1
175s  Named num(0) 
175s  - attr(*, "names")= chr(0) 
175s  Named num(0) 
175s  - attr(*, "names")= chr(0) 
175s double: NAs = TRUE, lag = 1, differences = 1, setNames = 0, useNames = 0
175s  num [1:9] NA 0.673 8.826 NA NA ...
175s  num [1:9] NA 0.673 8.826 NA NA ...
175s double: NAs = TRUE, lag = 1, differences = 2, setNames = 0, useNames = 0
175s  num [1:8] NA 8.15 NA NA NA ...
175s  num [1:8] NA 8.15 NA NA NA ...
175s double: NAs = TRUE, lag = 1, differences = 3, setNames = 0, useNames = 0
175s  num [1:7] NA NA NA NA NA NA NA
175s  num [1:7] NA NA NA NA NA NA NA
175s double: NAs = TRUE, lag = 1, differences = 4, setNames = 0, useNames = 0
175s  num [1:6] NA NA NA NA NA NA
175s  num [1:6] NA NA NA NA NA NA
175s double: NAs = TRUE, lag = 2, differences = 1, setNames = 0, useNames = 0
175s  num [1:8] NA 9.5 NA NA NA ...
175s  num [1:8] NA 9.5 NA NA NA ...
175s double: NAs = TRUE, lag = 2, differences = 2, setNames = 0, useNames = 0
175s  num [1:6] NA NA NA NA NA NA
175s  num [1:6] NA NA NA NA NA NA
175s double: NAs = TRUE, lag = 2, differences = 3, setNames = 0, useNames = 0
175s  num [1:4] NA NA NA NA
175s  num [1:4] NA NA NA NA
175s double: NAs = TRUE, lag = 2, differences = 4, setNames = 0, useNames = 0
175s  num [1:2] NA NA
175s  num [1:2] NA NA
175s double: NAs = TRUE, lag = 3, differences = 1, setNames = 0, useNames = 0
175s  num [1:7] NA NA NA NA NA NA NA
175s  num [1:7] NA NA NA NA NA NA NA
175s double: NAs = TRUE, lag = 3, differences = 2, setNames = 0, useNames = 0
175s  num [1:4] NA NA NA NA
175s  num [1:4] NA NA NA NA
175s double: NAs = TRUE, lag = 3, differences = 3, setNames = 0, useNames = 0
175s  num NA
175s  num NA
175s double: NAs = TRUE, lag = 3, differences = 4, setNames = 0, useNames = 0
175s  num(0) 
175s  num(0) 
175s > 
175s 
175s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
175s Copyright (C) 2025 The R Foundation for Statistical Computing
175s Platform: x86_64-pc-linux-gnu
175s 
175s R is free software and comes with ABSOLUTELY NO WARRANTY.
175s You are welcome to redistribute it under certain conditions.
175s Type 'license()' or 'licence()' for distribution details.
175s 
175s R is a collaborative project with many contributors.
175s Type 'contributors()' for more information and
175s 'citation()' on how to cite R or R packages in publications.
175s 
175s Type 'demo()' for some demos, 'help()' for on-line help, or
175s 'help.start()' for an HTML browser interface to help.
175s Type 'q()' to quit R.
175s 
175s > library("matrixStats")
175s > 
175s > diff2_R <- function(..., useNames=NA){
175s +   res <- diff(...)
175s +   if (!useNames) names(res) <- NULL
175s +   res
175s + }
175s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
175s > # Subsetted tests
175s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
175s > source("utils/validateIndicesFramework.R")
175s > x <- runif(6, min = -6, max = 6)
175s > for (setNames in c(TRUE, FALSE)) {
175s +   if (setNames) names(x) <- LETTERS[1:6]
175s +   else names(x) <- NULL
175s +   for (l in 1:2) {
175s +     for (d in 1:2) {
175s +       for (idxs in index_cases) {
175s +         for (useNames in c(TRUE, FALSE)) {
175s +           validateIndicesTestVector(x, idxs,
175s +                                     ftest = diff2, fsure = diff2_R,
175s +                                     lag = l, differences = d, useNames = useNames)
175s +         }
175s +       }
175s +     }
175s +   }
175s + }
175s > 
175s 
175s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
175s Copyright (C) 2025 The R Foundation for Statistical Computing
175s Platform: x86_64-pc-linux-gnu
175s 
175s R is free software and comes with ABSOLUTELY NO WARRANTY.
175s You are welcome to redistribute it under certain conditions.
175s Type 'license()' or 'licence()' for distribution details.
175s 
175s R is a collaborative project with many contributors.
175s Type 'contributors()' for more information and
175s 'citation()' on how to cite R or R packages in publications.
175s 
175s Type 'demo()' for some demos, 'help()' for on-line help, or
175s 'help.start()' for an HTML browser interface to help.
175s Type 'q()' to quit R.
175s 
175s > library("matrixStats")
175s > 
175s > indexByRow_R1 <- function(dim, idxs = NULL, ...) {
175s +   n <- prod(dim)
175s +   x <- matrix(seq_len(n), nrow = dim[2L], ncol = dim[1L], byrow = TRUE)
175s +   if (!is.null(idxs))
175s +     x <- x[idxs]
175s +   as.vector(x)
175s + }
175s > 
175s > 
175s > indexByRow_R2 <- function(dim, idxs = NULL, ...) {
175s +   n <- prod(dim)
175s +   if (is.null(idxs)) {
175s +     x <- matrix(seq_len(n), nrow = dim[2L], ncol = dim[1L], byrow = TRUE)
175s +     as.vector(x)
175s +   } else {
175s +     idxs <- idxs - 1L
175s +     cols <- idxs %/% dim[2L]
175s +     rows <- idxs  %% dim[2L]
175s +     cols + dim[1L] * rows + 1L
175s +   }
175s + }
175s > 
175s > 
175s > dim <- c(5L, 4L)
175s > x <- matrix(NA_integer_, nrow = dim[1L], ncol = dim[2L])
175s > y <- t(x)
175s > idxs_by_cols <- seq_along(x)
175s > 
175s > # Assign by columns
175s > x[idxs_by_cols] <- idxs_by_cols
175s > print(x)
175s      [,1] [,2] [,3] [,4]
175s [1,]    1    6   11   16
175s [2,]    2    7   12   17
175s [3,]    3    8   13   18
175s [4,]    4    9   14   19
175s [5,]    5   10   15   20
175s > 
175s > # Truth
175s > y0 <- t(x)
175s > idxs_by_rows <- as.vector(y0)
175s > 
175s > # Assert
175s > idxs <- indexByRow(dim)
175s > stopifnot(all.equal(idxs, idxs_by_rows))
175s > y <- x
175s > y[idxs_by_rows] <- idxs
175s > print(y)
175s      [,1] [,2] [,3] [,4]
175s [1,]    1    6   11   16
175s [2,]    2    7   12   17
175s [3,]    3    8   13   18
175s [4,]    4    9   14   19
175s [5,]    5   10   15   20
175s > stopifnot(all(as.vector(y) == as.vector(x)))
175s > 
175s > idxs_R1 <- indexByRow_R1(dim)
175s > stopifnot(all.equal(idxs_R1, idxs_by_rows))
175s > 
175s > idxs_R2 <- indexByRow_R2(dim)
175s > stopifnot(all.equal(idxs_R2, idxs_by_rows))
175s > 
175s > # Assert
175s > idxs_by_cols <- seq(from = 1, to = length(x), by = 3L)
175s > idxs_by_rows <- as.vector(t(x)[idxs_by_cols])
175s > 
175s > idxs <- indexByRow(dim, idxs = idxs_by_cols)
175s > stopifnot(all(idxs == idxs_by_rows))
175s > 
175s > idxs_R1 <- indexByRow_R1(dim, idxs = idxs_by_cols)
175s > stopifnot(all(idxs_R1 == idxs_by_rows))
175s > 
175s > idxs_R2 <- indexByRow_R2(dim, idxs = idxs_by_cols)
175s > stopifnot(all(idxs_R2 == idxs_by_rows))
175s > 
175s > 
175s > ## DEFUNCT: Backward compatibility
175s > res <- tryCatch({
175s +   idxs1 <- indexByRow(x)
175s + }, error = identity)
175s > stopifnot(inherits(res, "error"))
175s > 
175s > 
175s > ## Exceptions:
175s > ## Too large matrices are not supported, which happens
175s > ## when prod(dim) > .Machine$integer.max
175s > dim_too_large <- c(.Machine$integer.max, 2L)
175s > res <- tryCatch({
175s +   idxs <- indexByRow(dim_too_large, idxs = 1L)
175s + }, error = identity)
175s > stopifnot(inherits(res, "error"))
175s > 
175s > ## Non-positive indices are not supported
175s > res <- tryCatch({
175s +   idxs <- indexByRow(c(1,1), idxs = 0L)
175s + }, error = identity)
175s > stopifnot(inherits(res, "error"))
175s > 
175s > res <- tryCatch({
175s +   idxs <- indexByRow(c(1,1), idxs = -1L)
175s + }, error = identity)
175s > stopifnot(inherits(res, "error"))
175s > 
175s 
175s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
175s Copyright (C) 2025 The R Foundation for Statistical Computing
175s Platform: x86_64-pc-linux-gnu
175s 
175s R is free software and comes with ABSOLUTELY NO WARRANTY.
175s You are welcome to redistribute it under certain conditions.
175s Type 'license()' or 'licence()' for distribution details.
175s 
175s R is a collaborative project with many contributors.
175s Type 'contributors()' for more information and
175s 'citation()' on how to cite R or R packages in publications.
175s 
175s Type 'demo()' for some demos, 'help()' for on-line help, or
175s 'help.start()' for an HTML browser interface to help.
175s Type 'q()' to quit R.
175s 
175s > library("matrixStats")
175s > library("stats")
175s > 
175s > logSumExp_R <- function(lx, na.rm = FALSE) {
175s +   log(sum(exp(lx), na.rm = na.rm))
175s + }
175s > 
175s > ## R-help thread \emph{'[R] Beyond double-precision?'} on May 9, 2009.
175s > 
175s > for (mode in c("integer", "double")) {
175s +   cat("mode: ", mode, "\n", sep = "")
175s + 
175s +   set.seed(1)
175s +   x <- runif(20, min = 1.0, max = 3.0)
175s +   storage.mode(x) <- mode
175s +   str(x)
175s + 
175s +   ## The logarithm of the harmonic mean
175s +   y0 <- log(1 / mean(1 / x))
175s +   print(y0)  ## -1.600885
175s + 
175s +   lx <- log(x)
175s +   y1 <- log(length(x)) - logSumExp(-lx)
175s +   print(y1)  ## [1] -1.600885
175s + 
175s +   # Sanity check
175s +   stopifnot(all.equal(y1, y0))
175s + 
175s +   y2 <- log(length(x)) - logSumExp_R(-lx)
175s +   # Sanity check
175s +   stopifnot(all.equal(y2, y0))
175s + } # for (mode ...)
175s mode: integer
175s  int [1:20] 1 1 2 2 1 2 2 2 2 1 ...
175s [1] 0.3215836
175s [1] 0.3215836
175s mode: double
175s  num [1:20] 1.53 1.74 2.15 2.82 1.4 ...
175s [1] 0.6673156
175s [1] 0.6673156
175s > 
175s > 
175s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
175s > # Missing values
175s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
175s > ## NA values
175s > lx <- c(1, 2, 3)
175s > lx[2] <- NA_real_
175s > y0 <- logSumExp_R(lx, na.rm = FALSE)
175s > y <- logSumExp(lx, na.rm = FALSE)
175s > print(y)
175s [1] NA
175s > stopifnot(identical(y, NA_real_))
175s > stopifnot(all.equal(y, y0))
175s > 
175s > y0 <- logSumExp_R(lx, na.rm = TRUE)
175s > y <- logSumExp(lx, na.rm = TRUE)
175s > print(y)
175s [1] 3.126928
175s > stopifnot(all.equal(y, y0))
175s > 
175s > ## NaN values
175s > lx <- c(1, 2, 3)
175s > lx[2] <- NaN
175s > y0 <- logSumExp_R(lx, na.rm = FALSE)
175s > y <- logSumExp(lx, na.rm = FALSE)
175s > print(y)
175s [1] NA
175s > stopifnot(identical(y, NA_real_))
175s > stopifnot(all.equal(y, y0))
175s > 
175s > y0 <- logSumExp_R(lx, na.rm = TRUE)
175s > y <- logSumExp(lx, na.rm = TRUE)
175s > print(y)
175s [1] 3.126928
175s > stopifnot(all.equal(y, y0))
175s > 
175s > 
175s > 
175s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
175s > # Corner cases
175s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
175s > ## Zero-length vectors
175s > lx <- numeric(0L)
175s > y0 <- logSumExp_R(lx)
175s > y <- logSumExp(lx)
175s > print(y)
175s [1] -Inf
175s > stopifnot(identical(y, -Inf))
175s > stopifnot(all.equal(y, y0))
175s > 
175s > ## Vectors of length one
175s > lx <- 1.0
175s > y0 <- logSumExp_R(lx)
175s > y <- logSumExp(lx)
175s > print(y)
175s [1] 1
175s > stopifnot(identical(y, lx))
175s > stopifnot(all.equal(y, y0))
175s > 
175s > lx <- NA_real_
175s > y0 <- logSumExp_R(lx, na.rm = TRUE)
175s > y <- logSumExp(lx, na.rm = TRUE)
175s > print(y)
175s [1] -Inf
175s > stopifnot(identical(y, -Inf))
175s > stopifnot(all.equal(y, y0))
175s > 
175s > ## All missing values
175s > lx <- c(NA_real_, NA_real_)
175s > y0 <- logSumExp_R(lx, na.rm = TRUE)
175s > y <- logSumExp(lx, na.rm = TRUE)
175s > print(y)
175s [1] -Inf
175s > stopifnot(identical(y, -Inf))
175s > stopifnot(all.equal(y, y0))
175s > 
175s > lx <- c(NA_real_, NA_real_)
175s > y0 <- logSumExp_R(lx, na.rm = FALSE)
175s > y <- logSumExp(lx, na.rm = FALSE)
175s > print(y)
175s [1] NA
175s > stopifnot(identical(y, NA_real_))
175s > stopifnot(all.equal(y, y0))
175s > 
175s > 
175s > ## +Inf values
175s > lx <- c(1, 2, +Inf)
175s > y0 <- logSumExp_R(lx)
175s > y <- logSumExp(lx)
175s > print(y)
175s [1] Inf
175s > stopifnot(identical(y, +Inf))
175s > stopifnot(all.equal(y, y0))
175s > 
175s > ## First element is a missing value, cf. PR #33
175s > lx <- c(NA_real_, 1)
175s > y0 <- logSumExp_R(lx)
175s > print(y0)
175s [1] NA
175s > y <- logSumExp(lx, na.rm = FALSE)
175s > print(y)
175s [1] NA
175s > stopifnot(identical(y, NA_real_))
175s > stopifnot(all.equal(y, y0))
175s > 
175s > y0 <- logSumExp_R(lx, na.rm = TRUE)
175s > print(y0)
175s [1] 1
175s > y <- logSumExp(lx, na.rm = TRUE)
175s > print(y)
175s [1] 1
175s > stopifnot(identical(y, 1))
175s > stopifnot(all.equal(y, y0))
175s > 
175s > ## Multiple -Inf values, cf. issue #84
175s > lx <- c(-Inf, -Inf)
175s > y0 <- logSumExp_R(lx)
175s > y <- logSumExp(lx)
175s > print(y)
175s [1] -Inf
175s > stopifnot(identical(y, -Inf))
175s > stopifnot(all.equal(y, y0))
175s > 
175s > lx <- c(-Inf, 5, -Inf)
175s > y0 <- logSumExp_R(lx)
175s > y <- logSumExp(lx)
175s > print(y)
175s [1] 5
175s > stopifnot(identical(y, 5))
175s > stopifnot(all.equal(y, y0))
175s > 
176s 
176s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
176s Copyright (C) 2025 The R Foundation for Statistical Computing
176s Platform: x86_64-pc-linux-gnu
176s 
176s R is free software and comes with ABSOLUTELY NO WARRANTY.
176s You are welcome to redistribute it under certain conditions.
176s Type 'license()' or 'licence()' for distribution details.
176s 
176s R is a collaborative project with many contributors.
176s Type 'contributors()' for more information and
176s 'citation()' on how to cite R or R packages in publications.
176s 
176s Type 'demo()' for some demos, 'help()' for on-line help, or
176s 'help.start()' for an HTML browser interface to help.
176s Type 'q()' to quit R.
176s 
176s > library("matrixStats")
176s > 
176s > logSumExp_R <- function(lx, na.rm = FALSE) {
176s +   log(sum(exp(lx), na.rm = na.rm))
176s + }
176s > 
176s > 
176s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
176s > # Subsetted tests
176s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
176s > source("utils/validateIndicesFramework.R")
176s > x <- runif(6, min = -6, max = 6)
176s > for (idxs in index_cases) {
176s +   validateIndicesTestVector(x, idxs,
176s +                             ftest = logSumExp, fsure = logSumExp_R,
176s +                             na.rm = FALSE)
176s +   validateIndicesTestVector(x, idxs,
176s +                             ftest = logSumExp, fsure = logSumExp_R,
176s +                             na.rm = TRUE)
176s + }
176s > 
176s 
176s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
176s Copyright (C) 2025 The R Foundation for Statistical Computing
176s Platform: x86_64-pc-linux-gnu
176s 
176s R is free software and comes with ABSOLUTELY NO WARRANTY.
176s You are welcome to redistribute it under certain conditions.
176s Type 'license()' or 'licence()' for distribution details.
176s 
176s R is a collaborative project with many contributors.
176s Type 'contributors()' for more information and
176s 'citation()' on how to cite R or R packages in publications.
176s 
176s Type 'demo()' for some demos, 'help()' for on-line help, or
176s 'help.start()' for an HTML browser interface to help.
176s Type 'q()' to quit R.
176s 
176s > library("matrixStats")
176s > 
176s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
176s > # Consistency checks
176s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
176s > set.seed(1)
176s > 
176s > mean2_R <- function(x, na.rm = FALSE, idxs = NULL) {
176s +   if (is.null(idxs)) {
176s +     mean(x, na.rm = na.rm)
176s +   } else {
176s +     mean(x[idxs], na.rm = na.rm)
176s +   }
176s + } # mean2_R()
176s > 
176s > 
176s > cat("Consistency checks:\n")
176s Consistency checks:
176s > for (kk in 1:20) {
176s +   cat("Random test #", kk, "\n", sep = "")
176s + 
176s +   # Simulate data in a matrix of any shape
176s +   n <- sample(100L, size = 1L)
176s +   x <- rnorm(n, sd = 100)
176s + 
176s +   # Add NAs?
176s +   if ((kk %% 4) %in% c(3, 0)) {
176s +     cat("Adding NAs\n")
176s +     nna <- sample(n, size = 1L)
176s +     na_values <- c(NA_real_, NaN)
176s +     t <- sample(na_values, size = nna, replace = TRUE)
176s +     x[sample(length(x), size = nna)] <- t
176s +   }
176s + 
176s +   # Integer or double?
176s +   if ((kk %% 4) %in% c(2, 0)) {
176s +     cat("Coercing to integers\n")
176s +     storage.mode(x) <- "integer"
176s +   }
176s + 
176s +   na.rm <- sample(c(TRUE, FALSE), size = 1L)
176s + 
176s +   # Sum over all
176s +   y0 <- mean2_R(x, na.rm = na.rm)
176s +   y1 <- mean2(x, na.rm = na.rm)
176s +   stopifnot(all.equal(y1, y0))
176s + 
176s +   # Sum over subset
176s +   nidxs <- sample(n, size = 1L)
176s +   idxs <- sample(n, size = nidxs)
176s +   y0 <- mean2_R(x, na.rm = na.rm, idxs = idxs)
176s +   y1 <- mean2(x, na.rm = na.rm, idxs = idxs)
176s +   stopifnot(all.equal(y1, y0))
176s + 
176s +   if (storage.mode(x) == "integer") {
176s +     storage.mode(x) <- "logical"
176s +     
176s +     y0 <- mean2_R(x, na.rm = na.rm)
176s +     y1 <- mean2(x, na.rm = na.rm)
176s +     stopifnot(all.equal(y1, y0))
176s +     
176s +     y0 <- mean2_R(x, na.rm = na.rm, idxs = idxs)
176s +     y1 <- mean2(x, na.rm = na.rm, idxs = idxs)
176s +     stopifnot(all.equal(y1, y0))
176s +   }
176s + } # for (kk ...)
176s Random test #1
176s Random test #2
176s Coercing to integers
176s Random test #3
176s Adding NAs
176s Random test #4
176s Adding NAs
176s Coercing to integers
176s Random test #5
176s Random test #6
176s Coercing to integers
176s Random test #7
176s Adding NAs
176s Random test #8
176s Adding NAs
176s Coercing to integers
176s Random test #9
176s Random test #10
176s Coercing to integers
176s Random test #11
176s Adding NAs
176s Random test #12
176s Adding NAs
176s Coercing to integers
176s Random test #13
176s Random test #14
176s Coercing to integers
176s Random test #15
176s Adding NAs
176s Random test #16
176s Adding NAs
176s Coercing to integers
176s Random test #17
176s Random test #18
176s Coercing to integers
176s Random test #19
176s Adding NAs
176s Random test #20
176s Adding NAs
176s Coercing to integers
176s > 
176s > 
176s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
176s > # Special cases
176s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
176s > for (na.rm in c(FALSE, TRUE)) {
176s +   # Averaging over zero elements (integers)
176s +   x <- integer(0)
176s +   s1 <- mean(x, na.rm = na.rm)
176s +   s2 <- mean2(x, na.rm = na.rm)
176s +   stopifnot(identical(s1, s2))
176s + 
176s +   x <- 1:5
176s +   idxs <- integer(0)
176s +   s1 <- mean(x[idxs], na.rm = na.rm)
176s +   s2 <- mean2(x, idxs = idxs, na.rm = na.rm)
176s +   stopifnot(identical(s1, s2))
176s + 
176s +   # Averaging over NA_integer_:s
176s +   x <- rep(NA_integer_, times = 5L)
176s +   s1 <- mean(x, na.rm = na.rm)
176s +   s2 <- mean2(x, na.rm = na.rm)
176s +   stopifnot(identical(s1, s2))
176s + 
176s +   x <- rep(NA_integer_, times = 5L)
176s +   idxs <- 1:3
176s +   s1 <- mean(x[idxs], na.rm = na.rm)
176s +   s2 <- mean2(x, idxs = idxs, na.rm = na.rm)
176s +   stopifnot(identical(s1, s2))
176s + 
176s + 
176s +   # Averaging over zero elements (doubles)
176s +   x <- double(0)
176s +   s1 <- mean(x)
176s +   s2 <- mean2(x)
176s +   stopifnot(identical(s1, s2))
176s + 
176s +   x <- as.double(1:10)
176s +   idxs <- integer(0)
176s +   s1 <- mean(x[idxs])
176s +   s2 <- mean2(x, idxs = idxs)
176s +   stopifnot(identical(s1, s2))
176s + 
176s +   # Averaging over NA_real_:s
176s +   x <- rep(NA_real_, times = 5L)
176s +   s1 <- mean(x, na.rm = na.rm)
176s +   s2 <- mean2(x, na.rm = na.rm)
176s +   stopifnot(identical(s1, s2))
176s + 
176s +   x <- rep(NA_real_, times = 5L)
176s +   idxs <- 1:3
176s +   s1 <- mean(x[idxs], na.rm = na.rm)
176s +   s2 <- mean2(x, idxs = idxs, na.rm = na.rm)
176s +   stopifnot(identical(s1, s2))
176s + 
176s +   # Averaging over -Inf:s
176s +   x <- rep(-Inf, times = 3L)
176s +   s1 <- mean(x, na.rm = na.rm)
176s +   s2 <- mean2(x, na.rm = na.rm)
176s +   stopifnot(identical(s1, s2))
176s + 
176s +   # Averaging over +Inf:s
176s +   x <- rep(+Inf, times = 3L)
176s +   s1 <- mean(x, na.rm = na.rm)
176s +   s2 <- mean2(x, na.rm = na.rm)
176s +   stopifnot(identical(s1, s2))
176s + 
176s +   # Averaging over mix of -Inf:s and +Inf:s
176s +   x <- rep(c(-Inf, +Inf), times = 3L)
176s +   s1 <- mean(x, na.rm = na.rm)
176s +   s2 <- mean2(x, na.rm = na.rm)
176s +   stopifnot(identical(s1, s2))
176s + 
176s +   # Averaging over mix of -Inf:s and +Inf:s and numerics
176s +   x <- rep(c(-Inf, +Inf, 3.14), times = 2L)
176s +   s1 <- mean(x, na.rm = na.rm)
176s +   s2 <- mean2(x, na.rm = na.rm)
176s +   stopifnot(identical(s1, s2))
176s + 
176s +   # Averaging over mix of NaN, NA, +Inf, and numerics
176s +   x <- c(NaN, NA, +Inf, 3.14)
176s +   s1 <- mean(x, na.rm = na.rm)
176s +   s2 <- mean2(x, na.rm = na.rm)
176s +   if (na.rm) {
176s +     stopifnot(identical(s2, s1))
176s +   } else {
176s +     stopifnot(is.na(s1), is.na(s2))
176s +     ## NOTE, due to compiler optimization, it is not guaranteed that NA is
176s +     ## returned here (as one would expect). NaN might very well be returned,
176s +     ## when both NA and NaN are involved.  This is an accepted feature in R,
176s +     ## which is documented in help("is.nan").  See also
176s +     ## https://stat.ethz.ch/pipermail/r-devel/2017-April/074009.html.
176s +     ## Thus, we cannot guarantee that s1 is identical to s0.
176s +   }
176s + 
176s +   # Averaging over mix of NaN, NA_real_, +Inf, and numerics
176s +   x <- c(NA_real_, NaN, +Inf, 3.14)
176s +   s1 <- mean(x, na.rm = na.rm)
176s +   s2 <- mean2(x, na.rm = na.rm)
176s +   if (na.rm) {
176s +     stopifnot(identical(s2, s1))
176s +   } else {
176s +     stopifnot(is.na(s1), is.na(s2))
176s +     ## NOTE, due to compiler optimization, it is not guaranteed that NA is
176s +     ## returned here (as one would expect). NaN might very well be returned,
176s +     ## when both NA and NaN are involved.  This is an accepted feature in R,
176s +     ## which is documented in help("is.nan").  See also
176s +     ## https://stat.ethz.ch/pipermail/r-devel/2017-April/074009.html.
176s +     ## Thus, we cannot guarantee that s1 is identical to s0.
176s +   }
176s + }
176s > 
176s > 
176s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
176s > # Argument 'idxs'
176s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
176s > x <- 1:5
176s > idxs_list <- list(
176s +   integer = 1:3,
176s +   double  = as.double(1:3),
176s +   logical = (x <= 3)
176s + )
176s > 
176s > for (idxs in idxs_list) {
176s +   cat("idxs:\n")
176s +   str(idxs)
176s +   s1 <- mean(x[idxs], na.rm = TRUE)
176s +   s2 <- mean2(x, idxs = idxs, na.rm = TRUE)
176s +   stopifnot(identical(s1, s2))
176s + }
176s idxs:
176s  int [1:3] 1 2 3
176s idxs:
176s  num [1:3] 1 2 3
176s idxs:
176s  logi [1:5] TRUE TRUE TRUE FALSE FALSE
176s > 
176s 
176s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
176s Copyright (C) 2025 The R Foundation for Statistical Computing
176s Platform: x86_64-pc-linux-gnu
176s 
176s R is free software and comes with ABSOLUTELY NO WARRANTY.
176s You are welcome to redistribute it under certain conditions.
176s Type 'license()' or 'licence()' for distribution details.
176s 
176s R is a collaborative project with many contributors.
176s Type 'contributors()' for more information and
176s 'citation()' on how to cite R or R packages in publications.
176s 
176s Type 'demo()' for some demos, 'help()' for on-line help, or
176s 'help.start()' for an HTML browser interface to help.
176s Type 'q()' to quit R.
176s 
176s > library("matrixStats")
176s > 
176s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
176s > # Subsetted tests
176s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
176s > source("utils/validateIndicesFramework.R")
176s > x <- runif(6, min = -6, max = 6)
176s > storage.mode(x) <- "integer"
176s > for (idxs in index_cases) {
176s +   validateIndicesTestVector(x, idxs,
176s +                             ftest = mean2, fsure = mean,
176s +                             na.rm = FALSE)
176s +   validateIndicesTestVector(x, idxs,
176s +                             ftest = mean2, fsure = mean,
176s +                             na.rm = TRUE)
176s + }
176s > 
176s 
176s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
176s Copyright (C) 2025 The R Foundation for Statistical Computing
176s Platform: x86_64-pc-linux-gnu
176s 
176s R is free software and comes with ABSOLUTELY NO WARRANTY.
176s You are welcome to redistribute it under certain conditions.
176s Type 'license()' or 'licence()' for distribution details.
176s 
176s R is a collaborative project with many contributors.
176s Type 'contributors()' for more information and
176s 'citation()' on how to cite R or R packages in publications.
176s 
176s Type 'demo()' for some demos, 'help()' for on-line help, or
176s 'help.start()' for an HTML browser interface to help.
176s Type 'q()' to quit R.
176s 
176s > library("matrixStats")
176s > 
176s > for (mode in c("integer", "double")) {
176s +   cat("mode: ", mode, "\n", sep = "")
176s + 
176s +   # Empty vector
176s +   x <- 0
176s +   storage.mode(x) <- mode
176s +   y <- prod(x, na.rm = TRUE)
176s +   print(y)
176s +   z <- product(x, na.rm = TRUE)
176s +   print(z)
176s +   stopifnot(all.equal(z, y))
176s + 
176s +   # Test negative values
176s +   x <- c(1, -4, 2)
176s +   storage.mode(x) <- mode
176s +   y <- prod(x, na.rm = TRUE)
176s +   print(y)
176s +   z <- product(x, na.rm = TRUE)
176s +   print(z)
176s +   stopifnot(all.equal(z, y))
176s + 
176s +   # Test missing values
176s +   x <- c(1, NA, NaN, 2)
176s +   storage.mode(x) <- mode
176s +   y <- prod(x, na.rm = TRUE)
176s +   print(y)
176s +   z <- product(x, na.rm = TRUE)
176s +   print(z)
176s +   stopifnot(all.equal(z, y))
176s + 
176s +   x <- c(1, NA, NaN, 2)
176s +   storage.mode(x) <- mode
176s +   y <- prod(x, na.rm = FALSE)
176s +   print(y)
176s +   z <- product(x, na.rm = FALSE)
176s +   print(z)
176s +   stopifnot(all(is.na(z), is.na(y)))
176s + 
176s +   x <- c(1, NaN, 2)
176s +   storage.mode(x) <- mode
176s +   y <- prod(x, na.rm = FALSE)
176s +   print(y)
176s +   stopifnot(is.na(y))
176s +   z <- product(x, na.rm = FALSE)
176s +   print(z)
176s +   stopifnot(is.na(z))
176s + 
176s + } # for (mode ...)
176s mode: integer
176s [1] 0
176s [1] 0
176s [1] -8
176s [1] -8
176s [1] 2
176s [1] 2
176s [1] NA
176s [1] NA
176s [1] NA
176s [1] NA
176s mode: double
176s [1] 0
176s [1] 0
176s [1] -8
176s [1] -8
176s [1] 2
176s [1] 2
176s [1] NA
176s [1] NA
176s [1] NaN
176s [1] NA
176s > 
176s > 
176s > # NAs following 0s
176s > x <- c(0L, NA_integer_)
176s > y <- prod(x, na.rm = FALSE)
176s > print(y)
176s [1] NA
176s > z <- product(x, na.rm = FALSE)
176s > print(z)
176s [1] NA
176s > stopifnot(identical(z, y))
176s > 
176s 
176s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
176s Copyright (C) 2025 The R Foundation for Statistical Computing
176s Platform: x86_64-pc-linux-gnu
176s 
176s R is free software and comes with ABSOLUTELY NO WARRANTY.
176s You are welcome to redistribute it under certain conditions.
176s Type 'license()' or 'licence()' for distribution details.
176s 
176s R is a collaborative project with many contributors.
176s Type 'contributors()' for more information and
176s 'citation()' on how to cite R or R packages in publications.
176s 
176s Type 'demo()' for some demos, 'help()' for on-line help, or
176s 'help.start()' for an HTML browser interface to help.
176s Type 'q()' to quit R.
176s 
176s > library("matrixStats")
176s > 
176s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
176s > # Subsetted tests
176s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
176s > source("utils/validateIndicesFramework.R")
176s > x <- runif(6, min = -6, max = 6)
176s > storage.mode(x) <- "integer"
176s > for (idxs in index_cases) {
176s +   validateIndicesTestVector(x, idxs,
176s +                             ftest = product, fsure = prod,
176s +                             na.rm = TRUE)
176s +   validateIndicesTestVector(x, idxs,
176s +                             ftest = product, fsure = prod,
176s +                             na.rm = FALSE)
176s + }
176s > 
176s 
176s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
176s Copyright (C) 2025 The R Foundation for Statistical Computing
176s Platform: x86_64-pc-linux-gnu
176s 
176s R is free software and comes with ABSOLUTELY NO WARRANTY.
176s You are welcome to redistribute it under certain conditions.
176s Type 'license()' or 'licence()' for distribution details.
176s 
176s R is a collaborative project with many contributors.
176s Type 'contributors()' for more information and
176s 'citation()' on how to cite R or R packages in publications.
176s 
176s Type 'demo()' for some demos, 'help()' for on-line help, or
176s 'help.start()' for an HTML browser interface to help.
176s Type 'q()' to quit R.
176s 
176s > library("matrixStats")
176s > library("utils")  ## utils::str
176s > 
176s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
176s > # Local functions
176s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
176s > psortKM_R <- function(x, k, m) {
176s +   x <- sort(x)
176s +   x[(k - m + 1):k]
176s + }
176s > 
176s > psortKM_R2 <- function(x, k, m) {
176s +   partial <- (k - m + 1):k
176s +   x <- sort.int(x, partial = partial)
176s +   x[partial]
176s + }
176s > 
176s > 
176s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
176s > # Consistency checks
176s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
176s > set.seed(1)
176s > 
176s > cat("Consistency checks:\n")
176s Consistency checks:
176s > x <- 1:30
176s > x[18:20] <- 20
176s > y <- sample(x)
176s > cat("x:\n")
176s x:
176s > str(x)
176s  num [1:30] 1 2 3 4 5 6 7 8 9 10 ...
176s > cat("sample(x):\n")
176s sample(x):
176s > str(y)
176s  num [1:30] 25 4 7 1 2 23 11 14 20 20 ...
176s > 
176s > for (k in c(1L, 2L, 20L, 21L, length(x))) {
176s +   for (m in 1:min(5L, k)) {
176s +     px0 <- psortKM_R(x, k = k, m = m)
176s +     px0b <- psortKM_R2(x, k = k, m = m)
176s +     stopifnot(identical(px0b, px0))
176s +     px1 <- matrixStats:::.psortKM(x, k = k, m = m)
176s +     cat(sprintf(".psortKM(x, k = %d, m = %d):\n", k, m))
176s +     print(px1)
176s +     stopifnot(identical(px1, px0))
176s + 
176s +     py0 <- psortKM_R(y, k = k, m = m)
176s +     py0b <- psortKM_R2(y, k = k, m = m)
176s +     stopifnot(identical(py0b, py0))
176s +     py1 <- matrixStats:::.psortKM(y, k = k, m = m)
176s +     cat(sprintf(".psortKM(y, k = %d, m = %d):\n", k, m))
176s +     print(py1)
176s +     stopifnot(identical(py1, py0))
176s +     stopifnot(identical(py1, px1))
176s +   } # for (m ...)
176s + } # for (k ...)
176s .psortKM(x, k = 1, m = 1):
176s [1] 1
176s .psortKM(y, k = 1, m = 1):
176s [1] 1
176s .psortKM(x, k = 2, m = 1):
176s [1] 2
176s .psortKM(y, k = 2, m = 1):
176s [1] 2
176s .psortKM(x, k = 2, m = 2):
176s [1] 1 2
176s .psortKM(y, k = 2, m = 2):
176s [1] 1 2
176s .psortKM(x, k = 20, m = 1):
176s [1] 20
176s .psortKM(y, k = 20, m = 1):
176s [1] 20
176s .psortKM(x, k = 20, m = 2):
176s [1] 20 20
176s .psortKM(y, k = 20, m = 2):
176s [1] 20 20
176s .psortKM(x, k = 20, m = 3):
176s [1] 20 20 20
176s .psortKM(y, k = 20, m = 3):
176s [1] 20 20 20
176s .psortKM(x, k = 20, m = 4):
176s [1] 17 20 20 20
176s .psortKM(y, k = 20, m = 4):
176s [1] 17 20 20 20
176s .psortKM(x, k = 20, m = 5):
176s [1] 16 17 20 20 20
176s .psortKM(y, k = 20, m = 5):
176s [1] 16 17 20 20 20
176s .psortKM(x, k = 21, m = 1):
176s [1] 21
176s .psortKM(y, k = 21, m = 1):
176s [1] 21
176s .psortKM(x, k = 21, m = 2):
176s [1] 20 21
176s .psortKM(y, k = 21, m = 2):
176s [1] 20 21
176s .psortKM(x, k = 21, m = 3):
176s [1] 20 20 21
176s .psortKM(y, k = 21, m = 3):
176s [1] 20 20 21
176s .psortKM(x, k = 21, m = 4):
176s [1] 20 20 20 21
176s .psortKM(y, k = 21, m = 4):
176s [1] 20 20 20 21
176s .psortKM(x, k = 21, m = 5):
176s [1] 17 20 20 20 21
176s .psortKM(y, k = 21, m = 5):
176s [1] 17 20 20 20 21
176s .psortKM(x, k = 30, m = 1):
176s [1] 30
176s .psortKM(y, k = 30, m = 1):
176s [1] 30
176s .psortKM(x, k = 30, m = 2):
176s [1] 29 30
176s .psortKM(y, k = 30, m = 2):
176s [1] 29 30
176s .psortKM(x, k = 30, m = 3):
176s [1] 28 29 30
176s .psortKM(y, k = 30, m = 3):
176s [1] 28 29 30
176s .psortKM(x, k = 30, m = 4):
176s [1] 27 28 29 30
176s .psortKM(y, k = 30, m = 4):
176s [1] 27 28 29 30
176s .psortKM(x, k = 30, m = 5):
176s [1] 26 27 28 29 30
176s .psortKM(y, k = 30, m = 5):
176s [1] 26 27 28 29 30
176s > 
176s 
176s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
176s Copyright (C) 2025 The R Foundation for Statistical Computing
176s Platform: x86_64-pc-linux-gnu
176s 
176s R is free software and comes with ABSOLUTELY NO WARRANTY.
176s You are welcome to redistribute it under certain conditions.
176s Type 'license()' or 'licence()' for distribution details.
176s 
176s R is a collaborative project with many contributors.
176s Type 'contributors()' for more information and
176s 'citation()' on how to cite R or R packages in publications.
176s 
176s Type 'demo()' for some demos, 'help()' for on-line help, or
176s 'help.start()' for an HTML browser interface to help.
176s Type 'q()' to quit R.
176s 
176s > library("matrixStats")
176s > 
176s > rowAlls_R <- function(x, value = TRUE, na.rm = FALSE, ..., useNames = TRUE) {
176s +   if (is.na(value)) {
176s +     res <- apply(is.na(x), MARGIN = 1L, FUN = all, na.rm = na.rm)
176s +   } else {
176s +     y <- x == value
176s +     
176s +     # Preserve dimnames attribute
176s +     dim <- dim(x) # for 0xN and Mx0 cases; needed in R (< 3.4.0)
176s +     if (!isTRUE(all.equal(dim(y), dim))) {
176s +       dim(y) <- dim
176s +       dimnames(y) <- dimnames(x)
176s +     }
176s +     
176s +     res <- apply(y, MARGIN = 1L, FUN = all, na.rm = na.rm)
176s +   }
176s +   if (!useNames) names(res) <- NULL
176s +   res
176s + }
176s > 
176s > rowAnys_R <- function(x, value = TRUE, na.rm = FALSE, ..., useNames = TRUE) {
176s +   if (is.na(value)) {
176s +     res <- apply(is.na(x), MARGIN = 1L, FUN = any, na.rm = na.rm)
176s +   } else {
176s +     y <- x == value
176s +     
176s +     # Preserve dimnames attribute
176s +     dim <- dim(x) # for 0xN and Mx0 cases; needed in R (< 3.4.0)
176s +     if (!isTRUE(all.equal(dim(y), dim))) {
176s +       dim(y) <- dim
176s +       dimnames(y) <- dimnames(x)
176s +     }
176s +     
176s +     res <- apply(y, MARGIN = 1L, FUN = any, na.rm = na.rm)
176s +   }
176s +   if (!useNames) names(res) <- NULL
176s +   res
176s + }
176s > 
176s > rowAnyMissings_R <- function(x, ..., useNames = TRUE) {
176s +   res <- apply(x, MARGIN = 1L, FUN = anyMissing)
176s +   if (!useNames) names(res) <- NULL
176s +   res
176s + }
176s > 
176s > 
176s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
176s > # Data type: logical
176s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
176s > x <- matrix(FALSE, nrow = 10L, ncol = 4L)
176s > x[7:8, 2:3] <- TRUE
176s > x[1:3, ] <- TRUE
176s > x[, 1] <- TRUE
176s > x[4, ] <- FALSE
176s > x[, 4] <- FALSE
176s > x[2, ] <- FALSE
176s > x[3, ] <- TRUE
176s > 
176s > # To check names attribute
176s > dimnames <- list(letters[1:10], LETTERS[1:4])
176s > 
176s > for (kk in 1:3) {
176s +   if (kk == 2) {
176s +     x[2, 2] <- NA
176s +   } else if (kk == 3) {
176s +     x[, 2] <- NA
176s +     x[2, ] <- NA
176s +   }
176s + 
176s +   # Test with and without dimnames on x
176s +   for (setDimnames in c(TRUE, FALSE)) {
176s +     dimnames(x) <- if (setDimnames) dimnames else NULL
176s + 
176s +     for (na.rm in c(FALSE, TRUE)) {
176s +       # Check names attribute
176s +       for (useNames in c(TRUE, FALSE)) {
176s +         m0 <- rowAlls_R(x, na.rm = na.rm, useNames = useNames)
176s +         m1 <- rowAlls(x, na.rm = na.rm, useNames = useNames)
176s +         m2 <- colAlls(t(x), na.rm = na.rm, useNames = useNames)
176s +         str(list("all()", m0 = m0, m1 = m1, m2 = m2))
176s +         stopifnot(identical(m1, m0))
176s +         stopifnot(identical(m2, m0))        
176s + 
176s +         m0 <- rowAnys_R(x, na.rm = na.rm, useNames = useNames)
176s +         m1 <- rowAnys(x, na.rm = na.rm, useNames = useNames)
176s +         m2 <- colAnys(t(x), na.rm = na.rm, useNames = useNames)
176s +         str(list("any()", m0 = m0, m1 = m1, m2 = m2))
176s +         stopifnot(identical(m1, m0))
176s +         stopifnot(identical(m2, m0))
176s +         
176s +         m0 <- rowAnyMissings_R(x, useNames = useNames)
176s +         m1 <- rowAnyMissings(x, useNames = useNames)
176s +         m2 <- colAnyMissings(t(x), useNames = useNames)
176s +         str(list("anyMissing()", m0 = m0, m1 = m1, m2 = m2))
176s +         stopifnot(identical(m1, m0))
176s +         stopifnot(identical(m2, m0))
176s +       }
176s +     }
176s +   }
176s + } # for (kk ...)
176s List of 4
176s  $   : chr "all()"
176s  $ m0: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m1: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m2: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s List of 4
176s  $   : chr "any()"
176s  $ m0: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m1: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m2: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s List of 4
176s  $   : chr "anyMissing()"
176s  $ m0: Named logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m1: Named logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m2: Named logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s List of 4
176s  $   : chr "all()"
176s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s List of 4
176s  $   : chr "any()"
176s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s List of 4
176s  $   : chr "anyMissing()"
176s  $ m0: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s  $ m1: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s  $ m2: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s List of 4
176s  $   : chr "all()"
176s  $ m0: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m1: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m2: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s List of 4
176s  $   : chr "any()"
176s  $ m0: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m1: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m2: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s List of 4
176s  $   : chr "anyMissing()"
176s  $ m0: Named logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m1: Named logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m2: Named logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s List of 4
176s  $   : chr "all()"
176s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s List of 4
176s  $   : chr "any()"
176s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s List of 4
176s  $   : chr "anyMissing()"
176s  $ m0: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s  $ m1: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s  $ m2: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s List of 4
176s  $   : chr "all()"
176s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s List of 4
176s  $   : chr "any()"
176s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s List of 4
176s  $   : chr "anyMissing()"
176s  $ m0: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s  $ m1: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s  $ m2: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s List of 4
176s  $   : chr "all()"
176s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s List of 4
176s  $   : chr "any()"
176s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s List of 4
176s  $   : chr "anyMissing()"
176s  $ m0: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s  $ m1: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s  $ m2: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s List of 4
176s  $   : chr "all()"
176s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s List of 4
176s  $   : chr "any()"
176s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s List of 4
176s  $   : chr "anyMissing()"
176s  $ m0: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s  $ m1: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s  $ m2: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s List of 4
176s  $   : chr "all()"
176s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s List of 4
176s  $   : chr "any()"
176s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s List of 4
176s  $   : chr "anyMissing()"
176s  $ m0: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s  $ m1: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s  $ m2: logi [1:10] FALSE FALSE FALSE FALSE FALSE FALSE ...
176s List of 4
176s  $   : chr "all()"
176s  $ m0: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m1: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m2: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s List of 4
176s  $   : chr "any()"
176s  $ m0: Named logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m1: Named logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m2: Named logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s List of 4
176s  $   : chr "anyMissing()"
176s  $ m0: Named logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m1: Named logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m2: Named logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s List of 4
176s  $   : chr "all()"
176s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s List of 4
176s  $   : chr "any()"
176s  $ m0: logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
176s  $ m1: logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
176s  $ m2: logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
176s List of 4
176s  $   : chr "anyMissing()"
176s  $ m0: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
176s  $ m1: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
176s  $ m2: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
176s List of 4
176s  $   : chr "all()"
176s  $ m0: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m1: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m2: Named logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s List of 4
176s  $   : chr "any()"
176s  $ m0: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m1: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m2: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s List of 4
176s  $   : chr "anyMissing()"
176s  $ m0: Named logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m1: Named logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s  $ m2: Named logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
176s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
176s List of 4
176s  $   : chr "all()"
176s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s List of 4
176s  $   : chr "any()"
176s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
176s List of 4
176s  $   : chr "anyMissing()"
176s  $ m0: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
176s  $ m1: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
176s  $ m2: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
176s List of 4
176s  $   : chr "all()"
176s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s List of 4
176s  $   : chr "any()"
176s  $ m0: logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
176s  $ m1: logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
176s  $ m2: logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
176s List of 4
176s  $   : chr "anyMissing()"
176s  $ m0: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
176s  $ m1: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
176s  $ m2: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
176s List of 4
176s  $   : chr "all()"
176s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
176s List of 4
176s  $   : chr "any()"
176s  $ m0: logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
176s  $ m1: logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
176s  $ m2: logi [1:10] TRUE NA TRUE FALSE TRUE TRUE ...
176s List of 4
176s  $   : chr "anyMissing()"
176s  $ m0: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
176s  $ m1: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
176s  $ m2: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
176s List of 4
177s  $   : chr "all()"
177s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
177s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
177s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
177s List of 4
177s  $   : chr "any()"
177s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
177s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
177s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
177s List of 4
177s  $   : chr "anyMissing()"
177s  $ m0: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
177s  $ m1: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
177s  $ m2: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
177s List of 4
177s  $   : chr "all()"
177s  $ m0: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
177s  $ m1: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
177s  $ m2: logi [1:10] FALSE FALSE TRUE FALSE FALSE FALSE ...
177s List of 4
177s  $   : chr "any()"
177s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
177s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
177s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
177s List of 4
177s  $   : chr "anyMissing()"
177s  $ m0: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
177s  $ m1: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
177s  $ m2: logi [1:10] FALSE TRUE FALSE FALSE FALSE FALSE ...
177s List of 4
177s  $   : chr "all()"
177s  $ m0: Named logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
177s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
177s  $ m1: Named logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
177s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
177s  $ m2: Named logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
177s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
177s List of 4
177s  $   : chr "any()"
177s  $ m0: Named logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
177s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
177s  $ m1: Named logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
177s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
177s  $ m2: Named logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
177s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
177s List of 4
177s  $   : chr "anyMissing()"
177s  $ m0: Named logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
177s  $ m1: Named logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
177s  $ m2: Named logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
177s List of 4
177s  $   : chr "all()"
177s  $ m0: logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
177s  $ m1: logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
177s  $ m2: logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
177s List of 4
177s  $   : chr "any()"
177s  $ m0: logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
177s  $ m1: logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
177s  $ m2: logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
177s List of 4
177s  $   : chr "anyMissing()"
177s  $ m0: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s  $ m1: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s  $ m2: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s List of 4
177s  $   : chr "all()"
177s  $ m0: Named logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
177s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
177s  $ m1: Named logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
177s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
177s  $ m2: Named logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
177s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
177s List of 4
177s  $   : chr "any()"
177s  $ m0: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
177s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
177s  $ m1: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
177s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
177s  $ m2: Named logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
177s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
177s List of 4
177s  $   : chr "anyMissing()"
177s  $ m0: Named logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
177s  $ m1: Named logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
177s  $ m2: Named logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s   ..- attr(*, "names")= chr [1:10] "a" "b" "c" "d" ...
177s List of 4
177s  $   : chr "all()"
177s  $ m0: logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
177s  $ m1: logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
177s  $ m2: logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
177s List of 4
177s  $   : chr "any()"
177s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
177s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
177s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
177s List of 4
177s  $   : chr "anyMissing()"
177s  $ m0: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s  $ m1: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s  $ m2: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s List of 4
177s  $   : chr "all()"
177s  $ m0: logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
177s  $ m1: logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
177s  $ m2: logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
177s List of 4
177s  $   : chr "any()"
177s  $ m0: logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
177s  $ m1: logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
177s  $ m2: logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
177s List of 4
177s  $   : chr "anyMissing()"
177s  $ m0: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s  $ m1: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s  $ m2: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s List of 4
177s  $   : chr "all()"
177s  $ m0: logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
177s  $ m1: logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
177s  $ m2: logi [1:10] FALSE NA NA FALSE FALSE FALSE ...
177s List of 4
177s  $   : chr "any()"
177s  $ m0: logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
177s  $ m1: logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
177s  $ m2: logi [1:10] TRUE NA TRUE NA TRUE TRUE ...
177s List of 4
177s  $   : chr "anyMissing()"
177s  $ m0: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s  $ m1: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s  $ m2: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s List of 4
177s  $   : chr "all()"
177s  $ m0: logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
177s  $ m1: logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
177s  $ m2: logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
177s List of 4
177s  $   : chr "any()"
177s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
177s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
177s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
177s List of 4
177s  $   : chr "anyMissing()"
177s  $ m0: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s  $ m1: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s  $ m2: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s List of 4
177s  $   : chr "all()"
177s  $ m0: logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
177s  $ m1: logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
177s  $ m2: logi [1:10] FALSE TRUE TRUE FALSE FALSE FALSE ...
177s List of 4
177s  $   : chr "any()"
177s  $ m0: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
177s  $ m1: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
177s  $ m2: logi [1:10] TRUE FALSE TRUE FALSE TRUE TRUE ...
177s List of 4
177s  $   : chr "anyMissing()"
177s  $ m0: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s  $ m1: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s  $ m2: logi [1:10] TRUE TRUE TRUE TRUE TRUE TRUE ...
177s > 
177s > 
177s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
177s > # Data type: integer
177s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
177s > x <- matrix(rep(1:6, length.out = 4 * 5), nrow = 4L, ncol = 5L)
177s > x[2, ] <- 7L
177s > x[3, 1] <- 7L
177s > x[2:3, 3:4] <- NA_integer_
177s > 
177s > # To check names attribute
177s > dimnames <- list(letters[1:4], LETTERS[1:5])
177s > 
177s > # Row/column counts
177s > value <- 7L
177s > 
177s > # Test with and without dimnames on x
177s > for (setDimnames in c(TRUE, FALSE)) {
177s +   dimnames(x) <- if (setDimnames) dimnames else NULL
177s +   for (na.rm in c(FALSE, TRUE)) {
177s +     # Check names attribute
177s +     for (useNames in c(TRUE, FALSE)) {
177s +       r0 <- rowAlls_R(x, value = value, na.rm = na.rm, useNames = useNames)
177s +       r1 <- rowAlls(x, value = value, na.rm = na.rm, useNames = useNames)
177s +       r2 <- colAlls(t(x), value = value, na.rm = na.rm, useNames = useNames)
177s +       stopifnot(identical(r1, r0))
177s +       stopifnot(identical(r2, r1))
177s +       if (!useNames && !setDimnames) {
177s +         for (rr in seq_len(nrow(x))) {
177s +           c <- allValue(x[rr, ], value = value, na.rm = na.rm)
177s +           stopifnot(identical(c, r1[rr]))
177s +           c <- allValue(x[rr, ], value = value, na.rm = na.rm)
177s +           stopifnot(identical(c, r1[rr]))
177s +         }
177s +       }
177s + 
177s +       r0 <- rowAnys_R(x, value = value, na.rm = na.rm, useNames = useNames)
177s +       r1 <- rowAnys(x, value = value, na.rm = na.rm, useNames = useNames)
177s +       r2 <- colAnys(t(x), value = value, na.rm = na.rm, useNames = useNames)
177s +       stopifnot(identical(r1, r0))
177s +       stopifnot(identical(r2, r1))        
177s +       if (!useNames && !setDimnames) {
177s +         for (rr in seq_len(nrow(x))) {
177s +           c <- anyValue(x[rr, ], value = value, na.rm = na.rm)
177s +           stopifnot(identical(c, r1[rr]))
177s +           c <- anyValue(x[rr, ], value = value, na.rm = na.rm)
177s +           stopifnot(identical(c, r1[rr]))
177s +         }
177s +       }
177s +     }
177s +   }
177s + }
177s > 
177s > 
177s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
177s > # rowAlls(x) et al. on numeric 'x' with logical 'value'
177s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
177s > x <- matrix(0, nrow = 4L, ncol = 5L)
177s > x[2:4, 2] <- (1:3) / 4
177s > x[2, 2:4] <- (1:3) / 4
177s > x[3:4, 3] <- (3:4) / 4
177s > x[3, 3:4] <- (3:4) / 4
177s > x[1:4, 5] <- (1:4) / 5
177s > x[4, 4] <- NA_real_
177s > 
177s > # To check names attribute
177s > dimnames <- list(letters[1:4], LETTERS[1:5])
177s > 
177s > for (value in c(TRUE, FALSE)) {
177s +   for (na.rm in c(FALSE, TRUE)) {
177s +     y0 <- suppressWarnings(apply(x, MARGIN = 1L, FUN = function(e) any(as.logical(e) == value, na.rm = na.rm)))
177s +     y <- rowAnys(x, na.rm = na.rm, value = value)
177s +     stopifnot(identical(y, y0))
177s +     # Check names attribute
177s +     dimnames(x) <- dimnames
177s +     y <- rowAnys(x, na.rm = na.rm, value = value, useNames = FALSE)
177s +     stopifnot(all.equal(y, y0))
177s +     y0 <- suppressWarnings(apply(x, MARGIN = 1L, FUN = function(e) any(as.logical(e) == value, na.rm = na.rm)))
177s +     y <- rowAnys(x, na.rm = na.rm, value = value, useNames = TRUE)
177s +     stopifnot(all.equal(y, y0))
177s +     dimnames(x) <- NULL
177s +   
177s +     y0 <- suppressWarnings(apply(x, MARGIN = 2L, FUN = function(e) any(as.logical(e) == value, na.rm = na.rm)))
177s +     y <- colAnys(x, na.rm = na.rm, value = value)
177s +     stopifnot(identical(y, y0))
177s +     # Check names attribute
177s +     dimnames(x) <- dimnames
177s +     y <- colAnys(x, na.rm = na.rm, value = value, useNames = FALSE)
177s +     stopifnot(all.equal(y, y0))
177s +     y0 <- suppressWarnings(apply(x, MARGIN = 2L, FUN = function(e) any(as.logical(e) == value, na.rm = na.rm)))
177s +     y <- colAnys(x, na.rm = na.rm, value = value, useNames = TRUE)
177s +     stopifnot(all.equal(y, y0))
177s +     dimnames(x) <- NULL
177s +   
177s +     y0 <- suppressWarnings(apply(x, MARGIN = 1L, FUN = function(e) all(as.logical(e) == value, na.rm = na.rm)))
177s +     y <- rowAlls(x, na.rm = na.rm, value = value)
177s +     stopifnot(identical(y, y0))
177s +     # Check names attribute
177s +     dimnames(x) <- dimnames
177s +     y <- rowAlls(x, na.rm = na.rm, value = value, useNames = FALSE)
177s +     stopifnot(all.equal(y, y0))  
177s +     y0 <- suppressWarnings(apply(x, MARGIN = 1L, FUN = function(e) all(as.logical(e) == value, na.rm = na.rm)))
177s +     y <- rowAlls(x, na.rm = na.rm, value = value, useNames = TRUE)
177s +     stopifnot(all.equal(y, y0))    
177s +     dimnames(x) <- NULL
177s +   
177s +     y0 <- suppressWarnings(apply(x, MARGIN = 2L, FUN = function(e) all(as.logical(e) == value, na.rm = na.rm)))
177s +     y <- colAlls(x, na.rm = na.rm, value = value)
177s +     stopifnot(identical(y, y0))
177s +     print(y0)
177s +     # Check names attribute
177s +     dimnames(x) <- dimnames
177s +     y <- colAlls(x, na.rm = na.rm, value = value, useNames = FALSE)
177s +     stopifnot(all.equal(y, y0))     
177s +     y0 <- suppressWarnings(apply(x, MARGIN = 2L, FUN = function(e) all(as.logical(e) == value, na.rm = na.rm)))
177s +     y <- colAlls(x, na.rm = na.rm, value = value, useNames = TRUE)
177s +     stopifnot(all.equal(y, y0))     
177s +     dimnames(x) <- NULL
177s +   } ## for (na.rm ...)
177s + } ## for(value ...)
177s [1] FALSE FALSE FALSE FALSE  TRUE
177s [1] FALSE FALSE FALSE FALSE  TRUE
177s [1]  TRUE FALSE FALSE FALSE FALSE
177s [1]  TRUE FALSE FALSE FALSE FALSE
177s > 
177s > 
177s > 
177s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
177s > # Data type: character (not sure if this should be supported)
177s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
177s > all_R <- function(x, value = TRUE, ...) {
177s +   if (is.na(value)) {
177s +     all(is.na(x), ...)
177s +   } else {
177s +     all(x == value, ...)
177s +   }
177s + }
177s > 
177s > any_R <- function(x, value = TRUE, ...) {
177s +   if (is.na(value)) {
177s +     any(is.na(x), ...)
177s +   } else {
177s +     any(x == value, ...)
177s +   }
177s + }
177s > 
177s > x <- matrix(rep(letters, length.out = 10 * 5), nrow = 10L, ncol = 5L)
177s > x[2, ] <- "g"
177s > x[2:4, 3:4] <- NA_character_
177s > 
177s > # To check names attribute
177s > dimnames <- list(letters[1:10], LETTERS[1:5])
177s > 
177s > # Test with and without dimnames on x
177s > for (setDimnames in c(TRUE, FALSE)) {
177s +   dimnames(x) <- if (setDimnames) dimnames else NULL
177s + 
177s +   # Row/column counts
177s +   for (value in c("g", NA_character_)) {
177s +     for (na.rm in c(FALSE, TRUE)) {
177s +       # Check names attribute
177s +       for (useNames in c(TRUE, FALSE)) {
177s +         r0 <- rowAlls_R(x, value = value, na.rm = na.rm, useNames = useNames)
177s +         r1 <- rowAlls(x, value = value, na.rm = na.rm, useNames = useNames)
177s +         r2 <- colAlls(t(x), value = value, na.rm = na.rm, useNames = useNames)
177s +         stopifnot(identical(r1, r0))
177s +         stopifnot(identical(r2, r1))
177s +         if (!useNames && !setDimnames) {
177s +           for (rr in seq_len(nrow(x))) {
177s +             c0 <- all_R(x[rr, ], value, na.rm = na.rm)
177s +             c <- allValue(x[rr, ], value = value, na.rm = na.rm)
177s +             stopifnot(identical(c, r1[rr]))
177s +             stopifnot(identical(c, c0))
177s +           }
177s +         }
177s +         
177s +         r0 <- rowAnys_R(x, value = value, na.rm = na.rm, useNames = useNames)
177s +         r1 <- rowAnys(x, value = value, na.rm = na.rm, useNames = useNames)
177s +         r2 <- colAnys(t(x), value = value, na.rm = na.rm, useNames = useNames)
177s +         stopifnot(identical(r1, r0))
177s +         stopifnot(identical(r2, r1))        
177s +         if (!useNames && !setDimnames) {
177s +           for (rr in seq_len(nrow(x))) {
177s +             c0 <- any_R(x[rr, ], value, na.rm = na.rm)
177s +             c <- anyValue(x[rr, ], value = value, na.rm = na.rm)
177s +             stopifnot(identical(c, c0))
177s +             stopifnot(identical(c, r1[rr]))
177s +           }
177s +         }
177s +       }
177s +     }
177s +   }
177s + }
177s > 
177s > 
177s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
177s > # NA 0 test
177s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
177s > x <- matrix(0, nrow = 3L, ncol = 3L)
177s > x[1, ] <- c(NA_real_, NA_real_, 0)
177s > x[3, ] <- c(1, 0, 1)
177s > 
177s > dimnames <- list(letters[1:3], LETTERS[1:3])
177s > 
177s > # Test with and without dimnames on x
177s > for (setDimnames in c(TRUE, FALSE)) {
177s +   dimnames(x) <- if (setDimnames) dimnames else NULL
177s +   # Check names attribute
177s +   for (useNames in c(TRUE, FALSE)) {
177s +     r0 <- rowAnys_R(x, value = 0, useNames = useNames)
177s +     r1 <- rowAnys(x, value = 0, useNames = useNames)
177s +     stopifnot(identical(r0, r1))
177s +   }
177s + }
177s > 
177s 
177s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
177s Copyright (C) 2025 The R Foundation for Statistical Computing
177s Platform: x86_64-pc-linux-gnu
177s 
177s R is free software and comes with ABSOLUTELY NO WARRANTY.
177s You are welcome to redistribute it under certain conditions.
177s Type 'license()' or 'licence()' for distribution details.
177s 
177s R is a collaborative project with many contributors.
177s Type 'contributors()' for more information and
177s 'citation()' on how to cite R or R packages in publications.
177s 
177s Type 'demo()' for some demos, 'help()' for on-line help, or
177s 'help.start()' for an HTML browser interface to help.
177s Type 'q()' to quit R.
177s 
177s > library("matrixStats")
177s > 
177s > rowAlls_R <- function(x, value = TRUE, na.rm = FALSE, ..., useNames = TRUE) {
177s +   if (is.na(value)) {
177s +     res <- apply(is.na(x), MARGIN = 1L, FUN = all, na.rm = na.rm)
177s +   } else {
177s +     y <- x == value
177s +     
177s +     # Preserve dimnames attribute
177s +     dim <- dim(x) # for 0xN and Mx0 cases; needed in R (< 3.4.0)
177s +     if (!isTRUE(all.equal(dim(y), dim))) {
177s +       dim(y) <- dim
177s +       dimnames(y) <- dimnames(x)
177s +     }
177s +     
177s +     res <- apply(y, MARGIN = 1L, FUN = all, na.rm = na.rm)
177s +   }
177s +   if (!useNames) names(res) <- NULL
177s +   res
177s + }
177s > 
177s > rowAnys_R <- function(x, value = TRUE, na.rm = FALSE, ..., useNames = TRUE) {
177s +   if (is.na(value)) {
177s +     res <- apply(is.na(x), MARGIN = 1L, FUN = any, na.rm = na.rm)
177s +   } else {
177s +     y <- x == value
177s +     
177s +     # Preserve dimnames attribute
177s +     dim <- dim(x) # for 0xN and Mx0 cases; needed in R (< 3.4.0)
177s +     if (!isTRUE(all.equal(dim(y), dim))) {
177s +       dim(y) <- dim
177s +       dimnames(y) <- dimnames(x)
177s +     }
177s +     
177s +     res <- apply(y, MARGIN = 1L, FUN = any, na.rm = na.rm)
177s +   }
177s +   if (!useNames) names(res) <- NULL
177s +   res
177s + }
177s > 
177s > rowAnyMissings_R <- function(x, ..., useNames = TRUE) {
177s +   res <- apply(x, MARGIN = 1L, FUN = anyMissing)
177s +   if (!useNames) names(res) <- NULL
177s +   res
177s + }
177s > 
177s > 
177s > all_R <- function(x, value = TRUE, ...) {
177s +   if (is.na(value)) {
177s +     all(is.na(x), ...)
177s +   } else {
177s +     all(x == value, ...)
177s +   }
177s + }
177s > 
177s > any_R <- function(x, value = TRUE, ...) {
177s +   if (is.na(value)) {
177s +     any(is.na(x), ...)
177s +   } else {
177s +     any(x == value, ...)
177s +   }
177s + }
177s > 
177s > 
177s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
177s > # Subsetted tests
177s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
177s > source("utils/validateIndicesFramework.R")
177s > x <- matrix(runif(6 * 6, min = -3, max = 3), nrow = 6, ncol = 6)
177s > storage.mode(x) <- "integer"
177s > x[2:3, ] <- NA_integer_
177s > x[2, 1] <- 0L
177s > x[4:5, ] <- 0L
177s > x[4, 6] <- NA_integer_
177s > 
177s > # To check names attribute
177s > dimnames <- list(letters[1:6], LETTERS[1:6])
177s > 
177s > # Test with and without dimnames on x
177s > for (setDimnames in c(TRUE, FALSE)) {
177s +   if (setDimnames) dimnames(x) <- dimnames
177s +   else dimnames(x) <- NULL
177s +   
177s +   count <- 0L
177s +   for (rows in index_cases) {
177s +     for (cols in index_cases) {
177s +       count <- count + 1L
177s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
177s +       useNames <- c(TRUE, FALSE)
177s +       useNames <- useNames[count %% length(useNames) + 1]
177s +       
177s +       validateIndicesTestMatrix(x, rows, cols,
177s +                                 ftest = rowAlls, fsure = rowAlls_R,
177s +                                 value = 0, na.rm = TRUE, useNames = useNames)
177s +       validateIndicesTestMatrix(x, rows, cols,
177s +                                 ftest = rowAlls, fsure = rowAlls_R,
177s +                                 value = 0, na.rm = FALSE, useNames = useNames)
177s +       validateIndicesTestMatrix(x, rows, cols,
177s +                                 ftest = rowAlls, fsure = rowAlls_R,
177s +                                 value = NA_integer_, useNames = useNames)
177s +       validateIndicesTestMatrix(x, rows, cols,
177s +                                 fcoltest = colAlls, fsure = rowAlls_R,
177s +                                 value = 0, na.rm = TRUE, useNames = useNames)
177s +       validateIndicesTestMatrix(x, rows, cols,
177s +                                 fcoltest = colAlls, fsure = rowAlls_R,
177s +                                 value = 0, na.rm = FALSE, useNames = useNames)
177s +       validateIndicesTestMatrix(x, rows, cols,
177s +                                 fcoltest = colAlls, fsure = rowAlls_R,
177s +                                 value = NA_integer_, useNames = useNames)
177s +   
177s +       validateIndicesTestMatrix(x, rows, cols,
177s +                                 ftest = rowAnys, fsure = rowAnys_R,
177s +                                 value = 0, na.rm = TRUE, useNames = useNames)
177s +       validateIndicesTestMatrix(x, rows, cols,
177s +                                 ftest = rowAnys, fsure = rowAnys_R,
177s +                                 value = 0, na.rm = FALSE, useNames = useNames)
177s +       validateIndicesTestMatrix(x, rows, cols,
177s +                                 ftest = rowAnys, fsure = rowAnys_R,
177s +                                 value = NA_integer_, useNames = useNames)
177s +       validateIndicesTestMatrix(x, rows, cols,
177s +                                 fcoltest = colAnys, fsure = rowAnys_R,
177s +                                 value = 0, na.rm = TRUE, useNames = useNames)
177s +       validateIndicesTestMatrix(x, rows, cols,
177s +                                 fcoltest = colAnys, fsure = rowAnys_R,
177s +                                 value = 0, na.rm = FALSE, useNames = useNames)
177s +       validateIndicesTestMatrix(x, rows, cols,
177s +                                 fcoltest = colAnys, fsure = rowAnys_R,
177s +                                 value = NA_integer_, useNames = useNames)
177s +   
177s +       validateIndicesTestMatrix(x, rows, cols,
177s +                                 ftest = rowAnyMissings,
177s +                                 fsure = rowAnyMissings_R, useNames = useNames)
177s +       validateIndicesTestMatrix(x, rows, cols,
177s +                                 fcoltest = colAnyMissings,
177s +                                 fsure = rowAnyMissings_R, useNames = useNames)
177s +     }
177s +   }
177s + }
177s > 
177s > for (rr in seq_len(nrow(x))) {
177s +   for (idxs in index_cases) {
177s +     validateIndicesTestVector(x[rr, ], idxs,
177s +                               ftest = allValue, fsure = all_R,
177s +                               value = 0, na.rm = TRUE)
177s +     validateIndicesTestVector(x[rr, ], idxs,
177s +                               ftest = allValue, fsure = all_R,
177s +                               value = 0, na.rm = FALSE)
177s +     validateIndicesTestVector(x[rr, ], idxs,
177s +                               ftest = allValue, fsure = all_R,
177s +                               value = NA_integer_)
177s + 
177s +     validateIndicesTestVector(x[rr, ], idxs,
177s +                               ftest = anyValue, fsure = any_R,
177s +                               value = 0, na.rm = TRUE)
177s +     validateIndicesTestVector(x[rr, ], idxs,
177s +                               ftest = anyValue, fsure = any_R,
177s +                               value = 0, na.rm = FALSE)
177s +     validateIndicesTestVector(x[rr, ], idxs,
177s +                               ftest = anyValue, fsure = any_R,
177s +                               value = NA_integer_)
177s +   }
177s + }
178s > 
178s > 
178s > storage.mode(x) <- "character"
178s > # Test with and without dimnames on x
178s > for (setDimnames in c(TRUE, FALSE)) {
178s +   if (setDimnames) dimnames(x) <- dimnames
178s +   else dimnames(x) <- NULL
178s +   for (rows in index_cases) {
178s +     for (cols in index_cases) {
178s +       # Check names attribute
178s +       for (useNames in c(TRUE, FALSE)) {
178s +         validateIndicesTestMatrix(x, rows, cols,
178s +                                   ftest = rowAlls, fsure = rowAlls_R,
178s +                                   value = "0", na.rm = TRUE, useNames = useNames)
178s +         validateIndicesTestMatrix(x, rows, cols,
178s +                                   ftest = rowAlls, fsure = rowAlls_R,
178s +                                   value = "0", na.rm = FALSE, useNames = useNames)
178s +         validateIndicesTestMatrix(x, rows, cols,
178s +                                   ftest = rowAlls, fsure = rowAlls_R,
178s +                                   value = NA_character_, useNames = useNames)
178s +         validateIndicesTestMatrix(x, rows, cols,
178s +                                   fcoltest = colAlls, fsure = rowAlls_R,
178s +                                   value = "0", na.rm = TRUE, useNames = useNames)
178s +         validateIndicesTestMatrix(x, rows, cols,
178s +                                   fcoltest = colAlls, fsure = rowAlls_R,
178s +                                   value = "0", na.rm = FALSE, useNames = useNames)
178s +         validateIndicesTestMatrix(x, rows, cols,
178s +                                   fcoltest = colAlls, fsure = rowAlls_R,
178s +                                   value = NA_character_, useNames = useNames)
178s +     
178s +         validateIndicesTestMatrix(x, rows, cols,
178s +                                   ftest = rowAnys, fsure = rowAnys_R,
178s +                                   value = "0", na.rm = TRUE, useNames = useNames)
178s +         validateIndicesTestMatrix(x, rows, cols,
178s +                                   ftest = rowAnys, fsure = rowAnys_R,
178s +                                   value = "0", na.rm = FALSE, useNames = useNames)
178s +         validateIndicesTestMatrix(x, rows, cols,
178s +                                   ftest = rowAnys, fsure = rowAnys_R,
178s +                                   value = NA_character_, useNames = useNames)
178s +         validateIndicesTestMatrix(x, rows, cols,
178s +                                   fcoltest = colAnys, fsure = rowAnys_R,
178s +                                   value = "0", na.rm = TRUE, useNames = useNames)
178s +         validateIndicesTestMatrix(x, rows, cols,
178s +                                   fcoltest = colAnys, fsure = rowAnys_R,
178s +                                   value = "0", na.rm = FALSE, useNames = useNames)
178s +         validateIndicesTestMatrix(x, rows, cols,
178s +                                   fcoltest = colAnys, fsure = rowAnys_R,
178s +                                   value = NA_character_, useNames = useNames)
178s +     
178s +         validateIndicesTestMatrix(x, rows, cols,
178s +                                   ftest = rowAnyMissings,
178s +                                   fsure = rowAnyMissings_R, useNames = useNames)
178s +         validateIndicesTestMatrix(x, rows, cols,
178s +                                   fcoltest = colAnyMissings,
178s +                                   fsure = rowAnyMissings_R, useNames = useNames)        
178s +       }
178s +     }
178s +   }
178s + }
179s > 
179s > for (rr in seq_len(nrow(x))) {
179s +   for (idxs in index_cases) {
179s +     validateIndicesTestVector(x[rr, ], idxs,
179s +                               ftest = allValue, fsure = all_R,
179s +                               value = "0", na.rm = TRUE)
179s +     validateIndicesTestVector(x[rr, ], idxs,
179s +                               ftest = allValue, fsure = all_R,
179s +                               value = "0", na.rm = FALSE)
179s +     validateIndicesTestVector(x[rr, ], idxs,
179s +                               ftest = allValue, fsure = all_R,
179s +                               value = NA_integer_)
179s + 
179s +     validateIndicesTestVector(x[rr, ], idxs,
179s +                               ftest = anyValue, fsure = any_R,
179s +                               value = "0", na.rm = TRUE)
179s +     validateIndicesTestVector(x[rr, ], idxs,
179s +                               ftest = anyValue, fsure = any_R,
179s +                               value = "0", na.rm = FALSE)
179s +     validateIndicesTestVector(x[rr, ], idxs,
179s +                               ftest = anyValue, fsure = any_R,
179s +                               value = NA_integer_)
179s +   }
179s + }
179s > 
179s 
179s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
179s Copyright (C) 2025 The R Foundation for Statistical Computing
179s Platform: x86_64-pc-linux-gnu
179s 
179s R is free software and comes with ABSOLUTELY NO WARRANTY.
179s You are welcome to redistribute it under certain conditions.
179s Type 'license()' or 'licence()' for distribution details.
179s 
179s R is a collaborative project with many contributors.
179s Type 'contributors()' for more information and
179s 'citation()' on how to cite R or R packages in publications.
179s 
179s Type 'demo()' for some demos, 'help()' for on-line help, or
179s 'help.start()' for an HTML browser interface to help.
179s Type 'q()' to quit R.
179s 
179s > library("matrixStats")
179s > 
179s > X <- matrix(rnorm(20 * 6), nrow = 20, ncol = 6)
179s > rownames(X) <- LETTERS[1:nrow(X)]
179s > colnames(X) <- letters[1:ncol(X)]
179s > print(X)
179s             a            b           c          d            e           f
179s A  1.94584219 -1.603263553 -0.47979506 -0.7857903 -1.533983897 -0.93402043
179s B  0.70371354 -1.427618969 -1.04834507  0.2982445 -0.634595990 -0.14915733
179s C  1.35379266 -0.071805725  1.72135876 -1.3222530 -0.204011435 -0.24725248
179s D -1.62345950  0.083092047  0.33365884 -1.1718180  0.996811550  0.07601603
179s E  0.71973880 -0.788777707 -0.81815514  0.1652880 -1.120576833  1.34501152
179s F -2.16926799 -0.658771575  0.66657093  0.2746164  0.980405290  0.05342237
179s G  0.33952349  0.688110667 -0.17095846  0.1562647  0.632853395  1.69089988
179s H -1.17006069  1.323064011  0.60501914 -0.1720869 -1.408427388 -0.24538536
179s I  0.82384135 -0.320121268 -0.34840534  0.3885500  0.896246225  1.75460287
179s J -0.28124988  0.091220776 -0.47243215  0.7959029  0.003845496  0.30551558
179s K  0.01365748 -1.212228712 -1.73389374 -1.1119543  1.291546194  0.71617370
179s L -0.75271535  1.167948850  1.02773463  0.1261911 -0.715329612  1.18077428
179s M -0.81571773  0.494045857  0.38001746 -0.1460559 -0.477668518  0.06176001
179s N -1.07405293 -1.158730906 -0.04506403 -1.4658833 -0.160116717 -2.63949344
179s O -0.45323462  0.054818027  0.46290093  0.2924028 -1.243104812 -1.47923557
179s P  0.88250577 -0.247671235  0.32019341 -1.7806172  0.334743963  0.41319157
179s Q  0.28673726  0.044767011 -1.06995236  0.6408858 -2.531381088  0.34480331
179s R  0.26732366  1.303772498  1.15976451 -0.8895742  0.437345510  0.86987340
179s S -1.68909109 -1.566845836  0.60388267  1.7785579  0.326685509 -0.20401089
179s T -0.16832667 -0.009105228  0.96529033 -0.9077198 -0.365388512  1.91621014
179s > 
179s > 
179s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
179s > # Apply rowMeans() for 3 sets of 2 columns
179s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
179s > nbr_of_sets <- 3L
179s > S <- matrix(1:ncol(X), ncol = nbr_of_sets)
179s > colnames(S) <- sprintf("s%d", 1:nbr_of_sets)
179s > print(S)
179s      s1 s2 s3
179s [1,]  1  3  5
179s [2,]  2  4  6
179s > 
179s > Z <- rowAvgsPerColSet(X, S = S)
179s > print(Z)
179s            s1          s2          s3
179s A  0.17128932 -0.63279267 -1.23400216
179s B -0.36195271 -0.37505030 -0.39187666
179s C  0.64099347  0.19955288 -0.22563196
179s D -0.77018373 -0.41907960  0.53641379
179s E -0.03451945 -0.32643356  0.11221734
179s F -1.41401978  0.47059365  0.51691383
179s G  0.51381708 -0.00734686  1.16187664
179s H  0.07650166  0.21646610 -0.82690638
179s I  0.25186004  0.02007235  1.32542455
179s J -0.09501455  0.16173536  0.15468054
179s K -0.59928562 -1.42292402  1.00385995
179s L  0.20761675  0.57696288  0.23272233
179s M -0.16083594  0.11698078 -0.20795425
179s N -1.11639192 -0.75547366 -1.39980508
179s O -0.19920830  0.37765185 -1.36117019
179s P  0.31741727 -0.73021188  0.37396776
179s Q  0.16575213 -0.21453328 -1.09328889
179s R  0.78554808  0.13509517  0.65360946
179s S -1.62796847  1.19122028  0.06133731
179s T -0.08871595  0.02878527  0.77541081
179s > 
179s > # Validation
179s > Z0 <- cbind(s1 = rowMeans(X[, 1:2]), s2 = rowMeans(X[, 3:4]),
179s +             s3 = rowMeans(X[, 5:6]))
179s > stopifnot(identical(drop(Z), Z0))
179s > 
179s > 
179s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
179s > # Apply colMeans() for 5 sets of 4 rows
179s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
179s > nbr_of_sets <- 5L
179s > S <- matrix(1:nrow(X), ncol = nbr_of_sets)
179s > colnames(S) <- sprintf("s%d", 1:nbr_of_sets)
179s > print(S)
179s      s1 s2 s3 s4 s5
179s [1,]  1  5  9 13 17
179s [2,]  2  6 10 14 18
179s [3,]  3  7 11 15 19
179s [4,]  4  8 12 16 20
179s > 
179s > Z <- colAvgsPerRowSet(X, S = S)
179s > print(Z)
179s             a           b           c           d          e          f
179s s1  0.5949722 -0.75489905  0.13171937 -0.74540421 -0.3439449 -0.3136036
179s s2 -0.5700166  0.14090635  0.07061912  0.10602055 -0.2289364  0.7109871
179s s3 -0.0491166 -0.06829509 -0.38174915  0.04967244  0.3690771  0.9892666
179s s4 -0.3651249 -0.21438456  0.27951194 -0.77503840 -0.3865365 -0.9109444
179s s5 -0.3258392 -0.05685289  0.41474629  0.15553743 -0.5331846  0.7317190
179s > 
179s > # Validation
179s > Z0 <- rbind(s1 = colMeans(X[1:4, ]), s2 = colMeans(X[5:8, ]),
179s +             s3 = colMeans(X[9:12, ]), s4 = colMeans(X[13:16, ]),
179s +             s5 = colMeans(X[17:20, ]))
179s > stopifnot(identical(drop(Z), Z0))
179s > 
179s > 
179s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
179s > # When there is only one "complete" set
179s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
179s > nbr_of_sets <- 1L
179s > S <- matrix(1:ncol(X), ncol = nbr_of_sets)
179s > colnames(S) <- sprintf("s%d", 1:nbr_of_sets)
179s > print(S)
179s      s1
179s [1,]  1
179s [2,]  2
179s [3,]  3
179s [4,]  4
179s [5,]  5
179s [6,]  6
179s > 
179s > Z <- rowAvgsPerColSet(X, S = S, FUN = rowMeans)
179s > print(Z)
179s            s1
179s A -0.56516851
179s B -0.37629322
179s C  0.20497146
179s D -0.21761651
179s E -0.08291189
179s F -0.14217077
179s G  0.55611562
179s H -0.17797954
179s I  0.53245231
179s J  0.07380045
179s K -0.33944990
179s L  0.33910066
179s M -0.08393647
179s N -1.09055689
179s O -0.39424221
179s P -0.01294228
179s Q -0.38069001
179s R  0.52475090
179s S -0.12513696
179s T  0.23849338
179s > 
179s > Z0 <- rowMeans(X)
179s > stopifnot(identical(drop(Z), Z0))
179s > 
179s > 
179s > nbr_of_sets <- 1L
179s > S <- matrix(1:nrow(X), ncol = nbr_of_sets)
179s > colnames(S) <- sprintf("s%d", 1:nbr_of_sets)
179s > print(S)
179s       s1
179s  [1,]  1
179s  [2,]  2
179s  [3,]  3
179s  [4,]  4
179s  [5,]  5
179s  [6,]  6
179s  [7,]  7
179s  [8,]  8
179s  [9,]  9
179s [10,] 10
179s [11,] 11
179s [12,] 12
179s [13,] 13
179s [14,] 14
179s [15,] 15
179s [16,] 16
179s [17,] 17
179s [18,] 18
179s [19,] 19
179s [20,] 20
179s > 
179s > Z <- colAvgsPerRowSet(X, S = S, FUN = colMeans)
179s > print(Z)
179s            a         b         c          d          e        f
179s s1 -0.143025 -0.190705 0.1029695 -0.2418424 -0.2247051 0.241485
179s > 
179s > Z0 <- colMeans(X)
179s > stopifnot(identical(drop(Z), Z0))
179s > 
179s > 
179s > 
179s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
179s > # Use weights
179s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
179s > nbr_of_sets <- 3L
179s > S <- matrix(1:ncol(X), ncol = nbr_of_sets)
179s > colnames(S) <- sprintf("s%d", 1:nbr_of_sets)
179s > print(S)
179s      s1 s2 s3
179s [1,]  1  3  5
179s [2,]  2  4  6
179s > 
179s > W <- matrix(runif(length(X)), nrow = nrow(X), ncol = ncol(X))
179s > Z1 <- rowAvgsPerColSet(X, W = W, S = S, FUN = rowWeightedMeans)
179s > print(Z1)
179s            s1          s2          s3
179s A  0.17128932 -0.63279267 -1.23400216
179s B -0.36195271 -0.37505030 -0.39187666
179s C  0.64099347  0.19955288 -0.22563196
179s D -0.77018373 -0.41907960  0.53641379
179s E -0.03451945 -0.32643356  0.11221734
179s F -1.41401978  0.47059365  0.51691383
179s G  0.51381708 -0.00734686  1.16187664
179s H  0.07650166  0.21646610 -0.82690638
179s I  0.25186004  0.02007235  1.32542455
179s J -0.09501455  0.16173536  0.15468054
179s K -0.59928562 -1.42292402  1.00385995
179s L  0.20761675  0.57696288  0.23272233
179s M -0.16083594  0.11698078 -0.20795425
179s N -1.11639192 -0.75547366 -1.39980508
179s O -0.19920830  0.37765185 -1.36117019
179s P  0.31741727 -0.73021188  0.37396776
179s Q  0.16575213 -0.21453328 -1.09328889
179s R  0.78554808  0.13509517  0.65360946
179s S -1.62796847  1.19122028  0.06133731
179s T -0.08871595  0.02878527  0.77541081
179s > Z2 <- colAvgsPerRowSet(X, W = W, S = S, FUN = colWeightedMeans)
179s > print(Z2)
179s             a            b           c          d           e           f
179s s1  1.3247779 -1.515441261 -0.76407006 -0.2437729 -1.08428994 -0.54158888
179s s2 -0.1348334  0.005643161  1.02750880 -1.2470355  0.39640006 -0.08561823
179s s3 -0.7247646 -0.723774641 -0.07579211  0.2199522 -0.07008577  0.69921695
179s > 
179s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
179s > # Result should always be a matrix, including when nrow(X) <= 1
179s > # (https://github.com/HenrikBengtsson/matrixStats/issues/108)
179s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
179s > X <- matrix(1:3, nrow = 1L, ncol = 3L)
179s > S <- matrix(1, nrow = 1L, ncol = 1L)
179s > Z1 <- rowAvgsPerColSet(X, S = S)
179s > stopifnot(is.matrix(Z1))
179s > Z2 <- rowAvgsPerColSet(X, S = S, rows = 0)
179s > stopifnot(is.matrix(Z2))
179s > 
179s > 
179s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
179s > # Works with many, one or zero columns / rows
179s > # (https://github.com/HenrikBengtsson/matrixStats/issues/172)
179s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
179s > S <- cbind(1:2, 3:4, 5:6)
179s > X <- matrix(rnorm(2 * 6), nrow = 6, ncol = 2)
179s > Z2 <- colAvgsPerRowSet(X, S = S, FUN = colSums2)
179s > Z2_ref <- rbind(colSums2(X[S[,1], ,drop=FALSE]),
179s +                 colSums2(X[S[,2], ,drop=FALSE]),
179s +                 colSums2(X[S[,3], ,drop=FALSE]))
179s > stopifnot(identical(Z2, Z2_ref))
179s > X <- matrix(rnorm(6), nrow = 6, ncol = 1)
179s > Z1 <- colAvgsPerRowSet(X, S = S, FUN = colSums2)
179s > Z1_ref <- rbind(colSums2(X[S[,1], ,drop=FALSE]),
179s +                 colSums2(X[S[,2], ,drop=FALSE]),
179s +                 colSums2(X[S[,3], ,drop=FALSE]))
179s > stopifnot(identical(Z1, Z1_ref))
179s > X <- matrix(numeric(0), nrow = 6, ncol = 0)
179s > Z0 <- colAvgsPerRowSet(X, S = S, FUN = colSums2)
179s > Z0_ref <- matrix(numeric(0), nrow = ncol(S), ncol = 0)
179s > stopifnot(identical(Z0, unname(Z0_ref)))
179s > 
179s > 
179s > S <- rbind(1:4, 5:8)
179s > X <- matrix(rnorm(n = 2 * 8), nrow = 2, ncol = 8)
179s > Z2 <- rowAvgsPerColSet(X, S = S, FUN = rowMeans2)
179s > Z2_ref <- cbind(rowMeans2(X[,S[,1],drop=FALSE]),
179s +                 rowMeans2(X[,S[,2],drop=FALSE]),
179s +                 rowMeans2(X[,S[,3],drop=FALSE]),
179s +                 rowMeans2(X[,S[,4],drop=FALSE]))
179s > stopifnot(identical(Z2, Z2_ref))
179s > X <- matrix(rnorm(n = 8), nrow = 1, ncol = 8)
179s > Z1 <- rowAvgsPerColSet(X, S = S, FUN = rowMeans2)
179s > Z1_ref <- cbind(rowMeans2(X[,S[,1],drop=FALSE]),
179s +                 rowMeans2(X[,S[,2],drop=FALSE]),
179s +                 rowMeans2(X[,S[,3],drop=FALSE]),
179s +                 rowMeans2(X[,S[,4],drop=FALSE]))
179s > stopifnot(identical(Z1, Z1_ref))
179s > X <- matrix(numeric(0), nrow = 0, ncol = 8)
179s > Z0 <- rowAvgsPerColSet(X, S = S, FUN = rowMeans2)
179s > Z0_ref <- matrix(numeric(0), nrow = 0, ncol = ncol(S))
179s > stopifnot(identical(Z0, Z0_ref))
179s > 
179s 
179s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
179s Copyright (C) 2025 The R Foundation for Statistical Computing
179s Platform: x86_64-pc-linux-gnu
179s 
179s R is free software and comes with ABSOLUTELY NO WARRANTY.
179s You are welcome to redistribute it under certain conditions.
179s Type 'license()' or 'licence()' for distribution details.
179s 
179s R is a collaborative project with many contributors.
179s Type 'contributors()' for more information and
179s 'citation()' on how to cite R or R packages in publications.
179s 
179s Type 'demo()' for some demos, 'help()' for on-line help, or
179s 'help.start()' for an HTML browser interface to help.
179s Type 'q()' to quit R.
179s 
179s > library("matrixStats")
179s > 
179s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
179s > # Subsetted tests
179s > # - - - - - - - - - - - - - - - - - - - - - - - - - -
179s > source("utils/validateIndicesFramework.R")
179s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
179s > #W <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
179s > for (rows in index_cases) {
179s +   for (cols in index_cases) {
179s +     if (is.null(rows)) {
179s +       rows <- seq_len(nrow(x))
179s +       rows_finite <- rows
179s +     } else {
179s +       rows_finite <- rows[is.finite(rows)]
179s +     }
179s + 
179s +     if (is.null(cols)) {
179s +       cols <- seq_len(ncol(x))
179s +       cols_finite <- cols
179s +     } else {
179s +       cols_finite <- cols[is.finite(cols)]
179s +     }
179s + 
179s +     suppressWarnings({
179s +       actual <- tryCatch({
179s +         rowAvgsPerColSet(x, rows = rows, S = matrix(cols, ncol = 1),
179s +                          FUN = rowMeans)
179s +       }, error = function(c) "error")
179s +       expect <- tryCatch({
179s +         rowMeans(x[rows, cols_finite, drop = FALSE], na.rm = TRUE)
179s +       }, error = function(c) "error")
179s +     })
179s +     stopifnot(all.equal(as.vector(actual), expect))
179s + 
179s +     suppressWarnings({
179s +       actual <- tryCatch({
179s +         colAvgsPerRowSet(x, cols = cols, S = matrix(rows, ncol = 1),
179s +                          FUN = colMeans)
179s +       }, error = function(c) "error")
179s +       expect <- tryCatch({
179s +         colMeans(x[rows_finite, cols, drop = FALSE], na.rm = TRUE)
179s +       }, error = function(c) "error")
179s +     })
179s +     stopifnot(all.equal(as.vector(actual), expect))
179s +   }
179s + }
179s > 
179s 
179s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
179s Copyright (C) 2025 The R Foundation for Statistical Computing
179s Platform: x86_64-pc-linux-gnu
179s 
179s R is free software and comes with ABSOLUTELY NO WARRANTY.
179s You are welcome to redistribute it under certain conditions.
179s Type 'license()' or 'licence()' for distribution details.
179s 
179s R is a collaborative project with many contributors.
179s Type 'contributors()' for more information and
179s 'citation()' on how to cite R or R packages in publications.
179s 
179s Type 'demo()' for some demos, 'help()' for on-line help, or
179s 'help.start()' for an HTML browser interface to help.
179s Type 'q()' to quit R.
179s 
179s > library("matrixStats")
179s > 
179s > x <- matrix(1:27, ncol = 3)
179s > 
179s > # To check names attribute
179s > dimnames <- list(letters[1:9], LETTERS[1:3])
179s > 
179s > rowCollapse_R <- function(x, idxs, ..., useNames = TRUE) {
179s +   res <- x[, idxs]
179s +   # Preserve names attribute?
179s +   if (!useNames) names(res) <- NULL
179s +   res
179s + }
179s > 
179s > idxs <- 1L
179s > # Test with and without dimnames on x
179s > for (setDimnames in c(TRUE, FALSE)) {
179s +   if (setDimnames) dimnames(x) <- dimnames
179s +   else dimnames(x) <- NULL
179s +   # Check names attribute
179s +   for (useNames in c(TRUE, FALSE)) {
179s +     y_truth <- rowCollapse_R(x, idxs, useNames = useNames)
179s +     y <- rowCollapse(x, idxs, useNames = useNames)
179s +     stopifnot(identical(y, y_truth))
179s +     y2 <- colCollapse(t(x), idxs, useNames = useNames)
179s +     stopifnot(identical(y2, y))
179s +   }
179s + }
179s > 
179s > idxs <- 2L
179s > # Test with and without dimnames on x
179s > for (setDimnames in c(TRUE, FALSE)) {
179s +   if (setDimnames) dimnames(x) <- dimnames
179s +   else dimnames(x) <- NULL
179s +   # Check names attribute
179s +   for (useNames in c(TRUE, FALSE)) {
179s +     y_truth <- rowCollapse_R(x, idxs, useNames = useNames)
179s +     y <- rowCollapse(x, idxs, useNames = useNames)
179s +     stopifnot(identical(y, y_truth))
179s +     y2 <- colCollapse(t(x), idxs, useNames = useNames)
179s +     stopifnot(identical(y2, y))
179s +   }
179s + }
179s > 
179s > 
179s > rowCollapse_R <- function(x, idxs, ..., useNames = TRUE) {
179s +   res <- c(x[1:5, 1], x[6:9, 3])
179s +   # Preserve names attribute?
179s +   if (!useNames) names(res) <- NULL
179s +   res
179s + }
179s > 
179s > idxs <- c(1, 1, 1, 1, 1, 3, 3, 3, 3)
179s > # Test with and without dimnames on x
179s > for (setDimnames in c(TRUE, FALSE)) {
179s +   if (setDimnames) dimnames(x) <- dimnames
179s +   else dimnames(x) <- NULL
179s +   # Check names attribute
179s +   for (useNames in c(TRUE, FALSE)) {
179s +     y_truth <- rowCollapse_R(x, idxs, useNames = useNames)
179s +     y <- rowCollapse(x, idxs, useNames = useNames)
179s +     stopifnot(identical(y, y_truth))
179s +     y2 <- colCollapse(t(x), idxs, useNames = useNames)
179s +     stopifnot(identical(y2, y))
179s +   }
179s + }
179s > 
179s > 
179s > rowCollapse_R <- function(x, idxs, ..., useNames = TRUE) {
179s +   res <- c(x[1, 1], x[2, 2], x[3, 3], x[4, 1], x[5, 2],
179s +            x[6, 3], x[7, 1], x[8, 2], x[9, 3])
179s +   # Preserve names attribute?
179s +   if (useNames) {
179s +     names <- rownames(x)
179s +     if (!is.null(names)) names(res) <- names
179s +   }
179s +   res
179s + }
179s > 
179s > idxs <- 1:3
179s > # Test with and without dimnames on x
179s > for (setDimnames in c(TRUE, FALSE)) {
179s +   if (setDimnames) dimnames(x) <- dimnames
179s +   else dimnames(x) <- NULL
179s +   # Check names attribute
179s +   for (useNames in c(TRUE, FALSE)) {
179s +     y_truth <- rowCollapse_R(x, idxs, useNames = useNames)
179s +     y <- rowCollapse(x, idxs, useNames = useNames)
179s +     stopifnot(identical(y, y_truth))
179s +     y2 <- colCollapse(t(x), idxs, useNames = useNames)
179s +     stopifnot(identical(y2, y))
179s +   }
179s + }
180s > 
180s 
180s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
180s Copyright (C) 2025 The R Foundation for Statistical Computing
180s Platform: x86_64-pc-linux-gnu
180s 
180s R is free software and comes with ABSOLUTELY NO WARRANTY.
180s You are welcome to redistribute it under certain conditions.
180s Type 'license()' or 'licence()' for distribution details.
180s 
180s R is a collaborative project with many contributors.
180s Type 'contributors()' for more information and
180s 'citation()' on how to cite R or R packages in publications.
180s 
180s Type 'demo()' for some demos, 'help()' for on-line help, or
180s 'help.start()' for an HTML browser interface to help.
180s Type 'q()' to quit R.
180s 
180s > library("matrixStats")
180s > 
180s > rowCollapse_R <- function(x, idxs, ..., useNames = TRUE) {
180s +   ans <- c()
180s +   storage.mode(ans) <- storage.mode(x)
180s +   for (ii in seq_len(length(idxs))) {
180s +     ans[ii] <- x[ii, idxs[ii]]
180s +   }
180s +   
180s +   # Preserve names attribute
180s +   if (useNames) {
180s +     names <- rownames(x)
180s +     if (!is.null(names)) names(ans) <- names
180s +   }
180s + 
180s +   ans
180s + }
180s > 
180s > 
180s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
180s > # Subsetted tests
180s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
180s > source("utils/validateIndicesFramework.R")
180s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
180s > storage.mode(x) <- "integer"
180s > 
180s > # To check names attribute
180s > dimnames <- list(letters[1:6], LETTERS[1:6])
180s > 
180s > for (rows in index_cases) {
180s +   if (is.null(rows)) rows <- seq_len(nrow(x))
180s + 
180s +   for (idxs in list(2L, seq_len(6L))) {
180s +     for (useNames in c(TRUE, FALSE)) {
180s +       suppressWarnings({
180s +         actual <- tryCatch(rowCollapse(x, idxs, rows = rows, useNames = useNames),
180s +                            error = function(c) "error")
180s +         expect <- tryCatch({
180s +           idxs_0 <- rep(idxs, length.out = nrow(x))[rows]
180s +           rowCollapse_R(x[rows, , drop = FALSE], idxs_0, useNames = useNames)
180s +         }, error = function(c) "error")
180s +       })
180s +       stopifnot(all.equal(actual, expect))
180s +     
180s +       suppressWarnings({
180s +         actual <- tryCatch(colCollapse(t(x), idxs, cols = rows, useNames = useNames),
180s +                            error = function(c) "error")
180s +       })
180s +       stopifnot(all.equal(actual, expect))
180s +       
180s +       # Check names attribute
180s +       dimnames(x) <- dimnames
180s +       suppressWarnings({
180s +         actual <- tryCatch(rowCollapse(x, idxs, rows = rows, useNames = useNames),
180s +                            error = function(c) "error")
180s +         expect <- tryCatch({
180s +           idxs_0 <- rep(idxs, length.out = nrow(x))[rows]
180s +           rowCollapse_R(x[rows, , drop = FALSE], idxs_0, useNames = useNames)
180s +         }, error = function(c) "error")
180s +       })
180s +       stopifnot(all.equal(actual, expect))
180s +       
180s +       suppressWarnings({
180s +         actual <- tryCatch(colCollapse(t(x), idxs, cols = rows, useNames = useNames),
180s +                            error = function(c) "error")
180s +       })
180s +       stopifnot(all.equal(actual, expect))
180s +       
180s +       dimnames(x) <- NULL
180s +     }
180s +   }
180s + }
180s > 
180s 
180s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
180s Copyright (C) 2025 The R Foundation for Statistical Computing
180s Platform: x86_64-pc-linux-gnu
180s 
180s R is free software and comes with ABSOLUTELY NO WARRANTY.
180s You are welcome to redistribute it under certain conditions.
180s Type 'license()' or 'licence()' for distribution details.
180s 
180s R is a collaborative project with many contributors.
180s Type 'contributors()' for more information and
180s 'citation()' on how to cite R or R packages in publications.
180s 
180s Type 'demo()' for some demos, 'help()' for on-line help, or
180s 'help.start()' for an HTML browser interface to help.
180s Type 'q()' to quit R.
180s 
180s > library("matrixStats")
180s > 
180s > rowCounts_R <- function(x, value = TRUE, na.rm = FALSE, ...) {
180s +   if (is.na(value)) {
180s +     counts <- apply(x, MARGIN = 1L, FUN = function(x)
180s +       sum(is.na(x))
180s +     )
180s +   } else {
180s +     counts <- apply(x, MARGIN = 1L, FUN = function(x)
180s +       sum(x == value, na.rm = na.rm)
180s +     )
180s +   }
180s +   # Preserve names attribute
180s +   names <- names(counts)  
180s +   counts <- as.integer(counts)
180s +   if (useNames && !is.null(names)) names(counts) <- names
180s +   counts
180s + }
180s > 
180s > 
180s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
180s > # Data type: integer and numeric
180s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
180s > for (mode in c("integer", "double")) {
180s +   x <- matrix(runif(10 * 5, min = -3, max = 3), nrow = 10L, ncol = 5L)
180s +   x[sample.int(length(x), size = 7L)] <- 0
180s +   storage.mode(x) <- mode
180s +   
180s +   dimnames = list(letters[1:10], LETTERS[1:5])
180s +   
180s +   # Test with and without dimnames on x
180s +   for (setDimnames in c(TRUE, FALSE)) {
180s +     if (setDimnames) dimnames(x) <- dimnames
180s +     else dimnames(x) <- NULL    
180s +     for (na.rm in c(FALSE, TRUE)) {
180s +       # Check names attribute
180s +       for (useNames in c(TRUE, FALSE)) {
180s +         # Count zeros
180s +         r0 <- rowCounts_R(x, value = 0, na.rm = na.rm, useNames = useNames)
180s +         r1 <- rowCounts(x, value = 0, na.rm = na.rm, useNames = useNames)
180s +         r2 <- colCounts(t(x), value = 0, na.rm = na.rm, useNames = useNames)
180s +         stopifnot(identical(r1, r0))
180s +         stopifnot(identical(r2, r0))
180s +         
180s +         # Count NAs
180s +         r0 <- rowCounts_R(x, value = NA, na.rm = na.rm, useNames = useNames)
180s +         r1 <- rowCounts(x, value = NA, na.rm = na.rm, useNames = useNames)
180s +         r2 <- colCounts(t(x), value = NA, na.rm = na.rm, useNames = useNames)
180s +         stopifnot(identical(r1, r0))
180s +         stopifnot(identical(r2, r0))
180s +         
180s +         if (mode == "integer") {
180s +           ux <- unique(as.vector(x))
180s +           r0 <- r1 <- r2 <- integer(nrow(x))
180s +           for (value in ux) {
180s +             r0 <- r0 + rowCounts_R(x, value = value, na.rm = na.rm, useNames = useNames)
180s +             r1 <- r1 + rowCounts(x, value = value, na.rm = na.rm, useNames = useNames)
180s +             r2 <- r2 + colCounts(t(x), value = value, na.rm = na.rm, useNames = useNames)
180s +             stopifnot(identical(r1, r0))
180s +             stopifnot(identical(r2, r0))
180s +           }
180s +           stopifnot(all(r0 == ncol(x)))
180s +         } # if (mode == "integer")
180s +       } # for (useNames ...)
180s +     } # for (na.rm ...)
180s +   } # for (setDimnames ...)
180s + } # for (mode ...)
180s > 
180s > 
180s > # All NAs
180s > na_list <- list(NA_integer_, NA_real_, NaN)
180s > for (na_value in na_list) {
180s +   x <- matrix(na_value, nrow = 10L, ncol = 5L)
180s +   # Test with and without dimnames on x
180s +   for (setDimnames in c(TRUE, FALSE)) {
180s +     if (setDimnames) dimnames(x) <- dimnames
180s +     else dimnames(x) <- NULL    
180s +     for (na.rm in c(FALSE, TRUE)) {
180s +       # Check names attribute
180s +       for (useNames in c(TRUE, FALSE)) {
180s +         r0 <- rowCounts_R(x, na.rm = na.rm, useNames = useNames)
180s +         r1 <- rowCounts(x, na.rm = na.rm, useNames = useNames)
180s +         r2 <- colCounts(t(x), na.rm = na.rm, useNames = useNames)
180s +         stopifnot(identical(r1, r0))
180s +         stopifnot(identical(r2, r0))
180s +         
180s +         # Count NAs
180s +         r0 <- rowCounts_R(x, value = NA, na.rm = na.rm, useNames = useNames)
180s +         r1 <- rowCounts(x, value = NA, na.rm = na.rm, useNames = useNames)
180s +         r2 <- colCounts(t(x), value = NA, na.rm = na.rm, useNames = useNames)
180s +         stopifnot(all(r0 == ncol(x)))
180s +         stopifnot(identical(r1, r0))
180s +         stopifnot(identical(r2, r0))
180s +       }
180s +     }
180s +   }
180s + } # for (na_value ...)
180s > 
180s > 
180s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
180s > # Data type: logical
180s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
180s > x <- matrix(FALSE, nrow = 10L, ncol = 4L)
180s > x[7:8, 2:3] <- TRUE
180s > x[1:3, ] <- TRUE
180s > x[, 1] <- TRUE
180s > x[4, ] <- FALSE
180s > x[, 4] <- FALSE
180s > x[2, ] <- FALSE
180s > x[3, ] <- TRUE
180s > 
180s > # To check names attribute
180s > dimnames <- list(letters[1:10], LETTERS[1:4])
180s > 
180s > # Test with and without dimnames on x
180s > for (setDimnames in c(TRUE, FALSE)) {
180s +   if (setDimnames) dimnames(x) <- dimnames
180s +   else dimnames(x) <- NULL
180s +   # Row/column counts
180s +   for (na.rm in c(FALSE, TRUE)) {
180s +     # Check names attribute
180s +     for (useNames in c(TRUE, FALSE)) {
180s +       r0 <- rowCounts_R(x, na.rm = na.rm, useNames = useNames)
180s +       r1 <- rowCounts(x, na.rm = na.rm, useNames = useNames)
180s +       r2 <- colCounts(t(x), na.rm = na.rm, useNames = useNames)
180s +       stopifnot(identical(r1, r0))
180s +       stopifnot(identical(r2, r0))
180s +       
180s +       r_true <- rowCounts(x, value = TRUE, na.rm = na.rm, useNames = useNames)
180s +       r_false <- rowCounts(x, value = FALSE, na.rm = na.rm, useNames = useNames)
180s +       stopifnot(r_true + r_false == ncol(x))
180s +       
180s +       c_true <- colCounts(x, value = TRUE, na.rm = na.rm, useNames = useNames)
180s +       c_false <- colCounts(x, value = FALSE, na.rm = na.rm, useNames = useNames)
180s +       stopifnot(c_true + c_false == nrow(x))
180s +       
180s +       # Count NAs
180s +       r0 <- rowCounts_R(x, value = NA, na.rm = na.rm, useNames = useNames)
180s +       r1 <- rowCounts(x, value = NA, na.rm = na.rm, useNames = useNames)
180s +       r2 <- colCounts(t(x), value = NA, na.rm = na.rm, useNames = useNames)
180s +       stopifnot(identical(r1, r0))
180s +       stopifnot(identical(r2, r0))
180s +     }
180s +   }
180s + }
180s > 
180s > 
180s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
180s > # Data type: character (not sure if this should be supported)
180s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
180s > x <- matrix(rep(letters, length.out = 10 * 5), nrow = 10L, ncol = 5L)
180s > x[2:3, 3:4] <- NA_character_
180s > 
180s > # Row/column counts
180s > for (na.rm in c(FALSE, TRUE)) {
180s +   for (value in c("g", NA_character_)) {
180s +     r0 <- rowCounts_R(x, value = value, na.rm = na.rm)
180s +     r1 <- rowCounts(x, value = value, na.rm = na.rm)
180s +     r2 <- colCounts(t(x), value = value, na.rm = na.rm)
180s +     stopifnot(identical(r1, r0))
180s +     stopifnot(identical(r2, r0))
180s + 
180s +     c <- count(x[1, ], value = value, na.rm = na.rm)
180s +     stopifnot(identical(c, r1[1]))
180s + 
180s +     c <- count(x[2, ], value = value, na.rm = na.rm)
180s +     stopifnot(identical(c, r1[2]))
180s +   }
180s + }
180s > 
180s > # NA row
180s > x <- matrix(0, nrow = 2L, ncol = 2L)
180s > x[1, ] <- NA_integer_
180s > 
180s > dimnames <- list(letters[1:2], LETTERS[1:2])
180s > 
180s > # Test with and without dimnames on x
180s > for (setDimnames in c(TRUE, FALSE)) {
180s +   if (setDimnames) dimnames(x) <- dimnames
180s +   else dimnames(x) <- NULL    
180s +   # Check names attribute
180s +   for (useNames in c(TRUE, FALSE)) {
180s +     r0 <- rowCounts(x, value = 0, useNames = useNames)
180s +     r1 <- rowCounts_R(x, value = 0, useNames = useNames)
180s +     stopifnot(identical(r0, r1))
180s +   }
180s + }
180s > 
180s 
180s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
180s Copyright (C) 2025 The R Foundation for Statistical Computing
180s Platform: x86_64-pc-linux-gnu
180s 
180s R is free software and comes with ABSOLUTELY NO WARRANTY.
180s You are welcome to redistribute it under certain conditions.
180s Type 'license()' or 'licence()' for distribution details.
180s 
180s R is a collaborative project with many contributors.
180s Type 'contributors()' for more information and
180s 'citation()' on how to cite R or R packages in publications.
180s 
180s Type 'demo()' for some demos, 'help()' for on-line help, or
180s 'help.start()' for an HTML browser interface to help.
180s Type 'q()' to quit R.
180s 
180s > library("matrixStats")
180s > 
180s > rowCounts_R <- function(x, value = TRUE, na.rm = FALSE, ..., useNames = TRUE) {
180s +   if (is.na(value)) {
180s +     counts <- apply(x, MARGIN = 1L, FUN = function(x)
180s +       sum(is.na(x))
180s +     )
180s +   } else {
180s +     counts <- apply(x, MARGIN = 1L, FUN = function(x)
180s +       sum(x == value, na.rm = na.rm)
180s +     )
180s +   }
180s +   # Preserve names attribute
180s +   names <- names(counts)  
180s +   counts <- as.integer(counts)
180s +   if (useNames && !is.null(names)) names(counts) <- names
180s +   counts
180s + } # rowCounts_R()
180s > 
180s > 
180s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
180s > # Subsetted tests
180s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
180s > source("utils/validateIndicesFramework.R")
180s > x <- matrix(runif(6 * 6, min = -3, max = 3), nrow = 6, ncol = 6)
180s > x[2:3, 3:4] <- NA_real_
180s > storage.mode(x) <- "integer"
180s > 
180s > # To check names attribute
180s > dimnames <- list(letters[1:6], LETTERS[1:6])
180s > 
180s > # Test with and without dimnames on x
180s > for (setDimnames in c(TRUE, FALSE)) {
180s +   if (setDimnames) dimnames(x) <- dimnames
180s +   else dimnames(x) <- NULL
180s +   for (rows in index_cases) {
180s +     for (cols in index_cases) {
180s +       # Check names attribute
180s +       for (useNames in c(TRUE, FALSE)) {
180s +         validateIndicesTestMatrix(x, rows, cols,
180s +                                   ftest = rowCounts, fsure = rowCounts_R,
180s +                                   value = 0, na.rm = TRUE, useNames = useNames)
180s +         validateIndicesTestMatrix(x, rows, cols,
180s +                                   fcoltest = colCounts, fsure = rowCounts_R,
180s +                                   value = 0, na.rm = TRUE, useNames = useNames)
180s +         for (value in c(0, NA_integer_)) {
180s +           validateIndicesTestMatrix(x, rows, cols,
180s +                                     ftest = rowCounts, fsure = rowCounts_R,
180s +                                     value = value, useNames = useNames)
180s +           validateIndicesTestMatrix(x, rows, cols,
180s +                                     fcoltest = colCounts, fsure = rowCounts_R,
180s +                                     value = value, useNames = useNames)
180s +         }
180s +       }
180s +     }
180s +   }
180s + }
181s > 
181s > x <- matrix(rep(letters, length.out = 6 * 6), nrow = 6, ncol = 6)
181s > x[2:3, 3:4] <- NA_character_
181s > # Test with and without dimnames on x
181s > for (setDimnames in c(TRUE, FALSE)) {
181s +   if (setDimnames) dimnames(x) <- dimnames
181s +   else dimnames(x) <- NULL
181s +   
181s +   count <- 0L
181s +   for (rows in index_cases) {
181s +     for (cols in index_cases) {
181s +       count <- count + 1L
181s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
181s +       useNames <- c(TRUE, FALSE)
181s +       useNames <- useNames[count %% length(useNames) + 1]
181s +       
181s +       validateIndicesTestMatrix(x, rows, cols,
181s +                                 ftest = rowCounts, fsure = rowCounts_R,
181s +                                 value = "g", na.rm = TRUE, useNames = useNames)
181s +       validateIndicesTestMatrix(x, rows, cols,
181s +                                 fcoltest = colCounts, fsure = rowCounts_R,
181s +                                 value = "g", na.rm = TRUE, useNames = useNames)
181s +       for (value in c("g", NA_character_)) {
181s +         validateIndicesTestMatrix(x, rows, cols,
181s +                                   ftest = rowCounts, fsure = rowCounts_R,
181s +                                   value = value, useNames = useNames)
181s +         validateIndicesTestMatrix(x, rows, cols,
181s +                                   fcoltest = colCounts, fsure = rowCounts_R,
181s +                                   value = value, useNames = useNames)
181s +       }
181s +     }
181s +   }
181s + }
181s > 
181s 
181s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
181s Copyright (C) 2025 The R Foundation for Statistical Computing
181s Platform: x86_64-pc-linux-gnu
181s 
181s R is free software and comes with ABSOLUTELY NO WARRANTY.
181s You are welcome to redistribute it under certain conditions.
181s Type 'license()' or 'licence()' for distribution details.
181s 
181s R is a collaborative project with many contributors.
181s Type 'contributors()' for more information and
181s 'citation()' on how to cite R or R packages in publications.
181s 
181s Type 'demo()' for some demos, 'help()' for on-line help, or
181s 'help.start()' for an HTML browser interface to help.
181s Type 'q()' to quit R.
181s 
181s > library("matrixStats")
181s > 
181s > rowCummins_R <- function(x, ..., useNames = TRUE) {
181s +   suppressWarnings({
181s +     y <- t(apply(x, MARGIN = 1L, FUN = cummin))
181s +   })
181s +  
181s +   # Preserve dimnames attribute?
181s +   dim(y) <- dim(x)
181s +   dimnames(y) <- if (useNames) dimnames(x) else NULL
181s +   y
181s + }
181s > 
181s > rowCummaxs_R <- function(x, ..., useNames = TRUE) {
181s +   mode <- storage.mode(x)
181s +   # Change mode because a bug is detected on cummax for integer in R-3.2.0
181s +   storage.mode(x) <- "numeric"
181s +   suppressWarnings({
181s +     y <- t(apply(x, MARGIN = 1L, FUN = cummax))
181s +   })
181s +   
181s +   # Preserve dimnames attribute?
181s +   dim(y) <- dim(x)
181s +   dimnames(y) <- if (useNames) dimnames(x) else NULL
181s +   
181s +   y
181s + }
181s > 
181s > 
181s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
181s > # With and without some NAs
181s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
181s > for (mode in c("logical", "integer", "double")) {
181s +   for (add_na in c(FALSE, TRUE)) {
181s +     cat("add_na = ", add_na, "\n", sep = "")
181s + 
181s +     x <- matrix(1:50, nrow = 10L, ncol = 5L)
181s +     diag(x) <- 0
181s +     if (add_na) {
181s +       x[3:7, c(2, 4)] <- NA_real_
181s +     }
181s +     cat("mode: ", mode, "\n", sep = "")
181s +     storage.mode(x) <- mode
181s +     str(x)
181s +     
181s +     # To check dimnames attribute
181s +     dimnames <- list(letters[1:10], LETTERS[1:5])
181s +     
181s +     # Test with and without dimnames on x
181s +     for (setDimnames in c(TRUE, FALSE)) {
181s +       if (setDimnames) dimnames(x) <- dimnames
181s +       else dimnames(x) <- NULL    
181s +       # Check names attribute
181s +       for (useNames in c(TRUE, FALSE)) {
181s +         # Row/column ranges
181s +         r0 <- rowCummins_R(x, useNames = useNames)
181s +         r1 <- rowCummins(x, useNames = useNames)
181s +         r2 <- t(colCummins(t(x), useNames = useNames))
181s +         stopifnot(all.equal(r1, r2))
181s +         stopifnot(all.equal(r1, r0))
181s +         stopifnot(all.equal(r2, r0))
181s + 
181s +         r0 <- rowCummaxs_R(x, useNames = useNames)
181s +         r1 <- rowCummaxs(x, useNames = useNames)
181s +         r2 <- t(colCummaxs(t(x), useNames = useNames))
181s +         stopifnot(all.equal(r1, r2))
181s +         stopifnot(all.equal(r1, r0))
181s +         stopifnot(all.equal(r2, r0))
181s +       } # for (useNames ...)
181s +     } # for (setDimnames ...)
181s +   } # for (add_na ...)
181s + } # for (mode ...)
181s add_na = FALSE
181s mode: logical
181s  logi [1:10, 1:5] FALSE TRUE TRUE TRUE TRUE TRUE ...
181s add_na = TRUE
181s mode: logical
181s  logi [1:10, 1:5] FALSE TRUE TRUE TRUE TRUE TRUE ...
181s add_na = FALSE
181s mode: integer
181s  int [1:10, 1:5] 0 2 3 4 5 6 7 8 9 10 ...
181s add_na = TRUE
181s mode: integer
181s  int [1:10, 1:5] 0 2 3 4 5 6 7 8 9 10 ...
181s add_na = FALSE
181s mode: double
181s  num [1:10, 1:5] 0 2 3 4 5 6 7 8 9 10 ...
181s add_na = TRUE
181s mode: double
181s  num [1:10, 1:5] 0 2 3 4 5 6 7 8 9 10 ...
181s > 
181s > 
181s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
181s > # All NAs
181s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
181s > for (mode in c("logical", "integer", "double")) {
181s +   x <- matrix(NA_real_, nrow = 10L, ncol = 5L)
181s +   cat("mode: ", mode, "\n", sep = "")
181s +   storage.mode(x) <- mode
181s +   str(x)
181s +   
181s +   # Test with and without dimnames on x
181s +   for (setDimnames in c(TRUE, FALSE)) {
181s +     if (setDimnames) dimnames(x) <- dimnames
181s +     else dimnames(x) <- NULL    
181s +     # Check names attribute
181s +     for (useNames in c(TRUE, FALSE)) {
181s +       r0 <- rowCummins_R(x, useNames = useNames)
181s +       r1 <- rowCummins(x, useNames = useNames)
181s +       r2 <- t(colCummins(t(x), useNames = useNames))
181s +       stopifnot(all.equal(r1, r2))
181s +       stopifnot(all.equal(r1, r0))
181s +       stopifnot(all.equal(r2, r0))
181s +       
181s +       r0 <- rowCummaxs_R(x, useNames = useNames)
181s +       r1 <- rowCummaxs(x, useNames = useNames)
181s +       r2 <- t(colCummaxs(t(x), useNames = useNames))
181s +       stopifnot(all.equal(r1, r2))
181s +       stopifnot(all.equal(r1, r0))
181s +       stopifnot(all.equal(r2, r0))
181s +     } # for (useNames ...)
181s +   } # for (setDimnames ...)
181s + } # for (mode ...)
181s mode: logical
181s  logi [1:10, 1:5] NA NA NA NA NA NA ...
181s mode: integer
181s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
181s mode: double
181s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
181s > 
181s > 
181s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
181s > # A 1x1 matrix
181s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
181s > for (mode in c("logical", "integer", "double")) {
181s +   x <- matrix(0, nrow = 1L, ncol = 1L)
181s +   cat("mode: ", mode, "\n", sep = "")
181s +   storage.mode(x) <- mode
181s +   str(x)
181s + 
181s +   # To check dimnames attribute
181s +   dimnames <- list("a", "A")
181s +   
181s +   # Test with and without dimnames on x
181s +   for (setDimnames in c(TRUE, FALSE)) {
181s +     if (setDimnames) dimnames(x) <- dimnames
181s +     else dimnames(x) <- NULL    
181s +     # Check names attribute
181s +     for (useNames in c(TRUE, FALSE)) {
181s +       r0 <- rowCummins_R(x, useNames = useNames)
181s +       r1 <- rowCummins(x, useNames = useNames)
181s +       r2 <- t(colCummins(t(x), useNames = useNames))
181s +       stopifnot(all.equal(r1, r2))
181s +       stopifnot(all.equal(r1, r0))
181s +       stopifnot(all.equal(r2, r0))
181s +       
181s +       r0 <- rowCummaxs_R(x, useNames = useNames)
181s +       r1 <- rowCummaxs(x, useNames = useNames)
181s +       r2 <- t(colCummaxs(t(x), useNames = useNames))
181s +       stopifnot(all.equal(r1, r2))
181s +       stopifnot(all.equal(r1, r0))
181s +       stopifnot(all.equal(r2, r0))
181s +     } # for (useNames ...)
181s +   } # for (setDimnames ...)
181s + } # for (mode ...)
181s mode: logical
181s  logi [1, 1] FALSE
181s mode: integer
181s  int [1, 1] 0
181s mode: double
181s  num [1, 1] 0
181s > 
181s > 
181s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
181s > # Corner cases
181s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
181s > for (mode in c("logical", "integer", "double")) {
181s +   cat("mode: ", mode, "\n", sep = "")
181s +   value <- 0
181s +   storage.mode(value) <- mode
181s +   value0 <- if (mode == "logical") 0L else value
181s + 
181s +   # A 0x0 matrix
181s +   x <- matrix(value, nrow = 0L, ncol = 0L)
181s +   str(x)
181s +   r0 <- matrix(value0, nrow = nrow(x), ncol = ncol(x))
181s +   r1 <- rowCummins(x)
181s +   r2 <- t(colCummins(t(x)))
181s +   stopifnot(all.equal(r1, r2))
181s +   stopifnot(all.equal(r1, r0))
181s +   stopifnot(all.equal(r2, r0))
181s + 
181s +   # A 0xK matrix
181s +   x <- matrix(value, nrow = 0L, ncol = 5L)
181s +   str(x)
181s +   colnames <- LETTERS[1:5]
181s +   # Test with and without dimnames on x
181s +   for (setDimnames in c(TRUE, FALSE)) {
181s +     if (setDimnames) colnames(x) <- colnames
181s +     else dimnames(x) <- NULL
181s +     # Check names attribute
181s +     for (useNames in c(TRUE, FALSE)) {
181s +       r0 <- rowCummins_R(x, useNames = useNames)
181s +       r1 <- rowCummins(x, useNames = useNames)
181s +       r2 <- t(colCummins(t(x), useNames = useNames))
181s +       stopifnot(all.equal(r1, r2))
181s +       stopifnot(all.equal(r1, r0))
181s +       stopifnot(all.equal(r2, r0))
181s +       r0 <- rowCummaxs_R(x, useNames = useNames)
181s +       r1 <- rowCummaxs(x, useNames = useNames)
181s +       r2 <- t(colCummaxs(t(x), useNames = useNames))
181s +       stopifnot(all.equal(r1, r2))
181s +       stopifnot(all.equal(r1, r0))
181s +       stopifnot(all.equal(r2, r0))
181s +     } # for (useNames ...)
181s +   } # for (setDimnames ...)
181s + 
181s +   # A Nx0 matrix
181s +   x <- matrix(value, nrow = 5L, ncol = 0L)
181s +   str(x)
181s +   rownames <- LETTERS[1:5]
181s +   # Test with and without dimnames on x
181s +   for (setDimnames in c(TRUE, FALSE)) {
181s +     if (setDimnames) rownames(x) <- rownames
181s +     else dimnames(x) <- NULL
181s +     # Check names attribute
181s +     for (useNames in c(TRUE, FALSE)) {
181s +       r0 <- rowCummins_R(x, useNames = useNames)
181s +       r1 <- rowCummins(x, useNames = useNames)
181s +       r2 <- t(colCummins(t(x), useNames = useNames))
181s +       stopifnot(all.equal(r1, r2))
181s +       stopifnot(all.equal(r1, r0))
181s +       stopifnot(all.equal(r2, r0))
181s +       
181s +       r0 <- rowCummaxs_R(x, useNames = useNames)
181s +       r1 <- rowCummaxs(x, useNames = useNames)
181s +       r2 <- t(colCummaxs(t(x), useNames = useNames))
181s +       stopifnot(all.equal(r1, r2))
181s +       stopifnot(all.equal(r1, r0))
181s +       stopifnot(all.equal(r2, r0))
181s +     } # for (useNames ...)
181s +   } # for (setDimnames ...)
181s + } # for (mode ...)
181s mode: logical
181s  logi[0 , 0 ] 
181s  logi[0 , 1:5] 
181s  logi[1:5, 0 ] 
181s mode: integer
181s  int[0 , 0 ] 
181s  int[0 , 1:5] 
181s  int[1:5, 0 ] 
181s mode: double
181s  num[0 , 0 ] 
181s  num[0 , 1:5] 
181s  num[1:5, 0 ] 
181s > 
181s 
181s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
181s Copyright (C) 2025 The R Foundation for Statistical Computing
181s Platform: x86_64-pc-linux-gnu
181s 
181s R is free software and comes with ABSOLUTELY NO WARRANTY.
181s You are welcome to redistribute it under certain conditions.
181s Type 'license()' or 'licence()' for distribution details.
181s 
181s R is a collaborative project with many contributors.
181s Type 'contributors()' for more information and
181s 'citation()' on how to cite R or R packages in publications.
181s 
181s Type 'demo()' for some demos, 'help()' for on-line help, or
181s 'help.start()' for an HTML browser interface to help.
181s Type 'q()' to quit R.
181s 
181s > library("matrixStats")
181s > 
181s > rowCummins_R <- function(x, ..., useNames = TRUE) {
181s +   suppressWarnings({
181s +     y <- t(apply(x, MARGIN = 1L, FUN = cummin))
181s +   })
181s +   
181s +   # Preserve dimnames attribute?
181s +   dim(y) <- dim(x)
181s +   dimnames(y) <- if (useNames) dimnames(x) else NULL
181s +   
181s +   y
181s + }
181s > 
181s > rowCummaxs_R <- function(x, ..., useNames = TRUE) {
181s +   mode <- storage.mode(x)
181s +   # Change mode because a bug is detected on cummax for integer in R-3.2.0
181s +   storage.mode(x) <- "numeric"
181s +   suppressWarnings({
181s +     y <- t(apply(x, MARGIN = 1L, FUN = cummax))
181s +   })
181s +   
181s +   # Preserve dimnames attribute?
181s +   dim(y) <- dim(x)
181s +   dimnames(y) <- if (useNames) dimnames(x) else NULL
181s +   
181s +   storage.mode(y) <- mode
181s +   y
181s + }
181s > 
181s > 
181s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
181s > # Subsetted tests
181s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
181s > source("utils/validateIndicesFramework.R")
181s > x <- matrix(runif(6 * 6, min = -3, max = 3), nrow = 6, ncol = 6)
181s > storage.mode(x) <- "integer"
181s > 
181s > # To check dimnames attribute
181s > dimnames <- list(letters[1:6], LETTERS[1:6])
181s > 
181s > # Test with and without dimnames on x
181s > for (setDimnames in c(TRUE, FALSE)) {
181s +   if (setDimnames) dimnames(x) <- dimnames
181s +   else dimnames(x) <- NULL
181s +   for (rows in index_cases) {
181s +     for (cols in index_cases) {
181s +       # Check names attribute
181s +       for (useNames in c(TRUE, FALSE)) {
181s +         validateIndicesTestMatrix(x, rows, cols,
181s +                                   ftest = rowCummins, fsure = rowCummins_R, useNames = useNames,verbose=TRUE)
181s +         validateIndicesTestMatrix(x, rows, cols,
181s +                                   ftest = function(x, rows, cols, ..., useNames) {
181s +           t(colCummins(t(x), rows = cols, cols = rows, useNames = useNames))
181s +         }, fsure = rowCummins_R, useNames = useNames)
181s + 
181s +         validateIndicesTestMatrix(x, rows, cols,
181s +                                   ftest = rowCummaxs, fsure = rowCummaxs_R, useNames = useNames)
181s +         validateIndicesTestMatrix(x, rows, cols,
181s +                                   ftest = function(x, rows, cols, ..., useNames) {
181s +           t(colCummaxs(t(x), rows = cols, cols = rows, useNames = useNames))
181s +         }, fsure = rowCummaxs_R, useNames = useNames)
181s +       }
181s +     }
181s +   }
181s + }
182s > 
182s 
182s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
182s Copyright (C) 2025 The R Foundation for Statistical Computing
182s Platform: x86_64-pc-linux-gnu
182s 
182s R is free software and comes with ABSOLUTELY NO WARRANTY.
182s You are welcome to redistribute it under certain conditions.
182s Type 'license()' or 'licence()' for distribution details.
182s 
182s R is a collaborative project with many contributors.
182s Type 'contributors()' for more information and
182s 'citation()' on how to cite R or R packages in publications.
182s 
182s Type 'demo()' for some demos, 'help()' for on-line help, or
182s 'help.start()' for an HTML browser interface to help.
182s Type 'q()' to quit R.
182s 
182s > library("matrixStats")
182s > 
182s > rowCumprods_R <- function(x, ..., useNames = TRUE) {
182s +   suppressWarnings({
182s +     y <- t(apply(x, MARGIN = 1L, FUN = cumprod))
182s +   })
182s +   
182s +   # Preserve dimnames attribute?
182s +   dim(y) <- dim(x)
182s +   dimnames(y) <- if (useNames) dimnames(x) else NULL
182s +   
182s +   y
182s + }
182s > 
182s > 
182s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
182s > # With and without some NAs
182s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
182s > for (mode in c("logical", "integer", "double")) {
182s +   for (add_na in c(FALSE, TRUE)) {
182s +     cat("add_na = ", add_na, "\n", sep = "")
182s + 
182s +     x <- matrix(1:50, nrow = 10L, ncol = 5L)
182s +     if (add_na) {
182s +       x[3:7, c(2, 4)] <- NA_real_
182s +     }
182s +     cat("mode: ", mode, "\n", sep = "")
182s +     storage.mode(x) <- mode
182s +     str(x)
182s +     
182s +     # To check dimnames attribute
182s +     dimnames <- list(letters[1:10], LETTERS[1:5])
182s +     
182s +     # Test with and without dimnames on x
182s +     for (setDimnames in c(TRUE, FALSE)) {
182s +       if (setDimnames) dimnames(x) <- dimnames
182s +       else dimnames(x) <- NULL    
182s +       # Check names attribute
182s +       for (useNames in c(TRUE, FALSE)) {
182s +         # Row/column ranges
182s +         r0 <- rowCumprods_R(x, useNames = useNames)
182s +         r1 <- rowCumprods(x, useNames = useNames)
182s +         r2 <- t(colCumprods(t(x), useNames = useNames))
182s +         stopifnot(all.equal(r1, r2))
182s +         stopifnot(all.equal(r1, r0))
182s +         stopifnot(all.equal(r2, r0))
182s +       } # for (useNames ...)
182s +     } # for (setDimnames ...)
182s +   } # for (add_na ...)
182s + } # for (mode ...)
182s add_na = FALSE
182s mode: logical
182s  logi [1:10, 1:5] TRUE TRUE TRUE TRUE TRUE TRUE ...
182s add_na = TRUE
182s mode: logical
182s  logi [1:10, 1:5] TRUE TRUE TRUE TRUE TRUE TRUE ...
182s add_na = FALSE
182s mode: integer
182s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
182s add_na = TRUE
182s mode: integer
182s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
182s add_na = FALSE
182s mode: double
182s  num [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
182s add_na = TRUE
182s mode: double
182s  num [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
182s > 
182s > 
182s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
182s > # All NAs
182s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
182s > for (mode in c("logical", "integer", "double")) {
182s +   x <- matrix(NA_real_, nrow = 10L, ncol = 5L)
182s +   cat("mode: ", mode, "\n", sep = "")
182s +   storage.mode(x) <- mode
182s +   str(x)
182s +   
182s +   # Test with and without dimnames on x
182s +   for (setDimnames in c(TRUE, FALSE)) {
182s +     if (setDimnames) dimnames(x) <- dimnames
182s +     else dimnames(x) <- NULL    
182s +     # Check names attribute
182s +     for (useNames in c(TRUE, FALSE)) {
182s +       # Row/column ranges
182s +       r0 <- rowCumprods_R(x, useNames = useNames)
182s +       r1 <- rowCumprods(x, useNames = useNames)
182s +       r2 <- t(colCumprods(t(x), useNames = useNames))
182s +       stopifnot(all.equal(r1, r2))
182s +       stopifnot(all.equal(r1, r0))
182s +       stopifnot(all.equal(r2, r0))
182s +     } # for (useNames ...)
182s +   } # for (setDimnames ...)
182s + } # for (mode ...)
182s mode: logical
182s  logi [1:10, 1:5] NA NA NA NA NA NA ...
182s mode: integer
182s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
182s mode: double
182s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
182s > 
182s > 
182s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
182s > # A 1x1 matrix
182s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
182s > for (mode in c("logical", "integer", "double")) {
182s +   x <- matrix(0, nrow = 1L, ncol = 1L)
182s +   cat("mode: ", mode, "\n", sep = "")
182s +   storage.mode(x) <- mode
182s +   str(x)
182s +   
182s +   dimnames <- list("a", "A")
182s +   # Test with and without dimnames on x
182s +   for (setDimnames in c(TRUE, FALSE)) {
182s +     if (setDimnames) dimnames(x) <- dimnames
182s +     else dimnames(x) <- NULL    
182s +     # Check names attribute
182s +     for (useNames in c(TRUE, FALSE)) {
182s +       # Row/column ranges
182s +       r0 <- rowCumprods_R(x, useNames = useNames)
182s +       r1 <- rowCumprods(x, useNames = useNames)
182s +       r2 <- t(colCumprods(t(x), useNames = useNames))
182s +       stopifnot(all.equal(r1, r2))
182s +       stopifnot(all.equal(r1, r0))
182s +       stopifnot(all.equal(r2, r0))
182s +     } # for (useNames ...)
182s +   } # for (setDimnames ...)
182s + }
182s mode: logical
182s  logi [1, 1] FALSE
182s mode: integer
182s  int [1, 1] 0
182s mode: double
182s  num [1, 1] 0
182s > 
182s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
182s > # BUG FIX TEST: Assert zeros don't trump NAs in integer matrices
182s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
182s > for (mode in c("logical", "integer", "double")) {
182s +   x <- matrix(NA_real_, nrow = 3L, ncol = 2L)
182s +   x[1, 2] <- 0
182s +   x[2, 2] <- 1
182s +   x[3, 1] <- 0
182s +   storage.mode(x) <- mode
182s +   cat("mode: ", mode, "\n", sep = "")
182s +   str(x)
182s +   
182s +   dimnames <- list(letters[1:3], LETTERS[1:2])
182s +   # Test with and without dimnames on x
182s +   for (setDimnames in c(TRUE, FALSE)) {
182s +     if (setDimnames) dimnames(x) <- dimnames
182s +     else dimnames(x) <- NULL    
182s +     # Check names attribute
182s +     for (useNames in c(TRUE, FALSE)) {
182s +       # Row/column ranges
182s +       r0 <- rowCumprods_R(x, useNames = useNames)
182s +       r1 <- rowCumprods(x, useNames = useNames)
182s +       r2 <- t(colCumprods(t(x), useNames = useNames))
182s +       stopifnot(all.equal(r1, r2))
182s +       stopifnot(all.equal(r1, r0))
182s +       stopifnot(all.equal(r2, r0))
182s +     } # for (useNames ...)
182s +   } # for (setDimnames ...)
182s + }
182s mode: logical
182s  logi [1:3, 1:2] NA NA FALSE FALSE TRUE NA
182s mode: integer
182s  int [1:3, 1:2] NA NA 0 0 1 NA
182s mode: double
182s  num [1:3, 1:2] NA NA 0 0 1 NA
182s > 
182s > 
182s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
182s > # Corner cases
182s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
182s > for (mode in c("logical", "integer", "double")) {
182s +   cat("mode: ", mode, "\n", sep = "")
182s +   value <- 0
182s +   storage.mode(value) <- mode
182s +   if (mode == "logical") value2 <- 0L
182s + 
182s +   # A 0x0 matrix
182s +   x <- matrix(value, nrow = 0L, ncol = 0L)
182s +   str(x)
182s +   r0 <- matrix(value2, nrow = nrow(x), ncol = ncol(x))
182s +   r1 <- rowCumprods(x)
182s +   r2 <- t(colCumprods(t(x)))
182s +   stopifnot(all.equal(r1, r2))
182s +   stopifnot(all.equal(r1, r0))
182s +   stopifnot(all.equal(r2, r0))
182s + 
182s +   # A 0xK matrix
182s +   x <- matrix(value, nrow = 0L, ncol = 5L)
182s +   str(x)
182s +   colnames <- LETTERS[1:5]
182s +   # Test with and without dimnames on x
182s +   for (setDimnames in c(TRUE, FALSE)) {
182s +     if (setDimnames) colnames(x) <- colnames
182s +     else dimnames(x) <- NULL
182s +     # Check names attribute
182s +     for (useNames in c(TRUE, FALSE)) {
182s +       r0 <- rowCumprods_R(x, useNames = useNames)
182s +       r1 <- rowCumprods(x, useNames = useNames)
182s +       r2 <- t(rowCumprods(t(x), useNames = useNames))
182s +       stopifnot(all.equal(r1, r2))
182s +       stopifnot(all.equal(r1, r0))
182s +       stopifnot(all.equal(r2, r0))
182s +     } # for (useNames ...)
182s +   } # for (setDimnames ...)
182s + 
182s +   # A Nx0 matrix
182s +   x <- matrix(value, nrow = 5L, ncol = 0L)
182s +   str(x)
182s +   rownames <- LETTERS[1:5]
182s +   # Test with and without dimnames on x
182s +   for (setDimnames in c(TRUE, FALSE)) {
182s +     if (setDimnames) rownames(x) <- rownames
182s +     else dimnames(x) <- NULL
182s +     # Check names attribute
182s +     for (useNames in c(TRUE, FALSE)) {
182s +       r0 <- rowCumprods_R(x, useNames = useNames)
182s +       r1 <- rowCumprods(x, useNames = useNames)
182s +       r2 <- t(rowCumprods(t(x), useNames = useNames))
182s +       stopifnot(all.equal(r1, r2))
182s +       stopifnot(all.equal(r1, r0))
182s +       stopifnot(all.equal(r2, r0))
182s +     } # for (useNames ...)
182s +   } # for (setDimnames ...)
182s + } # for (mode ...)
182s mode: logical
182s  logi[0 , 0 ] 
182s  logi[0 , 1:5] 
182s  logi[1:5, 0 ] 
182s mode: integer
182s  int[0 , 0 ] 
182s  int[0 , 1:5] 
182s  int[1:5, 0 ] 
182s mode: double
182s  num[0 , 0 ] 
182s  num[0 , 1:5] 
182s  num[1:5, 0 ] 
182s > 
182s 
182s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
182s Copyright (C) 2025 The R Foundation for Statistical Computing
182s Platform: x86_64-pc-linux-gnu
182s 
182s R is free software and comes with ABSOLUTELY NO WARRANTY.
182s You are welcome to redistribute it under certain conditions.
182s Type 'license()' or 'licence()' for distribution details.
182s 
182s R is a collaborative project with many contributors.
182s Type 'contributors()' for more information and
182s 'citation()' on how to cite R or R packages in publications.
182s 
182s Type 'demo()' for some demos, 'help()' for on-line help, or
182s 'help.start()' for an HTML browser interface to help.
182s Type 'q()' to quit R.
182s 
182s > library("matrixStats")
182s > 
182s > rowCumprods_R <- function(x, ..., useNames = TRUE) {
182s +   suppressWarnings({
182s +     y <- t(apply(x, MARGIN = 1L, FUN = cumprod))
182s +   })
182s + 
182s +   # Preserve dimnames attribute?
182s +   dim(y) <- dim(x)
182s +   dimnames(y) <- if (useNames) dimnames(x) else NULL
182s +   
182s +   y
182s + }
182s > 
182s > 
182s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
182s > # Subsetted tests
182s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
182s > source("utils/validateIndicesFramework.R")
182s > x <- matrix(runif(6 * 6, min = -3, max = 3), nrow = 6, ncol = 6)
182s > storage.mode(x) <- "integer"
182s > 
182s > # To check dimnames attribute
182s > dimnames <- list(letters[1:6], LETTERS[1:6])
182s > 
182s > # Test with and without dimnames on x
182s > for (setDimnames in c(TRUE, FALSE)) {
182s +   if (setDimnames) dimnames(x) <- dimnames
182s +   else dimnames(x) <- NULL
182s +   for (rows in index_cases) {
182s +     for (cols in index_cases) {
182s +       # Check names attribute
182s +       for (useNames in c(TRUE, FALSE)) {
182s +         validateIndicesTestMatrix(x, rows, cols,
182s +                                   ftest = rowCumprods, fsure = rowCumprods_R, useNames = useNames)
182s +         validateIndicesTestMatrix(x, rows, cols,
182s +                                   ftest = function(x, rows, cols, ..., useNames) {
182s +           t(colCumprods(t(x), rows = cols, cols = rows, useNames = useNames))
182s +         }, fsure = rowCumprods_R, useNames = useNames)
182s +       }
182s +     }
182s +   }
182s + }
183s > 
183s 
183s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
183s Copyright (C) 2025 The R Foundation for Statistical Computing
183s Platform: x86_64-pc-linux-gnu
183s 
183s R is free software and comes with ABSOLUTELY NO WARRANTY.
183s You are welcome to redistribute it under certain conditions.
183s Type 'license()' or 'licence()' for distribution details.
183s 
183s R is a collaborative project with many contributors.
183s Type 'contributors()' for more information and
183s 'citation()' on how to cite R or R packages in publications.
183s 
183s Type 'demo()' for some demos, 'help()' for on-line help, or
183s 'help.start()' for an HTML browser interface to help.
183s Type 'q()' to quit R.
183s 
183s > library("matrixStats")
183s > 
183s > rowCumsums_R <- function(x, ..., useNames = TRUE) {
183s +   suppressWarnings({
183s +     y <- t(apply(x, MARGIN = 1L, FUN = cumsum))
183s +   })
183s +   
183s +   # Preserve dimnames attribute?
183s +   dim(y) <- dim(x)
183s +   dimnames(y) <- if (useNames) dimnames(x) else NULL
183s +   
183s +   y
183s + }
183s > 
183s > 
183s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
183s > # With and without some NAs
183s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
183s > dimnames <- list(letters[1:10], LETTERS[1:5]) # to check dimnames attribute
183s > for (mode in c("logical", "integer", "double")) {
183s +   for (add_na in c(FALSE, TRUE)) {
183s +     cat("add_na = ", add_na, "\n", sep = "")
183s + 
183s +     x <- matrix(1:50, nrow = 10L, ncol = 5L)
183s +     if (add_na) {
183s +       x[3:7, c(2, 4)] <- NA_real_
183s +     }
183s +     cat("mode: ", mode, "\n", sep = "")
183s +     storage.mode(x) <- mode
183s +     str(x)
183s +     
183s +     # Test with and without dimnames on x
183s +     for (setDimnames in c(TRUE, FALSE)) {
183s +       if (setDimnames) dimnames(x) <- dimnames
183s +       else dimnames(x) <- NULL    
183s +       # Check names attribute
183s +       for (useNames in c(TRUE, FALSE)) {
183s +         # Row/column ranges
183s +         r0 <- rowCumsums_R(x, useNames = useNames)
183s +         r1 <- rowCumsums(x, useNames = useNames)
183s +         r2 <- t(colCumsums(t(x), useNames = useNames))
183s +         stopifnot(all.equal(r1, r2))
183s +         stopifnot(all.equal(r1, r0))
183s +         stopifnot(all.equal(r2, r0))
183s +       } # for (useNames ...)
183s +     } # for (setDimnames ...)
183s +   } # for (add_na ...)
183s + }
183s add_na = FALSE
183s mode: logical
183s  logi [1:10, 1:5] TRUE TRUE TRUE TRUE TRUE TRUE ...
183s add_na = TRUE
183s mode: logical
183s  logi [1:10, 1:5] TRUE TRUE TRUE TRUE TRUE TRUE ...
183s add_na = FALSE
183s mode: integer
183s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
183s add_na = TRUE
183s mode: integer
183s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
183s add_na = FALSE
183s mode: double
183s  num [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
183s add_na = TRUE
183s mode: double
183s  num [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
183s > 
183s > 
183s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
183s > # All NAs
183s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
183s > for (mode in c("logical", "integer", "double")) {
183s +   x <- matrix(NA_real_, nrow = 10L, ncol = 5L)
183s +   cat("mode: ", mode, "\n", sep = "")
183s +   storage.mode(x) <- mode
183s +   str(x)
183s +   
183s +   # Test with and without dimnames on x
183s +   for (setDimnames in c(TRUE, FALSE)) {
183s +     if (setDimnames) dimnames(x) <- dimnames
183s +     else dimnames(x) <- NULL    
183s +     # Check names attribute
183s +     for (useNames in c(TRUE, FALSE)) {
183s +       # Row/column ranges
183s +       r0 <- rowCumsums_R(x, useNames = useNames)
183s +       r1 <- rowCumsums(x, useNames = useNames)
183s +       r2 <- t(colCumsums(t(x), useNames = useNames))
183s +       stopifnot(all.equal(r1, r2))
183s +       stopifnot(all.equal(r1, r0))
183s +       stopifnot(all.equal(r2, r0))
183s +     } # for (useNames ...)
183s +   } # for (setDimnames ...)
183s + } # for (mode ...)
183s mode: logical
183s  logi [1:10, 1:5] NA NA NA NA NA NA ...
183s mode: integer
183s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
183s mode: double
183s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
183s > 
183s > 
183s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
183s > # A 1x1 matrix
183s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
183s > dimnames <- list("a", "A") # to check dimnames attribute
183s > for (mode in c("logical", "integer", "double")) {
183s +   x <- matrix(0, nrow = 1L, ncol = 1L)
183s +   cat("mode: ", mode, "\n", sep = "")
183s +   storage.mode(x) <- mode
183s +   str(x)
183s + 
183s +   r0 <- rowCumsums_R(x)
183s +   r1 <- rowCumsums(x)
183s +   r2 <- t(colCumsums(t(x)))
183s +   stopifnot(all.equal(r1, r2))
183s +   stopifnot(all.equal(r1, r0))
183s +   stopifnot(all.equal(r2, r0))
183s +   
183s +   # Check dimnames attribute
183s +   dimnames(x) <- dimnames
183s +   # r0 <- rowCumsums_R(x)
183s +   # > r0
183s +   #        a
183s +   #   [1,] 0
183s +   r1 <- rowCumsums(x, useNames = TRUE)
183s +   r2 <- t(colCumsums(t(x), useNames = TRUE))
183s +   stopifnot(identical(dimnames(r1), dimnames))
183s +   stopifnot(identical(dimnames(r2), dimnames))    
183s +   dimnames(x) <- NULL
183s + }
183s mode: logical
183s  logi [1, 1] FALSE
183s mode: integer
183s  int [1, 1] 0
183s mode: double
183s  num [1, 1] 0
183s > 
183s > 
183s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
183s > # Corner cases
183s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
183s > names <- LETTERS[1:5] # to check dimnames attribute
183s > for (mode in c("logical", "integer", "double")) {
183s +   cat("mode: ", mode, "\n", sep = "")
183s +   value <- 0
183s +   storage.mode(value) <- mode
183s +   value2 <- value
183s +   if (mode == "logical") value2 <- 0L
183s +   
183s +   # A 0x0 matrix
183s +   x <- matrix(value, nrow = 0L, ncol = 0L)
183s +   str(x)
183s +   r0 <- matrix(value2, nrow = nrow(x), ncol = ncol(x))
183s +   r1 <- rowCumsums(x)
183s +   r2 <- t(colCumsums(t(x)))
183s +   stopifnot(all.equal(r1, r2))
183s +   stopifnot(all.equal(r1, r0))
183s +   stopifnot(all.equal(r2, r0))
183s + 
183s +   # A 0xK matrix
183s +   x <- matrix(value, nrow = 0L, ncol = 5L)
183s +   str(x)
183s +   colnames <- LETTERS[1:5]
183s +   # Test with and without dimnames on x
183s +   for (setDimnames in c(TRUE, FALSE)) {
183s +     if (setDimnames) colnames(x) <- colnames
183s +     else dimnames(x) <- NULL
183s +     # Check names attribute
183s +     for (useNames in c(TRUE, FALSE)) {
183s +       r0 <- rowCumsums_R(x, useNames = useNames)
183s +       r1 <- rowCumsums(x, useNames = useNames)
183s +       r2 <- t(rowCumsums(t(x), useNames = useNames))
183s +       stopifnot(all.equal(r1, r2))
183s +       stopifnot(all.equal(r1, r0))
183s +       stopifnot(all.equal(r2, r0))
183s +     } # for (useNames ...)
183s +   } # for (setDimnames ...)
183s + 
183s +   # A Nx0 matrix
183s +   x <- matrix(value, nrow = 5L, ncol = 0L)
183s +   str(x)
183s +   rownames <- LETTERS[1:5]
183s +   # Test with and without dimnames on x
183s +   for (setDimnames in c(TRUE, FALSE)) {
183s +     if (setDimnames) rownames(x) <- rownames
183s +     else dimnames(x) <- NULL
183s +     # Check names attribute
183s +     for (useNames in c(TRUE, FALSE)) {
183s +       r0 <- rowCumsums_R(x, useNames = useNames)
183s +       r1 <- rowCumsums(x, useNames = useNames)
183s +       r2 <- t(rowCumsums(t(x), useNames = useNames))
183s +       stopifnot(all.equal(r1, r2))
183s +       stopifnot(all.equal(r1, r0))
183s +       stopifnot(all.equal(r2, r0))
183s +     } # for (useNames ...)
183s +   } # for (setDimnames ...)
183s + } # for (mode ...)
183s mode: logical
183s  logi[0 , 0 ] 
183s  logi[0 , 1:5] 
183s  logi[1:5, 0 ] 
183s mode: integer
183s  int[0 , 0 ] 
183s  int[0 , 1:5] 
183s  int[1:5, 0 ] 
183s mode: double
183s  num[0 , 0 ] 
183s  num[0 , 1:5] 
183s  num[1:5, 0 ] 
183s > 
183s 
183s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
183s Copyright (C) 2025 The R Foundation for Statistical Computing
183s Platform: x86_64-pc-linux-gnu
183s 
183s R is free software and comes with ABSOLUTELY NO WARRANTY.
183s You are welcome to redistribute it under certain conditions.
183s Type 'license()' or 'licence()' for distribution details.
183s 
183s R is a collaborative project with many contributors.
183s Type 'contributors()' for more information and
183s 'citation()' on how to cite R or R packages in publications.
183s 
183s Type 'demo()' for some demos, 'help()' for on-line help, or
183s 'help.start()' for an HTML browser interface to help.
183s Type 'q()' to quit R.
183s 
183s > library("matrixStats")
183s > 
183s > rowCumsums_R <- function(x, ..., useNames = TRUE) {
183s +   suppressWarnings({
183s +     y <- t(apply(x, MARGIN = 1L, FUN = cumsum))
183s +   })
183s +   
183s +   # Preserve dimnames attribute?
183s +   dim(y) <- dim(x)
183s +   dimnames(y) <- if (useNames) dimnames(x) else NULL
183s + 
183s +   y
183s + }
183s > 
183s > 
183s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
183s > # Subsetted tests
183s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
183s > source("utils/validateIndicesFramework.R")
183s > x <- matrix(runif(6 * 6, min = -3, max = 3), nrow = 6, ncol = 6)
183s > storage.mode(x) <- "integer"
183s > 
183s > # To check dimnames attribute
183s > dimnames <- list(letters[1:6], LETTERS[1:6])
183s > 
183s > # Test with and without dimnames on x
183s > for (setDimnames in c(TRUE, FALSE)) {
183s +   if (setDimnames) dimnames(x) <- dimnames
183s +   else dimnames(x) <- NULL
183s +   for (rows in index_cases) {
183s +     for (cols in index_cases) {
183s +       # Check names attribute
183s +       for (useNames in c(TRUE, FALSE)) {
183s +         validateIndicesTestMatrix(x, rows, cols,
183s +                                   ftest = rowCumsums, fsure = rowCumsums_R, useNames = useNames)
183s +         validateIndicesTestMatrix(x, rows, cols,
183s +                                   ftest = function(x, rows, cols, ..., useNames) {
183s +           t(colCumsums(t(x), rows = cols, cols = rows, useNames = useNames))
183s +         }, fsure = rowCumsums_R, useNames = useNames)
183s +       }
183s +     }
183s +   }
183s + }
184s > 
184s 
184s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
184s Copyright (C) 2025 The R Foundation for Statistical Computing
184s Platform: x86_64-pc-linux-gnu
184s 
184s R is free software and comes with ABSOLUTELY NO WARRANTY.
184s You are welcome to redistribute it under certain conditions.
184s Type 'license()' or 'licence()' for distribution details.
184s 
184s R is a collaborative project with many contributors.
184s Type 'contributors()' for more information and
184s 'citation()' on how to cite R or R packages in publications.
184s 
184s Type 'demo()' for some demos, 'help()' for on-line help, or
184s 'help.start()' for an HTML browser interface to help.
184s Type 'q()' to quit R.
184s 
184s > library("matrixStats")
184s > 
184s > rowDiffs_R <- function(x, lag = 1L, differences = 1L, ..., useNames = TRUE) {
184s +   ncol2 <- ncol(x) - lag * differences
184s +   if (ncol2 <= 0) {
184s +     y <- matrix(x[integer(0L)], nrow = nrow(x), ncol = 0L)
184s +     # Preserve names attribute
184s +     if (useNames && !is.null(rownames(x))) rownames(y) <- rownames(x)
184s +     return(y)
184s +   }
184s +   suppressWarnings({
184s +     y <- apply(x, MARGIN = 1L, FUN = diff, lag = lag, differences = differences)
184s +   })
184s +   y <- t(y)
184s +   
184s +   # Preserve dimnames attribute
184s +   dim(y) <- c(nrow(x), ncol2)
184s +   if (useNames && !is.null(dimnames(x))) {
184s +     colnames <- colnames(x)
184s +     if (!is.null(colnames)) {
184s +       len <- length(colnames)
184s +       colnames <- colnames[(len - ncol2 + 1):len]
184s +     }
184s +     dimnames(y) <- list(rownames(x), colnames)      
184s +   }
184s +   else dimnames(y) <- NULL
184s +   
184s +   y
184s + }
184s > 
184s > 
184s > set.seed(0x42)
184s > 
184s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
184s > # With and without some NAs
184s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
184s > for (mode in c("integer", "double")) {
184s +   cat("mode: ", mode, "\n", sep = "")
184s + 
184s +   for (add_na in c(FALSE, TRUE)) {
184s +     cat("add_na = ", add_na, "\n", sep = "")
184s + 
184s +     x <- matrix(sample(10 * 8) + 0.1, nrow = 10L, ncol = 8L)
184s +     if (add_na) {
184s +       x[3:7, c(2, 4)] <- NA_real_
184s +     }
184s +     storage.mode(x) <- mode
184s +     str(x)
184s +     
184s +     dimnames <- list(letters[1:10], LETTERS[1:8])
184s + 
184s +     # Test with and without dimnames on x
184s +     for (setDimnames in c(TRUE, FALSE)) {
184s +       if (setDimnames) dimnames(x) <- dimnames
184s +       else dimnames(x) <- NULL
184s +       # Check dimnames attribute
184s +       for (useNames in c(TRUE, FALSE)) {
184s +         for (lag in 1:4) {
184s +           for (differences in 1:3) {
184s +             cat(sprintf("mode: %s, lag = %d, differences = %d\n",
184s +                         mode, lag, differences))
184s +             # Row/column ranges
184s +             r0 <- rowDiffs_R(x, lag = lag, differences = differences, useNames = useNames)
184s +             r1 <- rowDiffs(x, lag = lag, differences = differences, useNames = useNames)
184s +             r2 <- t(colDiffs(t(x), lag = lag, differences = differences, useNames = useNames))
184s +             stopifnot(all.equal(r1, r0))
184s +             stopifnot(all.equal(r2, r0))
184s +             stopifnot(all.equal(r1, r2))
184s +           }
184s +         }
184s +       } # for (useNames ...)
184s +     } # for (setDimnames ...)
184s +   } # for (add_na ...)
184s + } # for (mode ...)
184s mode: integer
184s add_na = FALSE
184s  int [1:10, 1:8] 68 26 29 47 48 10 1 38 16 40 ...
184s mode: integer, lag = 1, differences = 1
184s mode: integer, lag = 1, differences = 2
184s mode: integer, lag = 1, differences = 3
184s mode: integer, lag = 2, differences = 1
184s mode: integer, lag = 2, differences = 2
184s mode: integer, lag = 2, differences = 3
184s mode: integer, lag = 3, differences = 1
184s mode: integer, lag = 3, differences = 2
184s mode: integer, lag = 3, differences = 3
184s mode: integer, lag = 4, differences = 1
184s mode: integer, lag = 4, differences = 2
184s mode: integer, lag = 4, differences = 3
184s mode: integer, lag = 1, differences = 1
184s mode: integer, lag = 1, differences = 2
184s mode: integer, lag = 1, differences = 3
184s mode: integer, lag = 2, differences = 1
184s mode: integer, lag = 2, differences = 2
184s mode: integer, lag = 2, differences = 3
184s mode: integer, lag = 3, differences = 1
184s mode: integer, lag = 3, differences = 2
184s mode: integer, lag = 3, differences = 3
184s mode: integer, lag = 4, differences = 1
184s mode: integer, lag = 4, differences = 2
184s mode: integer, lag = 4, differences = 3
184s mode: integer, lag = 1, differences = 1
184s mode: integer, lag = 1, differences = 2
184s mode: integer, lag = 1, differences = 3
184s mode: integer, lag = 2, differences = 1
184s mode: integer, lag = 2, differences = 2
184s mode: integer, lag = 2, differences = 3
184s mode: integer, lag = 3, differences = 1
184s mode: integer, lag = 3, differences = 2
184s mode: integer, lag = 3, differences = 3
184s mode: integer, lag = 4, differences = 1
184s mode: integer, lag = 4, differences = 2
184s mode: integer, lag = 4, differences = 3
184s mode: integer, lag = 1, differences = 1
184s mode: integer, lag = 1, differences = 2
184s mode: integer, lag = 1, differences = 3
184s mode: integer, lag = 2, differences = 1
184s mode: integer, lag = 2, differences = 2
184s mode: integer, lag = 2, differences = 3
184s mode: integer, lag = 3, differences = 1
184s mode: integer, lag = 3, differences = 2
184s mode: integer, lag = 3, differences = 3
184s mode: integer, lag = 4, differences = 1
184s mode: integer, lag = 4, differences = 2
184s mode: integer, lag = 4, differences = 3
184s add_na = TRUE
184s  int [1:10, 1:8] 80 71 7 52 79 22 31 10 29 63 ...
184s mode: integer, lag = 1, differences = 1
184s mode: integer, lag = 1, differences = 2
184s mode: integer, lag = 1, differences = 3
184s mode: integer, lag = 2, differences = 1
184s mode: integer, lag = 2, differences = 2
184s mode: integer, lag = 2, differences = 3
184s mode: integer, lag = 3, differences = 1
184s mode: integer, lag = 3, differences = 2
184s mode: integer, lag = 3, differences = 3
184s mode: integer, lag = 4, differences = 1
184s mode: integer, lag = 4, differences = 2
184s mode: integer, lag = 4, differences = 3
184s mode: integer, lag = 1, differences = 1
184s mode: integer, lag = 1, differences = 2
184s mode: integer, lag = 1, differences = 3
184s mode: integer, lag = 2, differences = 1
184s mode: integer, lag = 2, differences = 2
184s mode: integer, lag = 2, differences = 3
184s mode: integer, lag = 3, differences = 1
184s mode: integer, lag = 3, differences = 2
184s mode: integer, lag = 3, differences = 3
184s mode: integer, lag = 4, differences = 1
184s mode: integer, lag = 4, differences = 2
184s mode: integer, lag = 4, differences = 3
184s mode: integer, lag = 1, differences = 1
184s mode: integer, lag = 1, differences = 2
184s mode: integer, lag = 1, differences = 3
184s mode: integer, lag = 2, differences = 1
184s mode: integer, lag = 2, differences = 2
184s mode: integer, lag = 2, differences = 3
184s mode: integer, lag = 3, differences = 1
184s mode: integer, lag = 3, differences = 2
184s mode: integer, lag = 3, differences = 3
184s mode: integer, lag = 4, differences = 1
184s mode: integer, lag = 4, differences = 2
184s mode: integer, lag = 4, differences = 3
184s mode: integer, lag = 1, differences = 1
184s mode: integer, lag = 1, differences = 2
184s mode: integer, lag = 1, differences = 3
184s mode: integer, lag = 2, differences = 1
184s mode: integer, lag = 2, differences = 2
184s mode: integer, lag = 2, differences = 3
184s mode: integer, lag = 3, differences = 1
184s mode: integer, lag = 3, differences = 2
184s mode: integer, lag = 3, differences = 3
184s mode: integer, lag = 4, differences = 1
184s mode: integer, lag = 4, differences = 2
184s mode: integer, lag = 4, differences = 3
184s mode: double
184s add_na = FALSE
184s  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 ...
184s mode: double, lag = 1, differences = 1
184s mode: double, lag = 1, differences = 2
184s mode: double, lag = 1, differences = 3
184s mode: double, lag = 2, differences = 1
184s mode: double, lag = 2, differences = 2
184s mode: double, lag = 2, differences = 3
184s mode: double, lag = 3, differences = 1
184s mode: double, lag = 3, differences = 2
184s mode: double, lag = 3, differences = 3
184s mode: double, lag = 4, differences = 1
184s mode: double, lag = 4, differences = 2
184s mode: double, lag = 4, differences = 3
184s mode: double, lag = 1, differences = 1
184s mode: double, lag = 1, differences = 2
184s mode: double, lag = 1, differences = 3
184s mode: double, lag = 2, differences = 1
184s mode: double, lag = 2, differences = 2
184s mode: double, lag = 2, differences = 3
184s mode: double, lag = 3, differences = 1
184s mode: double, lag = 3, differences = 2
184s mode: double, lag = 3, differences = 3
184s mode: double, lag = 4, differences = 1
184s mode: double, lag = 4, differences = 2
184s mode: double, lag = 4, differences = 3
184s mode: double, lag = 1, differences = 1
184s mode: double, lag = 1, differences = 2
184s mode: double, lag = 1, differences = 3
184s mode: double, lag = 2, differences = 1
184s mode: double, lag = 2, differences = 2
184s mode: double, lag = 2, differences = 3
184s mode: double, lag = 3, differences = 1
184s mode: double, lag = 3, differences = 2
184s mode: double, lag = 3, differences = 3
184s mode: double, lag = 4, differences = 1
184s mode: double, lag = 4, differences = 2
184s mode: double, lag = 4, differences = 3
184s mode: double, lag = 1, differences = 1
184s mode: double, lag = 1, differences = 2
184s mode: double, lag = 1, differences = 3
184s mode: double, lag = 2, differences = 1
184s mode: double, lag = 2, differences = 2
184s mode: double, lag = 2, differences = 3
184s mode: double, lag = 3, differences = 1
184s mode: double, lag = 3, differences = 2
184s mode: double, lag = 3, differences = 3
184s mode: double, lag = 4, differences = 1
184s mode: double, lag = 4, differences = 2
184s mode: double, lag = 4, differences = 3
184s add_na = TRUE
184s  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 ...
184s mode: double, lag = 1, differences = 1
184s mode: double, lag = 1, differences = 2
184s mode: double, lag = 1, differences = 3
184s mode: double, lag = 2, differences = 1
184s mode: double, lag = 2, differences = 2
184s mode: double, lag = 2, differences = 3
184s mode: double, lag = 3, differences = 1
184s mode: double, lag = 3, differences = 2
184s mode: double, lag = 3, differences = 3
184s mode: double, lag = 4, differences = 1
184s mode: double, lag = 4, differences = 2
184s mode: double, lag = 4, differences = 3
184s mode: double, lag = 1, differences = 1
184s mode: double, lag = 1, differences = 2
184s mode: double, lag = 1, differences = 3
184s mode: double, lag = 2, differences = 1
184s mode: double, lag = 2, differences = 2
184s mode: double, lag = 2, differences = 3
184s mode: double, lag = 3, differences = 1
184s mode: double, lag = 3, differences = 2
184s mode: double, lag = 3, differences = 3
184s mode: double, lag = 4, differences = 1
184s mode: double, lag = 4, differences = 2
184s mode: double, lag = 4, differences = 3
184s mode: double, lag = 1, differences = 1
184s mode: double, lag = 1, differences = 2
184s mode: double, lag = 1, differences = 3
184s mode: double, lag = 2, differences = 1
184s mode: double, lag = 2, differences = 2
184s mode: double, lag = 2, differences = 3
184s mode: double, lag = 3, differences = 1
184s mode: double, lag = 3, differences = 2
184s mode: double, lag = 3, differences = 3
184s mode: double, lag = 4, differences = 1
184s mode: double, lag = 4, differences = 2
184s mode: double, lag = 4, differences = 3
184s mode: double, lag = 1, differences = 1
184s mode: double, lag = 1, differences = 2
184s mode: double, lag = 1, differences = 3
184s mode: double, lag = 2, differences = 1
184s mode: double, lag = 2, differences = 2
184s mode: double, lag = 2, differences = 3
184s mode: double, lag = 3, differences = 1
184s mode: double, lag = 3, differences = 2
184s mode: double, lag = 3, differences = 3
184s mode: double, lag = 4, differences = 1
184s mode: double, lag = 4, differences = 2
184s mode: double, lag = 4, differences = 3
184s > 
184s > 
184s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
184s > # All NAs
184s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
184s > for (mode in c("integer", "double")) {
184s +   cat("mode: ", mode, "\n", sep = "")
184s +   x <- matrix(NA_real_, nrow = 10L, ncol = 5L)
184s +   storage.mode(x) <- mode
184s +   str(x)
184s +   
184s +   dimnames <- list(letters[1:10], LETTERS[1:5])
184s +   
184s +   # Test with and without dimnames on x
184s +   for (setDimnames in c(TRUE, FALSE)) {
184s +     if (setDimnames) dimnames(x) <- dimnames
184s +     else dimnames(x) <- NULL
184s +     # Check dimnames attribute
184s +     for (useNames in c(TRUE, FALSE)) {
184s +       r0 <- rowDiffs_R(x, useNames = useNames)
184s +       r1 <- rowDiffs(x, useNames = useNames)
184s +       r2 <- t(colDiffs(t(x), useNames = useNames))
184s +       stopifnot(all.equal(r1, r0))
184s +       stopifnot(all.equal(r2, r0))
184s +       stopifnot(all.equal(r1, r2))
184s +     } # for (useNames ...)
184s +   } # for (setDimnames ...)
184s + } # for (mode ...)
184s mode: integer
184s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
184s mode: double
184s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
184s > 
184s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
184s > # A 1x1 matrix
184s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
184s > x <- matrix(0, nrow = 1L, ncol = 1L)
184s > dimnames <- list("a", "A")
184s > # Test with and without dimnames on x
184s > for (setDimnames in c(TRUE, FALSE)) {
184s +   if (setDimnames) dimnames(x) <- dimnames
184s +   else dimnames(x) <- NULL
184s +   # Check dimnames attribute
184s +   for (useNames in c(TRUE, FALSE)) {
184s +     r0 <- rowDiffs_R(x, useNames = useNames)
184s +     r1 <- rowDiffs(x, useNames = useNames)
184s +     r2 <- t(colDiffs(t(x), useNames = useNames))
184s +     stopifnot(all.equal(r1, r0))
184s +     stopifnot(all.equal(r2, r0))
184s +     stopifnot(all.equal(r1, r2))
184s +   } # for (useNames ...)
184s + } # for (setDimnames ...)
184s > 
184s 
184s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
184s Copyright (C) 2025 The R Foundation for Statistical Computing
184s Platform: x86_64-pc-linux-gnu
184s 
184s R is free software and comes with ABSOLUTELY NO WARRANTY.
184s You are welcome to redistribute it under certain conditions.
184s Type 'license()' or 'licence()' for distribution details.
184s 
184s R is a collaborative project with many contributors.
184s Type 'contributors()' for more information and
184s 'citation()' on how to cite R or R packages in publications.
184s 
184s Type 'demo()' for some demos, 'help()' for on-line help, or
184s 'help.start()' for an HTML browser interface to help.
184s Type 'q()' to quit R.
184s 
184s > library("matrixStats")
184s > 
184s > rowDiffs_R <- function(x, lag = 1L, differences = 1L, ..., useNames = TRUE) {
184s +   ncol2 <- ncol(x) - lag * differences
184s +   if (ncol2 <= 0) {
184s +     y <- matrix(x[integer(0L)], nrow = nrow(x), ncol = 0L)
184s +     # Preserve names attribute
184s +     if (useNames && !is.null(rownames(x))) rownames(y) <- rownames(x)
184s +     return(y)
184s +   }
184s +   suppressWarnings({
184s +     y <- apply(x, MARGIN = 1L, FUN = diff, lag = lag, differences = differences)
184s +   })
184s +   y <- t(y)
184s +   
184s +   # Preserve dimnames attribute
184s +   dim(y) <- c(nrow(x), ncol2)
184s +   if (useNames && !is.null(dimnames(x))) {
184s +     colnames <- colnames(x)
184s +     if (!is.null(colnames)) {
184s +       len <- length(colnames)
184s +       colnames <- colnames[(len - ncol2 + 1):len]
184s +     }
184s +     dimnames(y) <- list(rownames(x), colnames)      
184s +   }
184s +   else dimnames(y) <- NULL
184s +   
184s +   y
184s + }
184s > 
184s > 
184s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
184s > # Subsetted tests
184s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
184s > source("utils/validateIndicesFramework.R")
184s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
184s > storage.mode(x) <- "integer"
184s > 
184s > # To check dimnames attribute
184s > dimnames <- list(letters[1:6], LETTERS[1:6])
184s > 
184s > # Test with and without dimnames on x
184s > for (setDimnames in c(TRUE, FALSE)) {
184s +   if (setDimnames) dimnames(x) <- dimnames
184s +   else dimnames(x) <- NULL
184s + 
184s +   count <- 0L
184s +   for (rows in index_cases) {
184s +     for (cols in index_cases) {
184s +       count <- count + 1L
184s +       for (lag in 1:2) {
184s +         for (differences in 1:3) {
184s +           # Check dimnames attribute
184s +           useNames <- c(TRUE, FALSE)
184s +           useNames <- useNames[count %% length(useNames) + 1]
184s +           validateIndicesTestMatrix(x, rows, cols,
184s +                                     ftest = rowDiffs, fsure = rowDiffs_R,
184s +                                     lag = lag, differences = differences, useNames = useNames)
184s +           validateIndicesTestMatrix(x, rows, cols,
184s +                                     ftest = function(x, rows, cols, ..., useNames) {
184s +             t(colDiffs(t(x), rows = cols, cols = rows, ..., useNames = useNames))
184s +                                     }, fsure = rowDiffs_R,
184s +                                     lag = lag, differences = differences, useNames = useNames)
184s +         }
184s +       }
184s +     }
184s +   }
184s + }
185s > 
185s 
185s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
185s Copyright (C) 2025 The R Foundation for Statistical Computing
185s Platform: x86_64-pc-linux-gnu
185s 
185s R is free software and comes with ABSOLUTELY NO WARRANTY.
185s You are welcome to redistribute it under certain conditions.
185s Type 'license()' or 'licence()' for distribution details.
185s 
185s R is a collaborative project with many contributors.
185s Type 'contributors()' for more information and
185s 'citation()' on how to cite R or R packages in publications.
185s 
185s Type 'demo()' for some demos, 'help()' for on-line help, or
185s 'help.start()' for an HTML browser interface to help.
185s Type 'q()' to quit R.
185s 
185s > library("matrixStats")
185s > 
185s > rowIQRs_R <- function(x, na.rm = FALSE, ..., useNames = TRUE) {
185s +   quantile_na <- function(x, ..., na.rm = FALSE) {
185s +     if (!na.rm && anyMissing(x))
185s +       return(c(NA_real_, NA_real_))
185s +     quantile(x, ..., na.rm = na.rm)
185s +   }
185s +   q <- apply(x, MARGIN = 1L, FUN = quantile_na,
185s +              probs = c(0.25, 0.75), na.rm = na.rm)
185s +   rownames(q) <- NULL # Not needed anymore
185s +   
185s +   # Preserve names attribute
185s +   dim(q) <- c(2L, nrow(x))
185s +   colnames(q) <- if (useNames) rownames(x) else NULL
185s +   
185s +   q[2L, , drop = TRUE] - q[1L, , drop = TRUE]
185s + }
185s > 
185s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
185s > # Test with multiple quantiles
185s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
185s > for (mode in c("integer", "double")) {
185s +   cat("mode: ", mode, "\n", sep = "")
185s +   x <- matrix(1:100 + 0.1, nrow = 10, ncol = 10)
185s +   storage.mode(x) <- mode
185s +   str(x)
185s +   
185s +   # To check names attribute
185s +   dimnames <- list(letters[1:10], LETTERS[1:10])
185s + 
185s +   for (add_na in c(FALSE, TRUE)) {
185s +     if (add_na) {
185s +       x[3:5, 6:9] <- NA
185s +     }
185s +     # Test with and without dimnames on x
185s +     for (setDimnames in c(TRUE, FALSE)) {
185s +       if (setDimnames) dimnames(x) <- dimnames
185s +       else dimnames(x) <- NULL
185s +       for (na.rm in c(FALSE, TRUE)) {
185s +         # Check names attribute
185s +         for (useNames in c(TRUE, FALSE)) {
185s +           probs <- c(0, 0.5, 1)
185s +           q0 <- rowIQRs_R(x, na.rm = na.rm, useNames = useNames)
185s +           print(q0)
185s +           q1 <- rowIQRs(x, na.rm = na.rm, useNames = useNames)
185s +           print(q1)
185s +           stopifnot(all.equal(q1, q0))
185s +           q2 <- colIQRs(t(x), na.rm = na.rm, useNames = useNames)
185s +           stopifnot(all.equal(q2, q0))
185s +           
185s +           q <- iqr(x[3, ], na.rm = na.rm)
185s +           print(q)
185s +         } # for (useNames ...)
185s +       } # for (na.rm ...)
185s +     } # for (setDimnames ...)
185s +   } # for (add_na ...)
185s + } # for (mode ...)
185s mode: integer
185s  int [1:10, 1:10] 1 2 3 4 5 6 7 8 9 10 ...
185s  a  b  c  d  e  f  g  h  i  j 
185s 45 45 45 45 45 45 45 45 45 45 
185s  a  b  c  d  e  f  g  h  i  j 
185s 45 45 45 45 45 45 45 45 45 45 
185s [1] 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s [1] 45
185s  a  b  c  d  e  f  g  h  i  j 
185s 45 45 45 45 45 45 45 45 45 45 
185s  a  b  c  d  e  f  g  h  i  j 
185s 45 45 45 45 45 45 45 45 45 45 
185s [1] 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s [1] 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s [1] 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s [1] 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s [1] 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s [1] 45
185s  a  b  c  d  e  f  g  h  i  j 
185s 45 45 NA NA NA 45 45 45 45 45 
185s  a  b  c  d  e  f  g  h  i  j 
185s 45 45 NA NA NA 45 45 45 45 45 
185s [1] NA
185s  [1] 45 45 NA NA NA 45 45 45 45 45
185s  [1] 45 45 NA NA NA 45 45 45 45 45
185s [1] NA
185s  a  b  c  d  e  f  g  h  i  j 
185s 45 45 25 25 25 45 45 45 45 45 
185s  a  b  c  d  e  f  g  h  i  j 
185s 45 45 25 25 25 45 45 45 45 45 
185s [1] 25
185s  [1] 45 45 25 25 25 45 45 45 45 45
185s  [1] 45 45 25 25 25 45 45 45 45 45
185s [1] 25
185s  [1] 45 45 NA NA NA 45 45 45 45 45
185s  [1] 45 45 NA NA NA 45 45 45 45 45
185s [1] NA
185s  [1] 45 45 NA NA NA 45 45 45 45 45
185s  [1] 45 45 NA NA NA 45 45 45 45 45
185s [1] NA
185s  [1] 45 45 25 25 25 45 45 45 45 45
185s  [1] 45 45 25 25 25 45 45 45 45 45
185s [1] 25
185s  [1] 45 45 25 25 25 45 45 45 45 45
185s  [1] 45 45 25 25 25 45 45 45 45 45
185s [1] 25
185s mode: double
185s  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 ...
185s  a  b  c  d  e  f  g  h  i  j 
185s 45 45 45 45 45 45 45 45 45 45 
185s  a  b  c  d  e  f  g  h  i  j 
185s 45 45 45 45 45 45 45 45 45 45 
185s [1] 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s [1] 45
185s  a  b  c  d  e  f  g  h  i  j 
185s 45 45 45 45 45 45 45 45 45 45 
185s  a  b  c  d  e  f  g  h  i  j 
185s 45 45 45 45 45 45 45 45 45 45 
185s [1] 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s [1] 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s [1] 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s [1] 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s [1] 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s  [1] 45 45 45 45 45 45 45 45 45 45
185s [1] 45
185s  a  b  c  d  e  f  g  h  i  j 
185s 45 45 NA NA NA 45 45 45 45 45 
185s  a  b  c  d  e  f  g  h  i  j 
185s 45 45 NA NA NA 45 45 45 45 45 
185s [1] NA
185s  [1] 45 45 NA NA NA 45 45 45 45 45
185s  [1] 45 45 NA NA NA 45 45 45 45 45
185s [1] NA
185s  a  b  c  d  e  f  g  h  i  j 
185s 45 45 25 25 25 45 45 45 45 45 
185s  a  b  c  d  e  f  g  h  i  j 
185s 45 45 25 25 25 45 45 45 45 45 
185s [1] 25
185s  [1] 45 45 25 25 25 45 45 45 45 45
185s  [1] 45 45 25 25 25 45 45 45 45 45
185s [1] 25
185s  [1] 45 45 NA NA NA 45 45 45 45 45
185s  [1] 45 45 NA NA NA 45 45 45 45 45
185s [1] NA
185s  [1] 45 45 NA NA NA 45 45 45 45 45
185s  [1] 45 45 NA NA NA 45 45 45 45 45
185s [1] NA
185s  [1] 45 45 25 25 25 45 45 45 45 45
185s  [1] 45 45 25 25 25 45 45 45 45 45
185s [1] 25
185s  [1] 45 45 25 25 25 45 45 45 45 45
185s  [1] 45 45 25 25 25 45 45 45 45 45
185s [1] 25
185s > 
185s > 
185s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
185s > # Test corner cases
185s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
185s > for (mode in c("integer", "double")) {
185s +   cat("mode: ", mode, "\n", sep = "")
185s +   # Empty vectors
185s +   x <- integer(0L)
185s +   storage.mode(x) <- mode
185s +   str(x)
185s +   q <- iqr(x)
185s +   print(q)
185s +   stopifnot(identical(q, NA_real_))
185s + 
185s +   # Scalar
185s +   x <- 1L
185s +   storage.mode(x) <- mode
185s +   str(x)
185s +   q <- iqr(x)
185s +   str(q)
185s +   stopifnot(identical(q, 0))
185s + }
185s mode: integer
185s  int(0) 
185s [1] NA
185s  int 1
185s  num 0
185s mode: double
185s  num(0) 
185s [1] NA
185s  num 1
185s  num 0
185s > 
185s > 
185s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
185s > # Single row matrices
185s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
185s > x <- matrix(1, nrow = 1L, ncol = 2L)
185s > dimnames <- list("a",  LETTERS[1:2])
185s > # Test with and without dimnames on x
185s > for (setDimnames in c(TRUE, FALSE)) {
185s +   if (setDimnames) dimnames(x) <- dimnames
185s +   else dimnames(x) <- NULL
185s +   # Check names attribute
185s +   for (useNames in c(TRUE, FALSE)) {
185s +     q0 <- rowIQRs_R(x, useNames = useNames)
185s +     q1 <- rowIQRs(x, useNames = useNames)
185s +     q2 <- colIQRs(t(x), useNames = useNames)
185s +     stopifnot(all.equal(q0, q1))
185s +     stopifnot(all.equal(q0, q2))
185s +   }
185s + }
185s > 
185s > x <- matrix(1, nrow = 2L, ncol = 1L)
185s > q <- colIQRs(x)
185s > stopifnot(identical(q, 0))
185s > 
185s 
185s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
185s Copyright (C) 2025 The R Foundation for Statistical Computing
185s Platform: x86_64-pc-linux-gnu
185s 
185s R is free software and comes with ABSOLUTELY NO WARRANTY.
185s You are welcome to redistribute it under certain conditions.
185s Type 'license()' or 'licence()' for distribution details.
185s 
185s R is a collaborative project with many contributors.
185s Type 'contributors()' for more information and
185s 'citation()' on how to cite R or R packages in publications.
185s 
185s Type 'demo()' for some demos, 'help()' for on-line help, or
185s 'help.start()' for an HTML browser interface to help.
185s Type 'q()' to quit R.
185s 
185s > library("matrixStats")
185s > 
185s > rowIQRs_R <- function(x, na.rm = FALSE, ..., useNames = TRUE) {
185s +   quantile_na <- function(x, ..., na.rm = FALSE) {
185s +     if (!na.rm && anyMissing(x))
185s +       return(c(NA_real_, NA_real_))
185s +     quantile(x, ..., na.rm = na.rm)
185s +   }
185s +   q <- apply(x, MARGIN = 1L, FUN = quantile_na,
185s +              probs = c(0.25, 0.75), na.rm = na.rm)
185s +   rownames(q) <- NULL # Not needed anymore
185s +   
185s +   # Preserve names attribute
185s +   dim(q) <- c(2L, nrow(x))
185s +   colnames(q) <- if (useNames) rownames(x) else NULL
185s +   
185s +   q[2L, , drop = TRUE] - q[1L, , drop = TRUE]
185s + }
185s > 
185s > 
185s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
185s > # Subsetted tests
185s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
185s > source("utils/validateIndicesFramework.R")
185s > x <- runif(6, min = -6, max = 6)
185s > for (idxs in index_cases) {
185s +   for (na.rm in c(TRUE, FALSE)) {
185s +     validateIndicesTestVector(x, idxs, ftest = iqr, fsure = function(x, na.rm) {
185s +       dim(x) <- c(1L, length(x))
185s +       rowIQRs_R(x, na.rm = na.rm)
185s +     }, na.rm = na.rm)
185s +   }
185s + }
185s > 
185s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
185s > 
185s > # To check names attribute
185s > dimnames <- list(letters[1:6], LETTERS[1:6])
185s > 
185s > # Test with and without dimnames on x
185s > for (setDimnames in c(TRUE, FALSE)) {
185s +   if (setDimnames) dimnames(x) <- dimnames
185s +   else dimnames(x) <- NULL
185s +   
185s +   count <- 0L
185s +   for (rows in index_cases) {
185s +     for (cols in index_cases) {
185s +       count <- count + 1L
185s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
185s +       useNames <- c(TRUE, FALSE)
185s +       useNames <- useNames[count %% length(useNames) + 1]
185s +       
185s +       validateIndicesTestMatrix(x, rows, cols,
185s +                                 ftest = rowIQRs, fsure = rowIQRs_R,
185s +                                 na.rm = na.rm, useNames = useNames)
185s +       validateIndicesTestMatrix(x, rows, cols,
185s +                                 fcoltest = colIQRs, fsure = rowIQRs_R,
185s +                                 na.rm = na.rm, useNames = useNames)
185s +     }
185s +   }
185s + }
186s > 
186s 
186s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
186s Copyright (C) 2025 The R Foundation for Statistical Computing
186s Platform: x86_64-pc-linux-gnu
186s 
186s R is free software and comes with ABSOLUTELY NO WARRANTY.
186s You are welcome to redistribute it under certain conditions.
186s Type 'license()' or 'licence()' for distribution details.
186s 
186s R is a collaborative project with many contributors.
186s Type 'contributors()' for more information and
186s 'citation()' on how to cite R or R packages in publications.
186s 
186s Type 'demo()' for some demos, 'help()' for on-line help, or
186s 'help.start()' for an HTML browser interface to help.
186s Type 'q()' to quit R.
186s 
186s > # Test inspired by the harmonic mean example in R-help
186s > # thread '[R] Beyond double-precision?' on May 9, 2009.
186s > 
186s > library("matrixStats")
186s > library("stats")
186s > 
186s > logSumExp0 <- function(lx) {
186s +   idx_max <- which.max(lx)
186s +   log1p(sum(exp(lx[-idx_max] - lx[idx_max]))) + lx[idx_max]
186s + }
186s > 
186s > n <- 200L
186s > set.seed(1)
186s > 
186s > for (mode in c("integer", "double")) {
186s +   cat("mode: ", mode, "\n", sep = "")
186s +   x <- matrix(runif(n, min = 1.0, max = 3.0), nrow = 20L)
186s +   storage.mode(x) <- mode
186s +   str(x)
186s + 
186s +   # The logarithm of the harmonic mean by rows
186s +   y_h <- log(1 / rowMeans(1 / x))
186s +   str(y_h)
186s + 
186s +   lx_neg <- -log(x)
186s + 
186s +   y0 <- log(ncol(x)) - apply(lx_neg, MARGIN = 1L, FUN = logSumExp0)
186s +   stopifnot(all.equal(y0, y_h))
186s + 
186s +   y1 <- log(ncol(x)) - apply(lx_neg, MARGIN = 1L, FUN = logSumExp)
186s +   stopifnot(all.equal(y1, y0))
186s + 
186s +   y2 <- log(ncol(x)) - rowLogSumExps(lx_neg)
186s +   stopifnot(all.equal(y2, y0))
186s + 
186s +   y3 <- log(ncol(x)) - colLogSumExps(t(lx_neg))
186s +   stopifnot(all.equal(y3, y0))
186s + 
186s + 
186s +   # The logarithm of the harmonic mean by columns
186s +   y_h <- log(1 / colMeans(1 / x))
186s +   str(y_h)
186s + 
186s +   y0 <- log(nrow(x)) - apply(lx_neg, MARGIN = 2L, FUN = logSumExp0)
186s +   stopifnot(all.equal(y0, y_h))
186s + 
186s +   y1 <- log(nrow(x)) - apply(lx_neg, MARGIN = 2L, FUN = logSumExp)
186s +   stopifnot(all.equal(y1, y0))
186s + 
186s +   y2 <- log(nrow(x)) - colLogSumExps(lx_neg)
186s +   stopifnot(all.equal(y2, y0))
186s + 
186s +   y3 <- log(nrow(x)) - rowLogSumExps(t(lx_neg))
186s +   stopifnot(all.equal(y3, y0))
186s + 
186s +   # Testing names
186s +   rownames(lx_neg) <- seq_len(nrow(x))
186s +   colnames(lx_neg) <- seq_len(ncol(x))
186s +   y2 <- rowLogSumExps(lx_neg, useNames = TRUE)
186s +   stopifnot(identical(names(y2), rownames(lx_neg)))
186s +   y3 <- colLogSumExps(t(lx_neg), useNames = TRUE)
186s +   stopifnot(identical(names(y3), rownames(lx_neg)))
186s + } # for (mode ...)
186s mode: integer
186s  int [1:20, 1:10] 1 1 2 2 1 2 2 2 2 1 ...
186s  num [1:20] 0.357 0.223 0.223 0.288 0.511 ...
186s  num [1:10] 0.322 0.223 0.322 0.255 0.255 ...
186s mode: double
186s  num [1:20, 1:10] 1.54 1.44 2.03 1.54 1.36 ...
186s  num [1:20] 0.526 0.466 0.734 0.638 0.604 ...
186s  num [1:10] 0.627 0.582 0.617 0.474 0.418 ...
186s > 
186s > 
186s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
186s > # Corner cases
186s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
186s > ## Zero-size matrices
186s > lx <- matrix(numeric(0L), nrow = 0L, ncol = 0L)
186s > y <- rowLogSumExps(lx)
186s > print(y)
186s numeric(0)
186s > stopifnot(length(y) == nrow(lx))
186s > 
186s > y <- colLogSumExps(lx)
186s > print(y)
186s numeric(0)
186s > stopifnot(length(y) == ncol(lx))
186s > 
186s > ## Zero-height matrices
186s > lx <- matrix(numeric(0L), nrow = 0L, ncol = 5L)
186s > y <- rowLogSumExps(lx)
186s > print(y)
186s numeric(0)
186s > stopifnot(length(y) == nrow(lx))
186s > 
186s > y <- colLogSumExps(lx)
186s > print(y)
186s [1] -Inf -Inf -Inf -Inf -Inf
186s > stopifnot(length(y) == ncol(lx))
186s > stopifnot(all(y == -Inf))
186s > 
186s > ## Zero-width matrices
186s > lx <- matrix(numeric(0L), nrow = 5L, ncol = 0L)
186s > y <- colLogSumExps(lx)
186s > print(y)
186s numeric(0)
186s > stopifnot(length(y) == ncol(lx))
186s > 
186s > y <- rowLogSumExps(lx)
186s > print(y)
186s [1] -Inf -Inf -Inf -Inf -Inf
186s > stopifnot(length(y) == nrow(lx))
186s > stopifnot(all(y == -Inf))
186s > 
186s > 
186s > ## Matrices with one element
186s > lx <- matrix(1.0, nrow = 1L, ncol = 1L)
186s > y <- rowLogSumExps(lx)
186s > print(y)
186s [1] 1
186s > stopifnot(length(y) == nrow(lx))
186s > stopifnot(all(y == lx))
186s > 
186s > y <- colLogSumExps(lx)
186s > print(y)
186s [1] 1
186s > stopifnot(length(y) == ncol(lx))
186s > stopifnot(all(y == lx))
186s > 
186s > ## All missing values
186s > lx <- matrix(NA_real_, nrow = 1L, ncol = 1L)
186s > y <- rowLogSumExps(lx, na.rm = TRUE)
186s > print(y)
186s [1] -Inf
186s > stopifnot(length(y) == nrow(lx))
186s > stopifnot(identical(y, -Inf))
186s > 
186s > lx <- matrix(NA_real_, nrow = 1L, ncol = 1L)
186s > y <- colLogSumExps(lx, na.rm = TRUE)
186s > print(y)
186s [1] -Inf
186s > stopifnot(length(y) == ncol(lx))
186s > stopifnot(identical(y, -Inf))
186s > 
186s > lx <- matrix(NA_real_, nrow = 2L, ncol = 2L)
186s > y <- rowLogSumExps(lx, na.rm = TRUE)
186s > print(y)
186s [1] -Inf -Inf
186s > stopifnot(length(y) == nrow(lx))
186s > stopifnot(all(y == -Inf))
186s > 
186s > y <- rowLogSumExps(lx, na.rm = FALSE)
186s > print(y)
186s [1] NA NA
186s > stopifnot(length(y) == nrow(lx))
186s > stopifnot(all(is.na(y) & !is.nan(y)))
186s > 
186s > lx <- matrix(NA_real_, nrow = 2L, ncol = 2L)
186s > y <- colLogSumExps(lx, na.rm = TRUE)
186s > print(y)
186s [1] -Inf -Inf
186s > stopifnot(length(y) == ncol(lx))
186s > stopifnot(all(y == -Inf))
186s > 
186s > y <- colLogSumExps(lx, na.rm = FALSE)
186s > print(y)
186s [1] NA NA
186s > stopifnot(length(y) == ncol(lx))
186s > stopifnot(all(is.na(y) & !is.nan(y)))
186s > 
186s > ## +Inf values
186s > lx <- matrix(c(1, 2, +Inf), nrow = 3L, ncol = 2L)
186s > y <- colLogSumExps(lx, na.rm = TRUE)
186s > print(y)
186s [1] Inf Inf
186s > stopifnot(length(y) == ncol(lx))
186s > stopifnot(all(y == +Inf))
186s > 
186s > ## multiple -Inf values
186s > lx <- matrix(c(-Inf, -Inf), nrow = 2L, ncol = 3L)
186s > y <- rowLogSumExps(lx)
186s > print(y)
186s [1] -Inf -Inf
186s > stopifnot(length(y) == nrow(lx))
186s > stopifnot(all(y == -Inf))
186s > 
186s > lx <- matrix(c(-Inf, 5, -Inf), nrow = 2L, ncol = 3L, byrow = TRUE)
186s > y <- rowLogSumExps(lx)
186s > print(y)
186s [1] 5 5
186s > stopifnot(length(y) == nrow(lx))
186s > stopifnot(all(y == 5))
186s > 
186s > ## Bug report #104 (https://github.com/HenrikBengtsson/matrixStats/issues/104)
186s > ## (This would core dump on Windows)
186s > x <- matrix(0.0, nrow = 2L, ncol = 32762L)
186s > y <- colLogSumExps(x)
186s > str(y)
186s  num [1:32762] 0.693 0.693 0.693 0.693 0.693 ...
186s > 
186s > ## Bug report #120 (https://github.com/HenrikBengtsson/matrixStats/issues/120)
186s > ## (This would error if x had rownames/colnames and non-NULL rows/cols were
186s > ## used)
186s > x <- matrix(runif(6), nrow = 2L, ncol = 3L,
186s +             dimnames = list(c("A", "B"), c("a", "b", "c")))
186s > y <- colLogSumExps(x, cols = 3:1, useNames = TRUE)
186s > stopifnot(names(y) == c("c", "b", "a"))
186s > y <- rowLogSumExps(x, rows = 2, useNames = TRUE)
186s > stopifnot(names(y) == "B")
186s > 
186s > 
186s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
186s > # Check names attributes
186s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
186s > 
186s > ## Create isFALSE() if running on an old version of R
186s > if (!exists("isFALSE", mode="function")) {
186s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
186s + }
186s > 
186s > rowLogSumExps_R <- function(x, ..., useNames = TRUE) {
186s +   res <- apply(x, MARGIN = 1L, FUN = function(rx, ...) {
186s +     log(sum(exp(rx), ...))
186s +   }, ...)
186s +   if (isFALSE(useNames)) names(res) <- NULL
186s +   res
186s + }
186s > 
186s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6L, ncol = 6L)
186s > 
186s > # To check names attribute
186s > dimnames <- list(letters[1:6], LETTERS[1:6])
186s > 
186s > # Test with and without dimnames on x
186s > for (setDimnames in c(TRUE, FALSE)) {
186s +   if (setDimnames) dimnames(x) <- dimnames
186s +   else dimnames(x) <- NULL
186s +   for (useNames in c(TRUE, FALSE)) {
186s +     y0 <- rowLogSumExps_R(x, useNames = useNames)
186s +     y1 <- rowLogSumExps(x, useNames = useNames)
186s +     y2 <- colLogSumExps(t(x), useNames = useNames)
186s +     stopifnot(all.equal(y1, y0))
186s +     stopifnot(all.equal(y2, y0))
186s +   }
186s + }
186s > 
186s 
186s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
186s Copyright (C) 2025 The R Foundation for Statistical Computing
186s Platform: x86_64-pc-linux-gnu
186s 
186s R is free software and comes with ABSOLUTELY NO WARRANTY.
186s You are welcome to redistribute it under certain conditions.
186s Type 'license()' or 'licence()' for distribution details.
186s 
186s R is a collaborative project with many contributors.
186s Type 'contributors()' for more information and
186s 'citation()' on how to cite R or R packages in publications.
186s 
186s Type 'demo()' for some demos, 'help()' for on-line help, or
186s 'help.start()' for an HTML browser interface to help.
186s Type 'q()' to quit R.
186s 
186s > library("matrixStats")
186s > 
186s > ## Create isFALSE() if running on an old version of R
186s > if (!exists("isFALSE", mode="function")) {
186s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
186s + }
186s > 
186s > rowLogSumExps_R <- function(x, ..., useNames = TRUE) {
186s +   res <- apply(x, MARGIN = 1L, FUN = function(rx, ...) {
186s +     log(sum(exp(rx), ...))
186s +   }, ...)
186s +   if (isFALSE(useNames)) names(res) <- NULL
186s +   res
186s + }
186s > 
186s > 
186s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
186s > # Subsetted tests
186s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
186s > source("utils/validateIndicesFramework.R")
186s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
186s > 
186s > # To check names attribute
186s > dimnames <- list(letters[1:6], LETTERS[1:6])
186s > 
186s > # Test with and without dimnames on x
186s > for (setDimnames in c(TRUE, FALSE)) {
186s +   if (setDimnames) dimnames(x) <- dimnames
186s +   else dimnames(x) <- NULL
186s +   for (rows in index_cases) {
186s +     for (cols in index_cases) {
186s +       for (na.rm in c(TRUE, FALSE)) {
186s +         for (useNames in c(TRUE, FALSE)) {
186s +           validateIndicesTestMatrix(x, rows, cols,
186s +                                     ftest = rowLogSumExps,
186s +                                     fsure = rowLogSumExps_R,
186s +                                     na.rm = na.rm, useNames = useNames)
186s +           validateIndicesTestMatrix(x, rows, cols,
186s +                                     fcoltest = colLogSumExps,
186s +                                     fsure = rowLogSumExps_R,
186s +                                     na.rm = na.rm, useNames = useNames)
186s +         }
186s +       }
186s +     }
186s +   }
186s + }
187s > 
187s 
187s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
187s Copyright (C) 2025 The R Foundation for Statistical Computing
187s Platform: x86_64-pc-linux-gnu
187s 
187s R is free software and comes with ABSOLUTELY NO WARRANTY.
187s You are welcome to redistribute it under certain conditions.
187s Type 'license()' or 'licence()' for distribution details.
187s 
187s R is a collaborative project with many contributors.
187s Type 'contributors()' for more information and
187s 'citation()' on how to cite R or R packages in publications.
187s 
187s Type 'demo()' for some demos, 'help()' for on-line help, or
187s 'help.start()' for an HTML browser interface to help.
187s Type 'q()' to quit R.
187s 
187s > library("matrixStats")
187s > 
187s > ## Always allow testing of the 'center' argument (as long as it's not defunct)
187s > options(matrixStats.center.onUse = "ignore")
187s > 
187s > rowMads_R <- function(x, na.rm = FALSE, ..., useNames = TRUE) {
187s +   suppressWarnings({
187s +     res <- apply(x, MARGIN = 1L, FUN = mad, na.rm = na.rm)
187s +   })
187s +   if (!useNames) names(res) <- NULL
187s +   res
187s + }
187s > 
187s > colMads_R <- function(x, na.rm = FALSE, ..., useNames = TRUE) {
187s +   suppressWarnings({
187s +     res <- apply(x, MARGIN = 2L, FUN = mad, na.rm = na.rm)
187s +   })
187s +   if (!useNames) names(res) <- NULL
187s +   res
187s + }
187s > 
187s > rowMads_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = TRUE) {
187s +   center <- rowMedians(x, cols = cols, na.rm = na.rm, useNames = FALSE)
187s +   rowMads(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
187s + }
187s > 
187s > colMads_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = TRUE) {
187s +   center <- colMedians(x, rows = rows, na.rm = na.rm, useNames = FALSE)
187s +   colMads(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
187s + }
187s > 
187s > 
187s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
187s > # A 3x3 matrix (no ties)
187s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
187s > for (mode in c("integer", "double")) {
187s +   x <- matrix(c(1, 2, 3, 2, 3, 4, 3, 4, 5) + 0.1, nrow = 3, ncol = 3)
187s +   cat("mode: ", mode, "\n", sep = "")
187s +   storage.mode(x) <- mode
187s +   str(x)
187s +   
187s +   # To check name attribute
187s +   dimnames <- list(letters[1:3], LETTERS[1:3])
187s +   
187s +   # Test with and without dimnames on x
187s +   for (setDimnames in c(TRUE, FALSE)) {
187s +     if (setDimnames) dimnames(x) <- dimnames
187s +     else dimnames(x) <- NULL
187s +     tx <- t(x)
187s +     # Check names attribute
187s +     for (useNames in c(TRUE, FALSE)) {
187s +       cat("rowMads():\n")
187s +       center <- rowMedians(x, na.rm = TRUE, useNames = useNames)
187s +       r0 <- rowMads_R(x, na.rm = TRUE, useNames = useNames)
187s +       r1 <- rowMads(x, na.rm = TRUE, useNames = useNames)
187s +       r1b <- rowMads_center(x, na.rm = TRUE, useNames = useNames)
187s +       r1c <- rowMads(x, center = center, na.rm = TRUE, useNames = useNames)
187s +       r2 <- colMads(tx, na.rm = TRUE, useNames = useNames)
187s +       r2b <- colMads_center(tx, na.rm = TRUE, useNames = useNames)
187s +       stopifnot(all.equal(r1, r2))
187s +       stopifnot(all.equal(r1, r0))
187s +       stopifnot(all.equal(r1b, r1))
187s +       stopifnot(all.equal(r1c, r1))
187s +       stopifnot(all.equal(r2, r0))
187s +       stopifnot(all.equal(r2b, r2))
187s +       
187s +       cat("colMads():\n")
187s +       center <- colMedians(x, na.rm = TRUE, useNames = useNames)
187s +       r0 <- colMads_R(x, na.rm = TRUE, useNames = useNames)
187s +       r1 <- colMads(x, na.rm = TRUE, useNames = useNames)
187s +       r1b <- colMads_center(x, na.rm = TRUE, useNames = useNames)
187s +       r1c <- colMads(x, center = center, na.rm = TRUE, useNames = useNames)
187s +       r2 <- rowMads(tx, na.rm = TRUE, useNames = useNames)
187s +       r2b <- rowMads_center(tx, na.rm = TRUE, useNames = useNames)
187s +       stopifnot(all.equal(r1, r2))
187s +       stopifnot(all.equal(r1, r0))
187s +       stopifnot(all.equal(r1b, r1))
187s +       stopifnot(all.equal(r1c, r1))
187s +       stopifnot(all.equal(r2, r0))
187s +       stopifnot(all.equal(r2b, r2))
187s +     }
187s +   }
187s + }
187s mode: integer
187s  int [1:3, 1:3] 1 2 3 2 3 4 3 4 5
187s rowMads():
187s colMads():
187s rowMads():
187s colMads():
187s rowMads():
187s colMads():
187s rowMads():
187s colMads():
187s mode: double
187s  num [1:3, 1:3] 1.1 2.1 3.1 2.1 3.1 4.1 3.1 4.1 5.1
187s rowMads():
187s colMads():
187s rowMads():
187s colMads():
187s rowMads():
187s colMads():
187s rowMads():
187s colMads():
187s > 
187s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
187s > # Ties: a 4x4 matrix
187s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
187s > for (mode in c("integer", "double")) {
187s +   x <- matrix(c(1:4, 2:5, 3:6, 4:7) + 0.1, nrow = 4, ncol = 4)
187s +   cat("mode: ", mode, "\n", sep = "")
187s +   storage.mode(x) <- mode
187s +   str(x)
187s +   tx <- t(x)
187s +   
187s +   # To check name attribute
187s +   dimnames <- list(letters[1:4], LETTERS[1:4])
187s +   
187s +   # Test with and without dimnames on x
187s +   for (setDimnames in c(TRUE, FALSE)) {
187s +     if (setDimnames) dimnames(x) <- dimnames
187s +     else dimnames(x) <- NULL
187s +     tx <- t(x)
187s +     # Check names attribute
187s +     for (useNames in c(TRUE, FALSE)) {
187s +       cat("rowMads():\n")
187s +       r0 <- rowMads_R(x, na.rm = TRUE, useNames = useNames)
187s +       r1 <- rowMads(x, na.rm = TRUE, useNames = useNames)
187s +       r2 <- colMads(tx, na.rm = TRUE, useNames = useNames)
187s +       stopifnot(all.equal(r1, r2))
187s +       stopifnot(all.equal(r1, r0))
187s +       stopifnot(all.equal(r2, r0))
187s +       
187s +       cat("colMads():\n")
187s +       r0 <- colMads_R(x, na.rm = TRUE, useNames = useNames)
187s +       r1 <- colMads(x, na.rm = TRUE, useNames = useNames)
187s +       r2 <- rowMads(tx, na.rm = TRUE, useNames = useNames)
187s +       stopifnot(all.equal(r1, r2))
187s +       stopifnot(all.equal(r1, r0))
187s +       stopifnot(all.equal(r2, r0))
187s +     }
187s +   }
187s + }
187s mode: integer
187s  int [1:4, 1:4] 1 2 3 4 2 3 4 5 3 4 ...
187s rowMads():
187s colMads():
187s rowMads():
187s colMads():
187s rowMads():
187s colMads():
187s rowMads():
187s colMads():
187s mode: double
187s  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 ...
187s rowMads():
187s colMads():
187s rowMads():
187s colMads():
187s rowMads():
187s colMads():
187s rowMads():
187s colMads():
187s > tx <- NULL
187s > 
187s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
187s > # No ties: a 3x3 matrix with an NA value
187s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
187s > for (mode in c("integer", "double")) {
187s +   x <- matrix(c(1, 2, 3, 2, 3, 4, 3, 4, 5) + 0.1, nrow = 3, ncol = 3)
187s +   x[2, 2] <- NA_real_
187s + 
187s +   cat("mode: ", mode, "\n", sep = "")
187s +   storage.mode(x) <- mode
187s +   str(x)
187s +   tx <- t(x)
187s +   
187s +   # To check name attribute
187s +   dimnames <- list(letters[1:3], LETTERS[1:3])
187s +   
187s +   # Test with and without dimnames on x
187s +   for (setDimnames in c(TRUE, FALSE)) {
187s +     if (setDimnames) dimnames(x) <- dimnames
187s +     else dimnames(x) <- NULL
187s +     tx <- t(x)
187s +     # Check names attribute
187s +     for (useNames in c(TRUE, FALSE)) {
187s +       cat("rowMads():\n")
187s +       r0 <- rowMads_R(x, na.rm = TRUE, useNames = useNames)
187s +       r1 <- rowMads(x, na.rm = TRUE, useNames = useNames)
187s +       r2 <- colMads(tx, na.rm = TRUE, useNames = useNames)
187s +       stopifnot(all.equal(r1, r2))
187s +       stopifnot(all.equal(r1, r0))
187s +       stopifnot(all.equal(r2, r0))
187s +       
187s +       cat("colMads():\n")
187s +       r0 <- colMads_R(x, na.rm = TRUE, useNames = useNames)
187s +       r1 <- colMads(x, na.rm = TRUE, useNames = useNames)
187s +       r2 <- rowMads(tx, na.rm = TRUE, useNames = useNames)
187s +       stopifnot(all.equal(r1, r2))
187s +       stopifnot(all.equal(r1, r0))
187s +       stopifnot(all.equal(r2, r0))
187s +     }
187s +   }
187s + }
187s mode: integer
187s  int [1:3, 1:3] 1 2 3 2 NA 4 3 4 5
187s rowMads():
187s colMads():
187s rowMads():
187s colMads():
187s rowMads():
187s colMads():
187s rowMads():
187s colMads():
187s mode: double
187s  num [1:3, 1:3] 1.1 2.1 3.1 2.1 NA 4.1 3.1 4.1 5.1
187s rowMads():
187s colMads():
187s rowMads():
187s colMads():
187s rowMads():
187s colMads():
187s rowMads():
187s colMads():
187s > tx <- NULL
187s > 
187s > 
187s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
187s > # With and without some NAs
187s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
187s > for (add_na in c(FALSE, TRUE)) {
187s +   cat("add_na = ", add_na, "\n", sep = "")
187s + 
187s +   x <- matrix(1:50, nrow = 10L, ncol = 5L)
187s +   if (add_na) {
187s +     x[3:7, c(2, 4)] <- NA_real_
187s +   }
187s +   
187s +   # To check name attribute
187s +   dimnames <- list(letters[1:10], LETTERS[1:5])
187s +   
187s +   # Test with and without dimnames on x
187s +   for (setDimnames in c(TRUE, FALSE)) {
187s +     if (setDimnames) dimnames(x) <- dimnames
187s +     else dimnames(x) <- NULL
187s +     tx <- t(x)
187s +     # Row/column ranges
187s +     for (na.rm in c(FALSE, TRUE)) {
187s +       # Check names attribute
187s +       for (useNames in c(TRUE, FALSE)) {
187s +       cat("na.rm = ", na.rm, "\n", sep = "")
187s +         cat("rowMads():\n")
187s +         center <- rowMedians(x, na.rm = na.rm, useNames = useNames)
187s +         r0 <- rowMads_R(x, na.rm = na.rm, useNames = useNames)
187s +         r1 <- rowMads(x, na.rm = na.rm, useNames = useNames)
187s +         r2 <- rowMads(x, center = center, na.rm = na.rm, useNames = useNames)
187s +         r3 <- colMads(tx, na.rm = na.rm, useNames = useNames)
187s +         stopifnot(all.equal(r1, r0))
187s +         stopifnot(all.equal(r2, r0))
187s +         stopifnot(all.equal(r2, r1))
187s +         stopifnot(all.equal(r3, r0))
187s +         stopifnot(all.equal(r3, r1))
187s +         stopifnot(all.equal(r3, r2))
187s +         
187s +         cat("colMads():\n")
187s +         center <- colMedians(x, na.rm = na.rm, useNames = useNames)
187s +         r0 <- colMads_R(x, na.rm = na.rm, useNames = useNames)
187s +         r1 <- colMads(x, na.rm = na.rm, useNames = useNames)
187s +         r2 <- colMads(x, center = center, na.rm = na.rm, useNames = useNames)
187s +         r3 <- rowMads(tx, na.rm = na.rm, useNames = useNames)
187s +         stopifnot(all.equal(r1, r0))
187s +         stopifnot(all.equal(r2, r0))
187s +         stopifnot(all.equal(r2, r1))
187s +         stopifnot(all.equal(r3, r0))
187s +         stopifnot(all.equal(r3, r1))
187s +         stopifnot(all.equal(r3, r2))
187s +       }
187s +     }
187s +   }
187s +   tx <- NULL
187s + } # for (add_na ...)
187s add_na = FALSE
187s na.rm = FALSE
187s rowMads():
187s colMads():
187s na.rm = FALSE
187s rowMads():
187s colMads():
187s na.rm = TRUE
187s rowMads():
187s colMads():
187s na.rm = TRUE
187s rowMads():
187s colMads():
187s na.rm = FALSE
187s rowMads():
187s colMads():
187s na.rm = FALSE
187s rowMads():
187s colMads():
187s na.rm = TRUE
187s rowMads():
187s colMads():
187s na.rm = TRUE
187s rowMads():
187s colMads():
187s add_na = TRUE
187s na.rm = FALSE
187s rowMads():
187s colMads():
187s na.rm = FALSE
187s rowMads():
187s colMads():
187s na.rm = TRUE
187s rowMads():
187s colMads():
187s na.rm = TRUE
187s rowMads():
187s colMads():
187s na.rm = FALSE
187s rowMads():
187s colMads():
187s na.rm = FALSE
187s rowMads():
187s colMads():
187s na.rm = TRUE
187s rowMads():
187s colMads():
187s na.rm = TRUE
187s rowMads():
187s colMads():
187s > 
187s > 
187s > 
187s > 
187s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
187s > # All NAs
187s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
187s > x <- matrix(NA_real_, nrow = 10L, ncol = 5L)
187s > # Test with and without dimnames on x
187s > for (setDimnames in c(TRUE, FALSE)) {
187s +   if (setDimnames) dimnames(x) <- dimnames
187s +   else dimnames(x) <- NULL
187s +   tx <- t(x)
187s +   # Row/column ranges
187s +   for (na.rm in c(FALSE, TRUE)) {
187s +     # Check names attribute
187s +     for (useNames in c(TRUE, FALSE)) {
187s +       cat("na.rm = ", na.rm, "\n", sep = "")
187s +       r0 <- rowMads_R(x, na.rm = na.rm, useNames = useNames)
187s +       if (na.rm) r0[is.na(r0)] <- NaN
187s +       r1 <- rowMads(x, na.rm = na.rm, useNames = useNames)
187s +       r2 <- colMads(tx, na.rm = na.rm, useNames = useNames)
187s +       stopifnot(all.equal(r1, r0))
187s +       stopifnot(all.equal(r2, r0))
187s +       stopifnot(all.equal(r1, r2))
187s +     }
187s +   }
187s + }
187s na.rm = FALSE
187s na.rm = FALSE
187s na.rm = TRUE
187s na.rm = TRUE
187s na.rm = FALSE
187s na.rm = FALSE
187s na.rm = TRUE
187s na.rm = TRUE
187s > tx <- NULL
187s > 
187s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
187s > # A 1x1 matrix
187s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
187s > x <- matrix(0, nrow = 1L, ncol = 1L)
187s > dimnames <- list("a", "A")
187s > # Test with and without dimnames on x
187s > for (setDimnames in c(TRUE, FALSE)) {
187s +   if (setDimnames) dimnames(x) <- dimnames
187s +   else dimnames(x) <- NULL
187s +   tx <- t(x)
187s +   # Row/column ranges
187s +   for (na.rm in c(FALSE, TRUE)) {
187s +     # Check names attribute
187s +     for (useNames in c(TRUE, FALSE)) {
187s +       cat("na.rm = ", na.rm, "\n", sep = "")
187s +       r0 <- rowMads_R(x, na.rm = na.rm, useNames = useNames)
187s +       r1 <- rowMads(x, na.rm = na.rm, useNames = useNames)
187s +       r2 <- colMads(tx, na.rm = na.rm, useNames = useNames)
187s +       stopifnot(all.equal(r1, r0))
187s +       stopifnot(all.equal(r2, r0))
187s +       stopifnot(all.equal(r1, r2))
187s +     }
187s +   }
187s + }
187s na.rm = FALSE
187s na.rm = FALSE
187s na.rm = TRUE
187s na.rm = TRUE
187s na.rm = FALSE
187s na.rm = FALSE
187s na.rm = TRUE
187s na.rm = TRUE
187s > 
187s > 
187s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
187s > # A 0x0 matrix
187s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
187s > x <- matrix(double(0), nrow = 0, ncol = 0)
187s > tx <- t(x)
187s > for (na.rm in c(FALSE, TRUE)) {
187s +   cat("na.rm = ", na.rm, "\n", sep = "")
187s +   r0 <- rowMads_R(x, na.rm = na.rm)
187s +   r1 <- rowMads(x, na.rm = na.rm)
187s +   r2 <- colMads(tx, na.rm = na.rm)
187s +   stopifnot(all.equal(r1, r2))
187s +   stopifnot(all.equal(r1, r0))
187s +   stopifnot(all.equal(r2, r0))
187s + }
187s na.rm = FALSE
187s na.rm = TRUE
187s > 
187s 
187s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
187s Copyright (C) 2025 The R Foundation for Statistical Computing
187s Platform: x86_64-pc-linux-gnu
187s 
187s R is free software and comes with ABSOLUTELY NO WARRANTY.
187s You are welcome to redistribute it under certain conditions.
187s Type 'license()' or 'licence()' for distribution details.
187s 
187s R is a collaborative project with many contributors.
187s Type 'contributors()' for more information and
187s 'citation()' on how to cite R or R packages in publications.
187s 
187s Type 'demo()' for some demos, 'help()' for on-line help, or
187s 'help.start()' for an HTML browser interface to help.
187s Type 'q()' to quit R.
187s 
187s > library("matrixStats")
187s > 
187s > ## Always allow testing of the 'center' argument (as long as it's not defunct)
187s > options(matrixStats.center.onUse = "ignore")
187s > 
187s > rowMads_R <- function(x, na.rm = FALSE, ..., useNames = TRUE) {
187s +   suppressWarnings({
187s +     res <- apply(x, MARGIN = 1L, FUN = mad, na.rm = na.rm)
187s +   })
187s +   if (!useNames) names(res) <- NULL
187s +   res
187s + }
187s > 
187s > colMads_R <- function(x, na.rm = FALSE, ..., useNames = TRUE) {
187s +   suppressWarnings({
187s +     res <- apply(x, MARGIN = 2L, FUN = mad, na.rm = na.rm)
187s +   })
187s +   if (!useNames) names(res) <- NULL
187s +   res
187s + }
187s > 
187s > rowMads_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = TRUE) {
187s +   center <- rowMedians(x, cols = cols, na.rm = na.rm, useNames = FALSE)
187s +   rowMads(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
187s + }
187s > 
187s > colMads_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = TRUE) {
187s +   center <- colMedians(x, rows = rows, na.rm = na.rm, useNames = FALSE)
187s +   colMads(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
187s + }
187s > 
187s > 
187s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
187s > # Subsetted tests
187s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
187s > source("utils/validateIndicesFramework.R")
187s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
187s > storage.mode(x) <- "integer"
187s > 
187s > # To check names attribute
187s > dimnames <- list(letters[1:6], LETTERS[1:6])
187s > 
187s > # Test with and without dimnames on x
187s > for (setDimnames in c(TRUE, FALSE)) {
187s +   if (setDimnames) dimnames(x) <- dimnames
187s +   else dimnames(x) <- NULL
187s + 
187s +   count <- 0L
187s +   for (rows in index_cases) {
187s +     for (cols in index_cases) {
187s +       count <- count + 1L
187s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
187s +       useNames <- c(TRUE, FALSE)
187s +       useNames <- useNames[count %% length(useNames) + 1]
187s +       
187s +       validateIndicesTestMatrix(x, rows, cols,
187s +                                 ftest = rowMads, fsure = rowMads_R,
187s +                                 na.rm = na.rm, useNames = useNames)
187s +       validateIndicesTestMatrix(x, rows, cols,
187s +                                 ftest = rowMads_center, fsure = rowMads_R,
187s +                                 na.rm = na.rm, useNames = useNames)
187s + 
187s +       validateIndicesTestMatrix(x, rows, cols,
187s +                                 fcoltest = colMads, fsure = rowMads_R,
187s +                                 na.rm = na.rm, useNames = useNames)
187s +       validateIndicesTestMatrix(x, rows, cols,
187s +                                 fcoltest = colMads_center, fsure = rowMads_R,
187s +                                 na.rm = na.rm, useNames = useNames)
187s +     }
187s +   }
187s + }
187s > 
187s 
187s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
187s Copyright (C) 2025 The R Foundation for Statistical Computing
187s Platform: x86_64-pc-linux-gnu
187s 
187s R is free software and comes with ABSOLUTELY NO WARRANTY.
187s You are welcome to redistribute it under certain conditions.
187s Type 'license()' or 'licence()' for distribution details.
187s 
187s R is a collaborative project with many contributors.
187s Type 'contributors()' for more information and
187s 'citation()' on how to cite R or R packages in publications.
187s 
187s Type 'demo()' for some demos, 'help()' for on-line help, or
187s 'help.start()' for an HTML browser interface to help.
187s Type 'q()' to quit R.
187s 
187s > library("matrixStats")
188s > 
188s > rowMeans_R <- function(x, na.rm = FALSE, ..., useNames = TRUE) {
188s +   res <- rowMeans(x, na.rm = na.rm)
188s +   if (!useNames) names(res) <- NULL
188s +   res
188s + }
188s > 
188s > colMeans_R <- function(x, na.rm = FALSE, ..., useNames = TRUE) {
188s +   res <- colMeans(x, na.rm = na.rm)
188s +   if (!useNames) names(res) <- NULL
188s +   res
188s + }
188s > 
188s > for (mode in c("integer", "logical", "double")) {
188s +   x <- matrix(-4:4, nrow = 3, ncol = 3)
188s +   storage.mode(x) <- mode
188s +   if (mode == "double") x <- x + 0.1
188s +   
188s +   # To check names attribute
188s +   dimnames <- list(letters[1:3], LETTERS[1:3])
188s +   
188s +   # Test with and without dimnames on x
188s +   for (setDimnames in c(TRUE, FALSE)) {
188s +     if (setDimnames) dimnames(x) <- dimnames
188s +     else dimnames(x) <- NULL
188s +     # Check names attribute
188s +     for (useNames in c(TRUE, FALSE)) {
188s +       y0 <- rowMeans_R(x, na.rm = FALSE, useNames = useNames)
188s +       y1 <- rowMeans2(x, na.rm = FALSE, useNames = useNames)
188s +       stopifnot(all.equal(y1, y0))
188s +       
188s +       y0 <- colMeans_R(x, na.rm = FALSE, useNames = useNames)
188s +       y1 <- colMeans2(x, na.rm = FALSE, useNames = useNames)
188s +       stopifnot(all.equal(y1, y0))
188s +     }
188s +   }
188s + }
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Special case: Single-element matrix
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > cat("Special case: Single-element matrix:\n")
188s Special case: Single-element matrix:
188s > for (mode in c("integer", "logical", "double")) {
188s +   x <- matrix(1, nrow = 1, ncol = 1)
188s +   storage.mode(x) <- mode
188s +   
188s +   # To check names attribute
188s +   dimnames <- list("a", "A")
188s +   
188s +   # Test with and without dimnames on x
188s +   for (setDimnames in c(TRUE, FALSE)) {
188s +     if (setDimnames) dimnames(x) <- dimnames
188s +     else dimnames(x) <- NULL
188s +     # Check names attribute
188s +     for (useNames in c(TRUE, FALSE)) {
188s +       y0 <- rowMeans_R(x, na.rm = FALSE, useNames = useNames)
188s +       y1 <- rowMeans2(x, na.rm = FALSE, useNames = useNames)
188s +       stopifnot(all.equal(y1, y0))
188s +       
188s +       y0 <- colMeans_R(x, na.rm = FALSE, useNames = useNames)
188s +       y1 <- colMeans2(x, na.rm = FALSE, useNames = useNames)
188s +       stopifnot(all.equal(y1, y0))
188s +     }
188s +   }
188s + }
188s > 
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Special case: Empty matrix
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > cat("Special case: Empty matrix:\n")
188s Special case: Empty matrix:
188s > for (mode in c("integer", "logical", "double")) {
188s +   x <- matrix(integer(0), nrow = 0, ncol = 0)
188s +   storage.mode(x) <- mode
188s + 
188s +   y0 <- rowMeans(x, na.rm = FALSE)
188s +   y1 <- rowMeans2(x, na.rm = FALSE)
188s +   stopifnot(all.equal(y1, y0))
188s + 
188s +   y0 <- colMeans(x, na.rm = FALSE)
188s +   y1 <- colMeans2(x, na.rm = FALSE)
188s +   stopifnot(all.equal(y1, y0))
188s + }
188s > 
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Special case: All NAs
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > cat("Special case: All NAs:\n")
188s Special case: All NAs:
188s > for (mode in c("integer", "logical", "double")) {
188s +   x <- matrix(NA_integer_, nrow = 3, ncol = 3)
188s +   storage.mode(x) <- mode
188s +   
188s +   # To check names attribute
188s +   dimnames <- list(letters[1:3], LETTERS[1:3])
188s +   
188s +   # Test with and without dimnames on x
188s +   for (setDimnames in c(TRUE, FALSE)) {
188s +     if (setDimnames) dimnames(x) <- dimnames
188s +     else dimnames(x) <- NULL
188s +     # Check names attribute
188s +     for (useNames in c(TRUE, FALSE)) {
188s +       y0 <- rowMeans_R(x, na.rm = TRUE, useNames = useNames)
188s +       y1 <- rowMeans2(x, na.rm = TRUE, useNames = useNames)
188s +       stopifnot(all.equal(y1, y0))
188s +       
188s +       y0 <- colMeans_R(x, na.rm = TRUE, useNames = useNames)
188s +       y1 <- colMeans2(x, na.rm = TRUE, useNames = useNames)
188s +       stopifnot(all.equal(y1, y0))
188s +     }
188s +   }
188s + }
188s > 
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Special case: All NaNs
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > cat("Special case: All NaNs:\n")
188s Special case: All NaNs:
188s > x <- matrix(NA_real_, nrow = 3, ncol = 3)
188s > 
188s > # Test with and without dimnames on x
188s > for (setDimnames in c(TRUE, FALSE)) {
188s +   if (setDimnames) dimnames(x) <- dimnames
188s +   else dimnames(x) <- NULL
188s +   # Check names attribute
188s +   for (useNames in c(TRUE, FALSE)) {
188s +     y0 <- rowMeans_R(x, na.rm = TRUE, useNames = useNames)
188s +     y1 <- rowMeans2(x, na.rm = TRUE, useNames = useNames)
188s +     stopifnot(all.equal(y1, y0))
188s +     
188s +     y0 <- colMeans_R(x, na.rm = TRUE, useNames = useNames)
188s +     y1 <- colMeans2(x, na.rm = TRUE, useNames = useNames)
188s +     stopifnot(all.equal(y1, y0))
188s +   }
188s + }
188s > 
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Special case: All Infs
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > cat("Special case: All Infs:\n")
188s Special case: All Infs:
188s > x <- matrix(Inf, nrow = 3, ncol = 3)
188s > 
188s > # Test with and without dimnames on x
188s > for (setDimnames in c(TRUE, FALSE)) {
188s +   if (setDimnames) dimnames(x) <- dimnames
188s +   else dimnames(x) <- NULL
188s +   # Check names attribute
188s +   for (useNames in c(TRUE, FALSE)) {
188s +     y0 <- rowMeans_R(x, na.rm = FALSE, useNames = useNames)
188s +     y1 <- rowMeans2(x, na.rm = FALSE, useNames = useNames)
188s +     stopifnot(all.equal(y1, y0))
188s +     
188s +     y0 <- colMeans_R(x, na.rm = FALSE, useNames = useNames)
188s +     y1 <- colMeans2(x, na.rm = FALSE, useNames = useNames)
188s +     stopifnot(all.equal(y1, y0))
188s +   }
188s + }
188s > 
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Special case: All -Infs
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > cat("Special case: All -Infs:\n")
188s Special case: All -Infs:
188s > x <- matrix(-Inf, nrow = 3, ncol = 3)
188s > 
188s > # Test with and without dimnames on x
188s > for (setDimnames in c(TRUE, FALSE)) {
188s +   if (setDimnames) dimnames(x) <- dimnames
188s +   else dimnames(x) <- NULL
188s +   # Check names attribute
188s +   for (useNames in c(TRUE, FALSE)) {
188s +     y0 <- rowMeans_R(x, na.rm = FALSE, useNames = useNames)
188s +     y1 <- rowMeans2(x, na.rm = FALSE, useNames = useNames)
188s +     stopifnot(all.equal(y1, y0))
188s +     
188s +     y0 <- colMeans_R(x, na.rm = FALSE, useNames = useNames)
188s +     y1 <- colMeans2(x, na.rm = FALSE, useNames = useNames)
188s +     stopifnot(all.equal(y1, y0))
188s +   }
188s + }
188s > 
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Special case: Infs and -Infs
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > cat("Special case: Infs and -Infs:\n")
188s Special case: Infs and -Infs:
188s > x <- matrix(c(-Inf, +Inf), nrow = 4, ncol = 4)
188s > 
188s > # To check names attribute
188s > dimnames <- list(letters[1:4], LETTERS[1:4])
188s > 
188s > # Test with and without dimnames on x
188s > for (setDimnames in c(TRUE, FALSE)) {
188s +   if (setDimnames) dimnames(x) <- dimnames
188s +   else dimnames(x) <- NULL
188s +   # Check names attribute
188s +   for (useNames in c(TRUE, FALSE)) {
188s +     y0 <- rowMeans_R(x, na.rm = FALSE, useNames = useNames)
188s +     y1 <- rowMeans2(x, na.rm = FALSE, useNames = useNames)
188s +     stopifnot(all.equal(y1, y0))
188s +     
188s +     y0 <- colMeans_R(x, na.rm = FALSE, useNames = useNames)
188s +     y1 <- colMeans2(x, na.rm = FALSE, useNames = useNames)
188s +     stopifnot(all.equal(y1, y0))
188s +   }
188s + }
188s > 
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Special case: NaNs and NAs
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > cat("Special case: NaNs and NAs:\n")
188s Special case: NaNs and NAs:
188s > x <- matrix(c(NaN, NA_real_), nrow = 4, ncol = 4)
188s > 
188s > # Test with and without dimnames on x
188s > for (setDimnames in c(TRUE, FALSE)) {
188s +   if (setDimnames) dimnames(x) <- dimnames
188s +   else dimnames(x) <- NULL
188s +   # Check names attribute
188s +   for (useNames in c(TRUE, FALSE)) {
188s +     y0 <- rowMeans_R(x, na.rm = FALSE, useNames = useNames)
188s +     str(y0)
188s +     stopifnot(all(is.na(y0)), length(unique(y0)) >= 1L)
188s +     y1 <- rowMeans2(x, na.rm = FALSE, useNames = useNames)
188s +     str(y1)
188s +     stopifnot(all(is.na(y1)), length(unique(y1)) >= 1L)
188s +     stopifnot(all.equal(y1, y0))
188s +     
188s +     y0 <- colMeans_R(x, na.rm = FALSE, useNames = useNames)
188s +     stopifnot(all(is.na(y0)), length(unique(y0)) == 1L)
188s +     y1 <- colMeans2(x, na.rm = FALSE, useNames = useNames)
188s +     stopifnot(all(is.na(y1)), length(unique(y1)) == 1L)
188s +     stopifnot(all.equal(y1, y0))
188s +   }
188s + }
188s  Named num [1:4] NaN NA NaN NA
188s  - attr(*, "names")= chr [1:4] "a" "b" "c" "d"
188s  Named num [1:4] NaN NA NaN NA
188s  - attr(*, "names")= chr [1:4] "a" "b" "c" "d"
188s  num [1:4] NaN NA NaN NA
188s  num [1:4] NaN NA NaN NA
188s  num [1:4] NaN NA NaN NA
188s  num [1:4] NaN NA NaN NA
188s  num [1:4] NaN NA NaN NA
188s  num [1:4] NaN NA NaN NA
188s > ## NOTE, due to compiler optimization, it is not guaranteed that NA is
188s > ## returned here (as one would expect). NaN might very well be returned,
188s > ## when both NA and NaN are involved.  This is an accepted feature in R,
188s > ## which is documented in help("is.nan").  See also
188s > ## https://stat.ethz.ch/pipermail/r-devel/2017-April/074009.html.
188s > ## Thus, we cannot guarantee that y1 is identical to y0.
188s > 
188s > 
188s > 
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Special case: Integer overflow with ties
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > cat("Special case: Integer overflow with ties:\n")
188s Special case: Integer overflow with ties:
188s > x <- matrix(.Machine$integer.max, nrow = 4, ncol = 4)
188s > 
188s > # Test with and without dimnames on x
188s > for (setDimnames in c(TRUE, FALSE)) {
188s +   if (setDimnames) dimnames(x) <- dimnames
188s +   else dimnames(x) <- NULL
188s +   # Check names attribute
188s +   for (useNames in c(TRUE, FALSE)) {
188s +     y0 <- rowMeans_R(x, na.rm = FALSE, useNames = useNames)
188s +     y1 <- rowMeans2(x, na.rm = FALSE, useNames = useNames)
188s +     stopifnot(all.equal(y1, y0))
188s +     
188s +     y0 <- colMeans_R(x, na.rm = FALSE, useNames = useNames)
188s +     y1 <- colMeans2(x, na.rm = FALSE, useNames = useNames)
188s +     stopifnot(all.equal(y1, y0))
188s +   }
188s + }
188s > 
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Consistency checks
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > set.seed(1)
188s > 
188s > cat("Consistency checks:\n")
188s Consistency checks:
188s > n_sims <- if (Sys.getenv("_R_CHECK_USE_VALGRIND_") != "") 4L else 20L
188s > for (kk in seq_len(n_sims)) {
188s +   cat("Random test #", kk, "\n", sep = "")
188s + 
188s +   # Simulate data in a matrix of any shape
188s +   dim <- sample(50:200, size = 2)
188s +   n <- prod(dim)
188s +   x <- rnorm(n, sd = 100)
188s +   dim(x) <- dim
188s + 
188s +   # Add NAs?
188s +   if ((kk %% 4) %in% c(3, 0)) {
188s +     cat("Adding NAs\n")
188s +     nna <- sample(n, size = 1)
188s +     na_values <- c(NA_real_, NaN)
188s +     t <- sample(na_values, size = nna, replace = TRUE)
188s +     x[sample(length(x), size = nna)] <- t
188s +   }
188s + 
188s +   # Mode?
188s +   modes <- "double"
188s +   if ((kk %% 4) %in% c(2, 0)) {
188s +     modes <- c("integer", "logical")
188s +   }
188s + 
188s +   for (mode in modes) {
188s +     if (mode != "double") {
188s +       cat(sprintf("Coercing from %s to %s\n", storage.mode(x), mode))
188s +       storage.mode(x) <- mode
188s +     }
188s + 
188s +     na.rm <- sample(c(TRUE, FALSE), size = 1)
188s +   
188s +     # rowMeans2():
188s +     y0 <- rowMeans(x, na.rm = na.rm)
188s +     y1 <- rowMeans2(x, na.rm = na.rm)
188s +     stopifnot(all.equal(y1, y0))
188s +     y2 <- colMeans2(t(x), na.rm = na.rm)
188s +     stopifnot(all.equal(y2, y0))
188s +   
188s +     # colMeans2():
188s +     y0 <- colMeans(x, na.rm = na.rm)
188s +     y1 <- colMeans2(x, na.rm = na.rm)
188s +     stopifnot(all.equal(y1, y0))
188s +     y2 <- rowMeans2(t(x), na.rm = na.rm)
188s +     stopifnot(all.equal(y2, y0))
188s +   }
188s + } # for (kk ...)
188s Random test #1
188s Random test #2
188s Coercing from double to integer
188s Coercing from integer to logical
188s Random test #3
188s Adding NAs
188s Random test #4
188s Adding NAs
188s Coercing from double to integer
188s Coercing from integer to logical
188s Random test #5
188s Random test #6
188s Coercing from double to integer
188s Coercing from integer to logical
188s Random test #7
188s Adding NAs
188s Random test #8
188s Adding NAs
188s Coercing from double to integer
188s Coercing from integer to logical
188s Random test #9
188s Random test #10
188s Coercing from double to integer
188s Coercing from integer to logical
188s Random test #11
188s Adding NAs
188s Random test #12
188s Adding NAs
188s Coercing from double to integer
188s Coercing from integer to logical
188s Random test #13
188s Random test #14
188s Coercing from double to integer
188s Coercing from integer to logical
188s Random test #15
188s Adding NAs
188s Random test #16
188s Adding NAs
188s Coercing from double to integer
188s Coercing from integer to logical
188s Random test #17
188s Random test #18
188s Coercing from double to integer
188s Coercing from integer to logical
188s Random test #19
188s Adding NAs
188s Random test #20
188s Adding NAs
188s Coercing from double to integer
188s Coercing from integer to logical
188s > 
188s 
188s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
188s Copyright (C) 2025 The R Foundation for Statistical Computing
188s Platform: x86_64-pc-linux-gnu
188s 
188s R is free software and comes with ABSOLUTELY NO WARRANTY.
188s You are welcome to redistribute it under certain conditions.
188s Type 'license()' or 'licence()' for distribution details.
188s 
188s R is a collaborative project with many contributors.
188s Type 'contributors()' for more information and
188s 'citation()' on how to cite R or R packages in publications.
188s 
188s Type 'demo()' for some demos, 'help()' for on-line help, or
188s 'help.start()' for an HTML browser interface to help.
188s Type 'q()' to quit R.
188s 
188s > library("matrixStats")
188s > 
188s > rowMeans_R <- function(x, na.rm = FALSE, ..., useNames = TRUE) {
188s +   res <- rowMeans(x, na.rm = na.rm)
188s +   if (!useNames) names(res) <- NULL
188s +   res
188s + }
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Subsetted tests
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > source("utils/validateIndicesFramework.R")
188s > x <- matrix(runif(6 * 6, min = -3, max = 3), nrow = 6, ncol = 6)
188s > storage.mode(x) <- "integer"
188s > 
188s > # To check names attribute
188s > dimnames <- list(letters[1:6], LETTERS[1:6])
188s > 
188s > # Test with and without dimnames on x
188s > for (setDimnames in c(TRUE, FALSE)) {
188s +   if (setDimnames) dimnames(x) <- dimnames
188s +   else dimnames(x) <- NULL
188s +   
188s +   count <- 0L
188s +   for (rows in index_cases) {
188s +     for (cols in index_cases) {
188s +       count <- count + 1L
188s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
188s +       useNames <- c(TRUE, FALSE)
188s +       useNames <- useNames[count %% length(useNames) + 1]
188s +       
188s +       validateIndicesTestMatrix(x, rows, cols,
188s +                                 ftest = rowMeans2, fsure = rowMeans_R,
188s +                                 na.rm = na.rm, useNames = useNames)
188s +       validateIndicesTestMatrix(x, rows, cols,
188s +                                 fcoltest = colMeans2, fsure = rowMeans_R,
188s +                                 na.rm = na.rm, useNames = useNames)
188s +     }
188s +   }
188s + }
188s > 
188s 
188s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
188s Copyright (C) 2025 The R Foundation for Statistical Computing
188s Platform: x86_64-pc-linux-gnu
188s 
188s R is free software and comes with ABSOLUTELY NO WARRANTY.
188s You are welcome to redistribute it under certain conditions.
188s Type 'license()' or 'licence()' for distribution details.
188s 
188s R is a collaborative project with many contributors.
188s Type 'contributors()' for more information and
188s 'citation()' on how to cite R or R packages in publications.
188s 
188s Type 'demo()' for some demos, 'help()' for on-line help, or
188s 'help.start()' for an HTML browser interface to help.
188s Type 'q()' to quit R.
188s 
188s > library("matrixStats")
188s > 
188s > rowMedians_R <- function(x, na.rm = FALSE, ..., useNames = TRUE) {
188s +   res <- apply(x, MARGIN = 1L, FUN = median, na.rm = na.rm)
188s +   if (!useNames) names(res) <- NULL
188s +   res
188s + }
188s > 
188s > colMedians_R <- function(x, na.rm = FALSE, ..., useNames = TRUE) {
188s +   res <- apply(x, MARGIN = 2L, FUN = median, na.rm = na.rm)
188s +   if (!useNames) names(res) <- NULL
188s +   res
188s + }
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Special case: Non-ties
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > cat("Special case: Non-ties:\n")
188s Special case: Non-ties:
188s > for (mode in c("integer", "double")) {
188s +   x <- matrix(1:9 + 0.1, nrow = 3, ncol = 3)
188s +   storage.mode(x) <- mode
188s +   
188s +   # To check names attribute
188s +   dimnames <- list(letters[1:3], LETTERS[1:3])
188s +   
188s +   # Test with and without dimnames on x
188s +   for (setDimnames in c(TRUE, FALSE)) {
188s +     if (setDimnames) dimnames(x) <- dimnames
188s +     else dimnames(x) <- NULL
188s +     # Check names attribute
188s +     for (useNames in c(TRUE, FALSE)) {
188s +       y0 <- rowMedians_R(x, na.rm = FALSE, useNames = useNames)
188s +       y1 <- rowMedians(x, na.rm = FALSE, useNames = useNames)
188s +       stopifnot(all.equal(y1, y0))
188s +       
188s +       y0 <- colMedians_R(x, na.rm = FALSE, useNames = useNames)
188s +       y1 <- colMedians(x, na.rm = FALSE, useNames = useNames)
188s +       stopifnot(all.equal(y1, y0))
188s +     }
188s +   }
188s + }
188s > 
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Special case: Ties
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > cat("Special case: Ties:\n")
188s Special case: Ties:
188s > for (mode in c("integer", "double")) {
188s +   x <- matrix(1:16 + 0.1, nrow = 4, ncol = 4)
188s +   storage.mode(x) <- mode
188s +   
188s +   # To check names attribute
188s +   dimnames <- list(letters[1:4], LETTERS[1:4])
188s + 
188s +   # Test with and without dimnames on x
188s +   for (setDimnames in c(TRUE, FALSE)) {
188s +     if (setDimnames) dimnames(x) <- dimnames
188s +     else dimnames(x) <- NULL
188s +     # Check names attribute
188s +     for (useNames in c(TRUE, FALSE)) {
188s +       y0 <- rowMedians_R(x, na.rm = FALSE, useNames = useNames)
188s +       y1 <- rowMedians(x, na.rm = FALSE, useNames = useNames)
188s +       stopifnot(all.equal(y1, y0))
188s +       
188s +       y0 <- colMedians_R(x, na.rm = FALSE, useNames = useNames)
188s +       y1 <- colMedians(x, na.rm = FALSE, useNames = useNames)
188s +       stopifnot(all.equal(y1, y0))
188s +     }
188s +   }
188s + }
188s > 
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Special case: Single-element matrix
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > cat("Special case: Single-element matrix:\n")
188s Special case: Single-element matrix:
188s > for (mode in c("integer", "double")) {
188s +   x <- matrix(1, nrow = 1, ncol = 1)
188s +   storage.mode(x) <- mode
188s +   
188s +   # To check names attribute
188s +   dimnames <- list("a", "A")
188s + 
188s +   # Test with and without dimnames on x
188s +   for (setDimnames in c(TRUE, FALSE)) {
188s +     if (setDimnames) dimnames(x) <- dimnames
188s +     else dimnames(x) <- NULL
188s +     # Check names attribute
188s +     for (useNames in c(TRUE, FALSE)) {
188s +       y0 <- rowMedians_R(x, na.rm = FALSE, useNames = useNames)
188s +       y1 <- rowMedians(x, na.rm = FALSE, useNames = useNames)
188s +       stopifnot(all.equal(y1, y0))
188s +       
188s +       y0 <- colMedians_R(x, na.rm = FALSE, useNames = useNames)
188s +       y1 <- colMedians(x, na.rm = FALSE, useNames = useNames)
188s +       stopifnot(all.equal(y1, y0))
188s +     }
188s +   }
188s + }
188s > 
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Special case: Empty matrix
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > cat("Special case: Empty matrix:\n")
188s Special case: Empty matrix:
188s > for (mode in c("integer", "double")) {
188s +   x <- matrix(integer(0), nrow = 0, ncol = 0)
188s +   storage.mode(x) <- mode
188s + 
188s +   y0 <- rowMedians_R(x, na.rm = FALSE)
188s +   y1 <- rowMedians(x, na.rm = FALSE)
188s +   stopifnot(all.equal(y1, y0))
188s + 
188s +   y0 <- colMedians_R(x, na.rm = FALSE)
188s +   y1 <- colMedians(x, na.rm = FALSE)
188s +   stopifnot(all.equal(y1, y0))
188s + }
188s > 
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Special case: All NAs
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > cat("Special case: All NAs:\n")
188s Special case: All NAs:
188s > for (mode in c("integer", "double")) {
188s +   x <- matrix(NA_integer_, nrow = 3, ncol = 3)
188s +   storage.mode(x) <- mode
188s +   
188s +   # To check names attribute
188s +   dimnames <- list(letters[1:3], LETTERS[1:3])
188s + 
188s +   # Test with and without dimnames on x
188s +   for (setDimnames in c(TRUE, FALSE)) {
188s +     if (setDimnames) dimnames(x) <- dimnames
188s +     else dimnames(x) <- NULL
188s +     # Check names attribute
188s +     for (useNames in c(TRUE, FALSE)) {
188s +       y0 <- rowMedians_R(x, na.rm = TRUE, useNames = useNames)
188s +       y1 <- rowMedians(x, na.rm = TRUE, useNames = useNames)
188s +       stopifnot(all.equal(y1, y0))
188s +       
188s +       y0 <- colMedians_R(x, na.rm = TRUE, useNames = useNames)
188s +       y1 <- colMedians(x, na.rm = TRUE, useNames = useNames)
188s +       stopifnot(all.equal(y1, y0))
188s +     }
188s +   }
188s + }
188s > 
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Special case: All NaNs
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > cat("Special case: All NaNs:\n")
188s Special case: All NaNs:
188s > x <- matrix(NA_real_, nrow = 3, ncol = 3)
188s > 
188s > # Test with and without dimnames on x
188s > for (setDimnames in c(TRUE, FALSE)) {
188s +   if (setDimnames) dimnames(x) <- dimnames
188s +   else dimnames(x) <- NULL
188s +   # Check names attribute
188s +   for (useNames in c(TRUE, FALSE)) {
188s +     y0 <- rowMedians_R(x, na.rm = TRUE, useNames = useNames)
188s +     y1 <- rowMedians(x, na.rm = TRUE, useNames = useNames)
188s +     stopifnot(all.equal(y1, y0))
188s +     
188s +     y0 <- colMedians_R(x, na.rm = TRUE, useNames = useNames)
188s +     y1 <- colMedians(x, na.rm = TRUE, useNames = useNames)
188s +     stopifnot(all.equal(y1, y0))
188s +   }
188s + }
188s > 
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Special case: All Infs
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > cat("Special case: All Infs:\n")
188s Special case: All Infs:
188s > x <- matrix(Inf, nrow = 3, ncol = 3)
188s > 
188s > # Test with and without dimnames on x
188s > for (setDimnames in c(TRUE, FALSE)) {
188s +   if (setDimnames) dimnames(x) <- dimnames
188s +   else dimnames(x) <- NULL
188s +   # Check names attribute
188s +   for (useNames in c(TRUE, FALSE)) {
188s +     y0 <- rowMedians_R(x, na.rm = FALSE, useNames = useNames)
188s +     y1 <- rowMedians(x, na.rm = FALSE, useNames = useNames)
188s +     stopifnot(all.equal(y1, y0))
188s +     
188s +     y0 <- colMedians_R(x, na.rm = FALSE, useNames = useNames)
188s +     y1 <- colMedians(x, na.rm = FALSE, useNames = useNames)
188s +     stopifnot(all.equal(y1, y0))
188s +   }
188s + }
188s > 
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Special case: All -Infs
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > cat("Special case: All -Infs:\n")
188s Special case: All -Infs:
188s > x <- matrix(-Inf, nrow = 3, ncol = 3)
188s > 
188s > # Test with and without dimnames on x
188s > for (setDimnames in c(TRUE, FALSE)) {
188s +   if (setDimnames) dimnames(x) <- dimnames
188s +   else dimnames(x) <- NULL
188s +   # Check names attribute
188s +   for (useNames in c(TRUE, FALSE)) {
188s +     y0 <- rowMedians_R(x, na.rm = FALSE, useNames = useNames)
188s +     y1 <- rowMedians(x, na.rm = FALSE, useNames = useNames)
188s +     stopifnot(all.equal(y1, y0))
188s +     
188s +     y0 <- colMedians_R(x, na.rm = FALSE, useNames = useNames)
188s +     y1 <- colMedians(x, na.rm = FALSE, useNames = useNames)
188s +     stopifnot(all.equal(y1, y0))
188s +   }
188s + }
188s > 
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Special case: Infs and -Infs
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > cat("Special case: Infs and -Infs:\n")
188s Special case: Infs and -Infs:
188s > x <- matrix(c(-Inf, +Inf), nrow = 4, ncol = 4)
188s > 
188s > # To check names attribute
188s > dimnames <- list(letters[1:4], LETTERS[1:4])
188s > 
188s > # Test with and without dimnames on x
188s > for (setDimnames in c(TRUE, FALSE)) {
188s +   if (setDimnames) dimnames(x) <- dimnames
188s +   else dimnames(x) <- NULL
188s +   # Check names attribute
188s +   for (useNames in c(TRUE, FALSE)) {
188s +     y0 <- rowMedians_R(x, na.rm = FALSE, useNames = useNames)
188s +     y1 <- rowMedians(x, na.rm = FALSE, useNames = useNames)
188s +     stopifnot(all.equal(y1, y0))
188s +     
188s +     y0 <- colMedians_R(x, na.rm = FALSE, useNames = useNames)
188s +     y1 <- colMedians(x, na.rm = FALSE, useNames = useNames)
188s +     stopifnot(all.equal(y1, y0))
188s +   }
188s + }
188s > 
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Special case: Integer overflow with ties
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > cat("Special case: Integer overflow with ties:\n")
188s Special case: Integer overflow with ties:
188s > x <- matrix(.Machine$integer.max, nrow = 4, ncol = 4)
188s > 
188s > # Test with and without dimnames on x
188s > for (setDimnames in c(TRUE, FALSE)) {
188s +   if (setDimnames) dimnames(x) <- dimnames
188s +   else dimnames(x) <- NULL
188s +   # Check names attribute
188s +   for (useNames in c(TRUE, FALSE)) {
188s +     y0 <- rowMedians_R(x, na.rm = FALSE, useNames = useNames)
188s +     y1 <- rowMedians(x, na.rm = FALSE, useNames = useNames)
188s +     stopifnot(all.equal(y1, y0))
188s +     
188s +     y0 <- colMedians_R(x, na.rm = FALSE, useNames = useNames)
188s +     y1 <- colMedians(x, na.rm = FALSE, useNames = useNames)
188s +     stopifnot(all.equal(y1, y0))
188s +   }
188s + }
188s > 
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Consistency checks
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > set.seed(1)
188s > 
188s > cat("Consistency checks:\n")
188s Consistency checks:
188s > n_sims <- if (Sys.getenv("_R_CHECK_USE_VALGRIND_") != "") 4L else 20L
188s > for (kk in seq_len(n_sims)) {
188s +   cat("Random test #", kk, "\n", sep = "")
188s + 
188s +   # Simulate data in a matrix of any shape
188s +   dim <- sample(50:200, size = 2)
188s +   n <- prod(dim)
188s +   x <- rnorm(n, sd = 100)
188s +   dim(x) <- dim
188s + 
188s +   # Add NAs?
188s +   if ((kk %% 4) %in% c(3, 0)) {
188s +     cat("Adding NAs\n")
188s +     nna <- sample(n, size = 1)
188s +     na_values <- c(NA_real_, NaN)
188s +     t <- sample(na_values, size = nna, replace = TRUE)
188s +     x[sample(length(x), size = nna)] <- t
188s +   }
188s + 
188s +   # Integer or double?
188s +   if ((kk %% 4) %in% c(2, 0)) {
188s +     cat("Coercing to integers\n")
188s +     storage.mode(x) <- "integer"
188s +   }
188s + 
188s +   na.rm <- sample(c(TRUE, FALSE), size = 1)
188s + 
188s +   # rowMedians():
188s +   y0 <- rowMedians_R(x, na.rm = na.rm)
188s +   y1 <- rowMedians(x, na.rm = na.rm)
188s +   stopifnot(all.equal(y1, y0))
188s +   y2 <- colMedians(t(x), na.rm = na.rm)
188s +   stopifnot(all.equal(y2, y0))
188s + 
188s +   # colMedians():
188s +   y0 <- colMedians_R(x, na.rm = na.rm)
188s +   y1 <- colMedians(x, na.rm = na.rm)
188s +   stopifnot(all.equal(y1, y0))
188s +   y2 <- rowMedians(t(x), na.rm = na.rm)
188s +   stopifnot(all.equal(y2, y0))
188s + } # for (kk ...)
188s Random test #1
188s Random test #2
188s Coercing to integers
188s Random test #3
188s Adding NAs
188s Random test #4
188s Adding NAs
188s Coercing to integers
188s Random test #5
188s Random test #6
188s Coercing to integers
188s Random test #7
188s Adding NAs
188s Random test #8
188s Adding NAs
188s Coercing to integers
188s Random test #9
188s Random test #10
188s Coercing to integers
188s Random test #11
188s Adding NAs
188s Random test #12
188s Adding NAs
188s Coercing to integers
188s Random test #13
188s Random test #14
188s Coercing to integers
188s Random test #15
188s Adding NAs
188s Random test #16
188s Adding NAs
188s Coercing to integers
188s Random test #17
188s Random test #18
188s Coercing to integers
188s Random test #19
188s Adding NAs
188s Random test #20
188s Adding NAs
188s Coercing to integers
188s > 
188s 
188s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
188s Copyright (C) 2025 The R Foundation for Statistical Computing
188s Platform: x86_64-pc-linux-gnu
188s 
188s R is free software and comes with ABSOLUTELY NO WARRANTY.
188s You are welcome to redistribute it under certain conditions.
188s Type 'license()' or 'licence()' for distribution details.
188s 
188s R is a collaborative project with many contributors.
188s Type 'contributors()' for more information and
188s 'citation()' on how to cite R or R packages in publications.
188s 
188s Type 'demo()' for some demos, 'help()' for on-line help, or
188s 'help.start()' for an HTML browser interface to help.
188s Type 'q()' to quit R.
188s 
188s > library("matrixStats")
188s > 
188s > rowMedians_R <- function(x, na.rm = FALSE, ..., useNames = TRUE) {
188s +   res <- apply(x, MARGIN = 1L, FUN = median, na.rm = na.rm)
188s +   if (!useNames) names(res) <- NULL
188s +   res
188s + }
188s > 
188s > colMedians_R <- function(x, na.rm = FALSE, ..., useNames = TRUE) {
188s +   res <- apply(x, MARGIN = 2L, FUN = median, na.rm = na.rm)
188s +   if (!useNames) names(res) <- NULL
188s +   res
188s + }
188s > 
188s > 
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > # Subsetted tests
188s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188s > source("utils/validateIndicesFramework.R")
188s > x <- matrix(runif(6 * 6, min = -3, max = 3), nrow = 6, ncol = 6)
188s > storage.mode(x) <- "integer"
188s > 
188s > # To check names attribute
188s > dimnames <- list(letters[1:6], LETTERS[1:6])
188s > 
188s > # Test with and without dimnames on x
188s > for (setDimnames in c(TRUE, FALSE)) {
188s +   if (setDimnames) dimnames(x) <- dimnames
188s +   else dimnames(x) <- NULL
188s + 
188s +   count <- 0L
188s +   for (rows in index_cases) {
188s +     for (cols in index_cases) {
188s +       count <- count + 1L
188s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
188s +       useNames <- c(TRUE, FALSE)
188s +       useNames <- useNames[count %% length(useNames) + 1]
188s +       
188s +       validateIndicesTestMatrix(x, rows, cols,
188s +                                 ftest = rowMedians, fsure = rowMedians_R,
188s +                                 na.rm = na.rm, useNames = useNames)
188s +       validateIndicesTestMatrix(x, rows, cols,
188s +                                 fcoltest = colMedians, fsure = rowMedians_R,
188s +                                 na.rm = na.rm, useNames = useNames)
188s +     }
188s +   }
188s + }
188s > 
189s 
189s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
189s Copyright (C) 2025 The R Foundation for Statistical Computing
189s Platform: x86_64-pc-linux-gnu
189s 
189s R is free software and comes with ABSOLUTELY NO WARRANTY.
189s You are welcome to redistribute it under certain conditions.
189s Type 'license()' or 'licence()' for distribution details.
189s 
189s R is a collaborative project with many contributors.
189s Type 'contributors()' for more information and
189s 'citation()' on how to cite R or R packages in publications.
189s 
189s Type 'demo()' for some demos, 'help()' for on-line help, or
189s 'help.start()' for an HTML browser interface to help.
189s Type 'q()' to quit R.
189s 
189s > library("matrixStats")
189s > library("stats")
189s > 
189s > asWhich <- function(probs, max) {
189s +   idx <- as.integer(round(probs * max))
189s +   if (idx < 1L) {
189s +     idx <- 1L
189s +   } else if (idx > max) {
189s +     idx <- max
189s +   }
189s +   idx
189s + } # asWhich()
189s > 
189s > rowOrderStats_R <- function(x, probs, ..., useNames = TRUE) {
189s +   ans <- apply(x, MARGIN = 1L, FUN = quantile, probs = probs, type = 3L)
189s +   
189s +   # Remove Attributes
189s +   if (!useNames || length(ans) == 0L) attributes(ans) <- NULL
189s +   ans
189s + } # rowOrderStats_R()
189s > 
189s > 
189s > set.seed(1)
189s > 
189s > 
189s > # Simulate data in a matrix of any shape
189s > nrow <- 60L
189s > ncol <- 30L
189s > x <- rnorm(nrow * ncol)
189s > dim(x) <- c(nrow, ncol)
189s > probs <- 0.3
189s > which <- asWhich(probs, max = ncol)
189s > 
189s > y0 <- rowOrderStats_R(x, probs = probs)
189s > y1 <- rowOrderStats(x, which = which)
189s > stopifnot(all.equal(y1, y0))
189s > y2 <- colOrderStats(t(x), which = which)
189s > stopifnot(all.equal(y2, y0))
189s > 
189s > 
189s > 
189s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
189s > # Consistency checks
189s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
189s > for (mode in c("integer", "double")) {
189s +   cat("Consistency checks without NAs:\n")
189s +   for (kk in 1:3) {
189s +     cat("Random test #", kk, "\n", sep = "")
189s + 
189s +     # Simulate data in a matrix of any shape
189s +     nrow <- sample(20L, size = 1L)
189s +     ncol <- sample(20L, size = 1L)
189s +     x <- rnorm(nrow * ncol)
189s +     dim(x) <- c(nrow, ncol)
189s + 
189s +     cat("mode: ", mode, "\n", sep = "")
189s +     storage.mode(x) <- mode
189s +     str(x)
189s + 
189s +     probs <- runif(1)
189s +     which <- asWhich(probs, max = ncol)
189s + 
189s +     y0 <- rowOrderStats_R(x, probs = probs)
189s +     y1 <- rowOrderStats(x, which = which)
189s +     stopifnot(all.equal(y1, y0))
189s +     y2 <- colOrderStats(t(x), which = which)
189s +     stopifnot(all.equal(y2, y0))
189s +   } # for (kk in ...)
189s + } # for (mode ...)
189s Consistency checks without NAs:
189s Random test #1
189s mode: integer
189s  int [1:14, 1:6] 0 0 1 0 2 -1 1 0 0 0 ...
189s Random test #2
189s mode: integer
189s  int [1:8, 1:13] 0 0 1 -2 0 0 0 0 1 0 ...
189s Random test #3
189s mode: integer
189s  int [1:20, 1:17] 0 0 0 0 1 0 1 0 0 -1 ...
189s Consistency checks without NAs:
189s Random test #1
189s mode: double
189s  num [1:9, 1:5] -1.4286 -0.00386 -0.70456 -0.29242 -0.49607 ...
189s Random test #2
189s mode: double
189s  num [1:11, 1:20] -0.796 0.482 -0.952 0.5 1.242 ...
189s Random test #3
189s mode: double
189s  num [1:7, 1:18] 1.553 -2.405 0.167 -0.403 -1.746 ...
189s > 
189s > 
189s > # Check names attribute
189s > x <- matrix(1:9 + 0.1, nrow = 3L, ncol = 3L)
189s > 
189s > probs <- runif(1)
189s > which <- asWhich(probs, max = ncol(x))
189s > 
189s > dimnames <- list(letters[1:3], LETTERS[1:3])
189s > 
189s > # Test with and without dimnames on x
189s > for (setDimnames in c(TRUE, FALSE)) {
189s +   if (setDimnames) dimnames(x) <- dimnames
189s +   else dimnames(x) <- NULL
189s +   # Check names attribute
189s +   for (useNames in c(TRUE, FALSE)) {
189s +     y0 <- rowOrderStats_R(x, probs = probs, useNames = useNames)
189s +     y1 <- rowOrderStats(x, which = which, useNames = useNames)
189s +     stopifnot(all.equal(y1, y0))
189s +     y2 <- colOrderStats(t(x), which = which, useNames = useNames)
189s +     stopifnot(all.equal(y2, y0))    
189s +   }
189s + }
189s > 
189s 
189s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
189s Copyright (C) 2025 The R Foundation for Statistical Computing
189s Platform: x86_64-pc-linux-gnu
189s 
189s R is free software and comes with ABSOLUTELY NO WARRANTY.
189s You are welcome to redistribute it under certain conditions.
189s Type 'license()' or 'licence()' for distribution details.
189s 
189s R is a collaborative project with many contributors.
189s Type 'contributors()' for more information and
189s 'citation()' on how to cite R or R packages in publications.
189s 
189s Type 'demo()' for some demos, 'help()' for on-line help, or
189s 'help.start()' for an HTML browser interface to help.
189s Type 'q()' to quit R.
189s 
189s > library("matrixStats")
189s > 
189s > rowOrderStats_R <- function(x, probs, ..., useNames = TRUE) {
189s +   ans <- apply(x, MARGIN = 1L, FUN = quantile, probs = probs, type = 3L)
189s + 
189s +   # Remove Attributes
189s +   if (!useNames || length(ans) == 0L) attributes(ans) <- NULL
189s +   ans
189s + } # rowOrderStats_R()
189s > 
189s > 
189s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
189s > # Subsetted tests
189s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
189s > source("utils/validateIndicesFramework.R")
189s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
189s > storage.mode(x) <- "integer"
189s > 
189s > # To check names attribute
189s > dimnames <- list(letters[1:6], LETTERS[1:6])
189s > 
189s > probs <- 0.3
189s > # Test with and without dimnames on x
189s > for (setDimnames in c(TRUE, FALSE)) {
189s +   if (setDimnames) dimnames(x) <- dimnames
189s +   else dimnames(x) <- NULL
189s +   for (rows in index_cases) {
189s +     for (cols in index_cases) {
189s +       # Check names attribute
189s +       for (useNames in c(TRUE, FALSE)) {
189s +         if (is.null(cols)) which <- round(probs * ncol(x))
189s +         else {
189s +           xxrows <- rows
189s +           suppressWarnings({
189s +             xx <- tryCatch(x[, cols, drop = FALSE], error = function(c) "error")
189s +             if (identical(xx, "error")) which <- 0L
189s +             else which <- round(probs * ncol(xx))
189s +           })
189s +         }
189s +         if (which == 0L) next
189s +     
189s +         validateIndicesTestMatrix(x, rows, cols,
189s +                                   ftest = rowOrderStats, fsure = rowOrderStats_R,
189s +                                   which = which, probs = probs, useNames = useNames)
189s +         validateIndicesTestMatrix(x, rows, cols,
189s +                                   fcoltest = colOrderStats, fsure = rowOrderStats_R,
189s +                                   which = which, probs = probs, useNames = useNames)
189s +       }
189s +     }
189s +   }
189s + }
189s > 
189s 
189s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
189s Copyright (C) 2025 The R Foundation for Statistical Computing
189s Platform: x86_64-pc-linux-gnu
189s 
189s R is free software and comes with ABSOLUTELY NO WARRANTY.
189s You are welcome to redistribute it under certain conditions.
189s Type 'license()' or 'licence()' for distribution details.
189s 
189s R is a collaborative project with many contributors.
189s Type 'contributors()' for more information and
189s 'citation()' on how to cite R or R packages in publications.
189s 
189s Type 'demo()' for some demos, 'help()' for on-line help, or
189s 'help.start()' for an HTML browser interface to help.
189s Type 'q()' to quit R.
189s 
189s > library("matrixStats")
189s > 
189s > rowProds_R <- function(x, FUN = prod, na.rm = FALSE, ..., useNames = TRUE) {
189s +   res <- apply(x, MARGIN = 1L, FUN = FUN, na.rm = na.rm)
189s +   if (!useNames) names(res) <- NULL
189s +   res
189s + }
189s > 
189s > all.equal.na <- function(target, current, ...) {
189s +   # Computations involving NaN may return NaN or NA, cf. ?is.nan
189s +   current[is.nan(current)] <- NA_real_
189s +   target[is.nan(target)] <- NA_real_
189s +   all.equal(target, current, ...)
189s + }
189s > 
189s > for (mode in c("integer", "double")) {
189s +   # Missing values
189s +   x <- matrix(c(1, NA, NaN, 1, 1, 0, 1, 0), nrow = 4, ncol = 2)
189s +   cat("mode: ", mode, "\n", sep = "")
189s +   storage.mode(x) <- mode
189s +   str(x)
189s +   
189s +   # To check names attribute
189s +   dimnames <- list(letters[1:4], LETTERS[1:2])
189s +   
189s +   # Test with and without dimnames on x
189s +   for (setDimnames in c(TRUE, FALSE)) {
189s +     if (setDimnames) dimnames(x) <- dimnames
189s +     else dimnames(x) <- NULL
189s +     # Check names attribute
189s +     for (useNames in c(TRUE, FALSE)) {
189s +       y0 <- rowProds_R(x, na.rm = TRUE, useNames = useNames)
189s +       print(y0)
189s +       y1 <- rowProds(x, na.rm = TRUE, useNames = useNames)
189s +       print(y1)
189s +       y2 <- colProds(t(x), na.rm = TRUE, useNames = useNames)
189s +       print(y2)
189s +       stopifnot(all.equal(y1, y0))
189s +       stopifnot(all.equal(y2, y1))
189s +       
189s +       # Missing values
189s +       y0 <- rowProds_R(x, na.rm = FALSE, useNames = useNames)
189s +       print(y0)
189s +       y1 <- rowProds(x, na.rm = FALSE, useNames = useNames)
189s +       print(y1)
189s +       y2 <- colProds(t(x), na.rm = FALSE, useNames = useNames)
189s +       print(y2)
189s +       stopifnot(all.equal(y1, y0))
189s +       stopifnot(all.equal(y2, y1))
189s +       
189s +       # "Empty" rows
189s +       y0 <- rowProds_R(x[integer(0), , drop = FALSE], na.rm = FALSE, useNames = useNames)
189s +       print(y0)
189s +       y1 <- rowProds(x[integer(0), , drop = FALSE], na.rm = FALSE, useNames = useNames)
189s +       print(y1)
189s +       y2 <- colProds(t(x[integer(0), , drop = FALSE]), na.rm = FALSE, useNames = useNames)
189s +       print(y2)
189s +       stopifnot(all.equal.na(y1, y0))
189s +       stopifnot(all.equal(y2, y1))
189s +       stopifnot(length(y1) == 0L)
189s +       
189s +       # Using product()
189s +       y1 <- rowProds(x, method = "expSumLog", na.rm = FALSE, useNames = useNames)
189s +       print(y1)
189s +       y2 <- colProds(t(x), method = "expSumLog", na.rm = FALSE, useNames = useNames)
189s +       print(y2)
189s +       stopifnot(all.equal(y2, y1))
189s +     }
189s +   }
189s + } # for (mode ...)
189s mode: integer
189s  int [1:4, 1:2] 1 NA NA 1 1 0 1 0
189s a b c d 
189s 1 0 1 0 
189s a b c d 
189s 1 0 1 0 
189s a b c d 
189s 1 0 1 0 
189s  a  b  c  d 
189s  1 NA NA  0 
189s  a  b  c  d 
189s  1 NA NA  0 
189s  a  b  c  d 
189s  1 NA NA  0 
189s numeric(0)
189s numeric(0)
189s numeric(0)
189s  a  b  c  d 
189s  1 NA NA  0 
189s  a  b  c  d 
189s  1 NA NA  0 
189s [1] 1 0 1 0
189s [1] 1 0 1 0
189s [1] 1 0 1 0
189s [1]  1 NA NA  0
189s [1]  1 NA NA  0
189s [1]  1 NA NA  0
189s numeric(0)
189s numeric(0)
189s numeric(0)
189s [1]  1 NA NA  0
189s [1]  1 NA NA  0
189s [1] 1 0 1 0
189s [1] 1 0 1 0
189s [1] 1 0 1 0
189s [1]  1 NA NA  0
189s [1]  1 NA NA  0
189s [1]  1 NA NA  0
189s numeric(0)
189s numeric(0)
189s numeric(0)
189s [1]  1 NA NA  0
189s [1]  1 NA NA  0
189s [1] 1 0 1 0
189s [1] 1 0 1 0
189s [1] 1 0 1 0
189s [1]  1 NA NA  0
189s [1]  1 NA NA  0
189s [1]  1 NA NA  0
189s numeric(0)
189s numeric(0)
189s numeric(0)
189s [1]  1 NA NA  0
189s [1]  1 NA NA  0
189s mode: double
189s  num [1:4, 1:2] 1 NA NaN 1 1 0 1 0
189s a b c d 
189s 1 0 1 0 
189s a b c d 
189s 1 0 1 0 
189s a b c d 
189s 1 0 1 0 
189s   a   b   c   d 
189s   1  NA NaN   0 
189s   a   b   c   d 
189s   1  NA NaN   0 
189s   a   b   c   d 
189s   1  NA NaN   0 
189s numeric(0)
189s numeric(0)
189s numeric(0)
189s  a  b  c  d 
189s  1 NA NA  0 
189s  a  b  c  d 
189s  1 NA NA  0 
189s [1] 1 0 1 0
189s [1] 1 0 1 0
189s [1] 1 0 1 0
189s [1]   1  NA NaN   0
189s [1]   1  NA NaN   0
189s [1]   1  NA NaN   0
189s numeric(0)
189s numeric(0)
189s numeric(0)
189s [1]  1 NA NA  0
189s [1]  1 NA NA  0
189s [1] 1 0 1 0
189s [1] 1 0 1 0
189s [1] 1 0 1 0
189s [1]   1  NA NaN   0
189s [1]   1  NA NaN   0
189s [1]   1  NA NaN   0
189s numeric(0)
189s numeric(0)
189s numeric(0)
189s [1]  1 NA NA  0
189s [1]  1 NA NA  0
189s [1] 1 0 1 0
189s [1] 1 0 1 0
189s [1] 1 0 1 0
189s [1]   1  NA NaN   0
189s [1]   1  NA NaN   0
189s [1]   1  NA NaN   0
189s numeric(0)
189s numeric(0)
189s numeric(0)
189s [1]  1 NA NA  0
189s [1]  1 NA NA  0
189s > 
189s > 
189s > # Bug report 2012-06-25
189s > x <- matrix(c(1, 1, 1, 1, 1, 0, 1, 0), nrow = 4, ncol = 2)
189s > y0 <- rowProds_R(x)
189s > print(y0)
189s [1] 1 0 1 0
189s > y1 <- rowProds(x)
189s > print(y1)
189s [1] 1 0 1 0
189s > y2 <- colProds(t(x))
189s > print(y2)
189s [1] 1 0 1 0
189s > stopifnot(all.equal.na(y1, y0))
189s > stopifnot(all.equal.na(y1, x[, 1] * x[, 2]))
189s > stopifnot(all.equal.na(y2, y1))
189s > # Check names attribute
189s > dimnames(x) <- dimnames
189s > y0 <- rowProds_R(x, useNames = TRUE)
189s > print(y0)
189s a b c d 
189s 1 0 1 0 
189s > y1 <- rowProds(x, useNames = TRUE)
189s > print(y1)
189s a b c d 
189s 1 0 1 0 
189s > y2 <- colProds(t(x), useNames = TRUE)
189s > print(y2)
189s a b c d 
189s 1 0 1 0 
189s > stopifnot(all.equal.na(y1, y0))
189s > stopifnot(all.equal.na(y1, x[, 1] * x[, 2]))
189s > stopifnot(all.equal.na(y2, y1))
189s > 
189s > # Bug report 2014-03-25 ("all rows contains a zero")
189s > x <- matrix(c(0, 1, 1, 0), nrow = 2, ncol = 2)
189s > # To check names attribute
189s > dimnames <- list(letters[1:2], LETTERS[1:2])
189s > y0 <- rowProds_R(x)
189s > print(y0)
189s [1] 0 0
189s > y1 <- rowProds(x)
189s > print(y1)
189s [1] 0 0
189s > y2 <- colProds(t(x))
189s > print(y2)
189s [1] 0 0
189s > stopifnot(all.equal.na(y1, y0))
189s > stopifnot(all.equal.na(y1, c(0, 0)))
189s > stopifnot(all.equal.na(y2, y1))
189s > # Check names attribute
189s > dimnames(x) <- dimnames
189s > y0 <- rowProds_R(x, useNames = TRUE)
189s > print(y0)
189s a b 
189s 0 0 
189s > y1 <- rowProds(x, useNames = TRUE)
189s > print(y1)
189s a b 
189s 0 0 
189s > y2 <- colProds(t(x), useNames = TRUE)
189s > print(y2)
189s a b 
189s 0 0 
189s > stopifnot(all.equal.na(y1, y0))
189s > stopifnot(all.equal.na(y2, y1))
189s > 
189s 
189s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
189s Copyright (C) 2025 The R Foundation for Statistical Computing
189s Platform: x86_64-pc-linux-gnu
189s 
189s R is free software and comes with ABSOLUTELY NO WARRANTY.
189s You are welcome to redistribute it under certain conditions.
189s Type 'license()' or 'licence()' for distribution details.
189s 
189s R is a collaborative project with many contributors.
189s Type 'contributors()' for more information and
189s 'citation()' on how to cite R or R packages in publications.
189s 
189s Type 'demo()' for some demos, 'help()' for on-line help, or
189s 'help.start()' for an HTML browser interface to help.
189s Type 'q()' to quit R.
189s 
189s > library("matrixStats")
189s > 
189s > rowProds_R <- function(x, FUN = prod, na.rm = FALSE, ..., useNames = TRUE) {
189s +   res <- apply(x, MARGIN = 1L, FUN = FUN, na.rm = na.rm)
189s +   if (!useNames) names(res) <- NULL
189s +   res
189s + }
189s > 
189s > 
189s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
189s > # Subsetted tests
189s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
189s > source("utils/validateIndicesFramework.R")
189s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
189s > storage.mode(x) <- "integer"
189s > 
189s > # To check names attribute
189s > dimnames <- list(letters[1:6], LETTERS[1:6])
189s > 
189s > # Test with and without dimnames on x
189s > for (setDimnames in c(TRUE, FALSE)) {
189s +   if (setDimnames) dimnames(x) <- dimnames
189s +   else dimnames(x) <- NULL
189s +   for (rows in index_cases) {
189s +     for (cols in index_cases) {
189s +       for (na.rm in c(TRUE, FALSE)) {
189s +         for (useNames in c(TRUE, FALSE)) {
189s +           validateIndicesTestMatrix(x, rows, cols,
189s +                                     ftest = rowProds, fsure = rowProds_R,
189s +                                     method = "expSumLog",
189s +                                     FUN = product, na.rm = na.rm, useNames = useNames)
189s +           validateIndicesTestMatrix(x, rows, cols,
189s +                                     fcoltest = colProds, fsure = rowProds_R,
189s +                                     method = "expSumLog",
189s +                                     FUN = product, na.rm = na.rm, useNames = useNames)
189s +         }
189s +       }
189s +     }
189s +   }
189s + }
190s > 
190s 
190s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
190s Copyright (C) 2025 The R Foundation for Statistical Computing
190s Platform: x86_64-pc-linux-gnu
190s 
190s R is free software and comes with ABSOLUTELY NO WARRANTY.
190s You are welcome to redistribute it under certain conditions.
190s Type 'license()' or 'licence()' for distribution details.
190s 
190s R is a collaborative project with many contributors.
190s Type 'contributors()' for more information and
190s 'citation()' on how to cite R or R packages in publications.
190s 
190s Type 'demo()' for some demos, 'help()' for on-line help, or
190s 'help.start()' for an HTML browser interface to help.
190s Type 'q()' to quit R.
190s 
190s > library("matrixStats")
190s > 
190s > ## Create isFALSE() if running on an old version of R
190s > if (!exists("isFALSE", mode="function")) {
190s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
190s + }
190s > 
190s > rowQuantiles_R <- function(x, probs = c(0, 0.25, 0.50, 0.75, 1), na.rm = FALSE, drop = TRUE, type = 7L, ..., useNames = TRUE) {
190s +   q <- apply(x, MARGIN = 1L, FUN = function(x, probs, na.rm) {
190s +     if (!na.rm && any(is.na(x))) {
190s +       na_value <- NA_real_
190s +       if (type != 7L) storage.mode(na_value) <- storage.mode(x)
190s +       rep(na_value, times = length(probs))
190s +     } else {
190s +       as.vector(quantile(x, probs = probs, na.rm = na.rm, type = type, names = FALSE, ...))
190s +     }
190s +   }, probs = probs, na.rm = na.rm)
190s + 
190s +   if (!is.null(dim(q))) q <- t(q)
190s +   else dim(q) <- c(nrow(x), length(probs))
190s + 
190s +   colnames(q) <- matrixStats:::quantile_probs_names(probs)
190s +   rownames(q) <- rownames(x)
190s +   if (isFALSE(useNames)) dimnames(q) <- NULL
190s + 
190s +   if (drop) q <- drop(q)
190s +   q
190s + }
190s > 
190s > 
190s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
190s > # Test with multiple quantiles
190s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
190s > for (mode in c("logical", "integer", "double")) {
190s +   cat("mode: ", mode, "\n", sep = "")
190s +   x <- matrix(1:40 + 0.1, nrow = 8, ncol = 5)
190s +   storage.mode(x) <- mode
190s +   dimnames <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
190s +   str(x)
190s + 
190s +   probs <- c(0, 0.5, 1)
190s +   # Test with and without dimnames on x
190s +   for (setDimnames in c(TRUE, FALSE)) {
190s +     if (setDimnames) dimnames(x) <- dimnames
190s +     else dimnames(x) <- NULL    
190s +     # Check names attribute
190s +     for (useNames in c(TRUE, FALSE)) {
190s +       q0 <- rowQuantiles_R(x, probs = probs, useNames = useNames)
190s +       print(q0)
190s +       q1 <- rowQuantiles(x, probs = probs, useNames = useNames)
190s +       print(q1)
190s +       stopifnot(all.equal(q1, q0))
190s +       q2 <- colQuantiles(t(x), probs = probs, useNames = useNames)
190s +       stopifnot(all.equal(q2, q0))      
190s +     }
190s +   }
190s + } # for (mode ...)
190s mode: logical
190s  logi [1:8, 1:5] TRUE TRUE TRUE TRUE TRUE TRUE ...
190s   0% 50% 100%
190s a  1   1    1
190s b  1   1    1
190s c  1   1    1
190s d  1   1    1
190s e  1   1    1
190s f  1   1    1
190s g  1   1    1
190s h  1   1    1
190s   0% 50% 100%
190s a  1   1    1
190s b  1   1    1
190s c  1   1    1
190s d  1   1    1
190s e  1   1    1
190s f  1   1    1
190s g  1   1    1
190s h  1   1    1
190s      [,1] [,2] [,3]
190s [1,]    1    1    1
190s [2,]    1    1    1
190s [3,]    1    1    1
190s [4,]    1    1    1
190s [5,]    1    1    1
190s [6,]    1    1    1
190s [7,]    1    1    1
190s [8,]    1    1    1
190s      [,1] [,2] [,3]
190s [1,]    1    1    1
190s [2,]    1    1    1
190s [3,]    1    1    1
190s [4,]    1    1    1
190s [5,]    1    1    1
190s [6,]    1    1    1
190s [7,]    1    1    1
190s [8,]    1    1    1
190s      0% 50% 100%
190s [1,]  1   1    1
190s [2,]  1   1    1
190s [3,]  1   1    1
190s [4,]  1   1    1
190s [5,]  1   1    1
190s [6,]  1   1    1
190s [7,]  1   1    1
190s [8,]  1   1    1
190s      0% 50% 100%
190s [1,]  1   1    1
190s [2,]  1   1    1
190s [3,]  1   1    1
190s [4,]  1   1    1
190s [5,]  1   1    1
190s [6,]  1   1    1
190s [7,]  1   1    1
190s [8,]  1   1    1
190s      [,1] [,2] [,3]
190s [1,]    1    1    1
190s [2,]    1    1    1
190s [3,]    1    1    1
190s [4,]    1    1    1
190s [5,]    1    1    1
190s [6,]    1    1    1
190s [7,]    1    1    1
190s [8,]    1    1    1
190s      [,1] [,2] [,3]
190s [1,]    1    1    1
190s [2,]    1    1    1
190s [3,]    1    1    1
190s [4,]    1    1    1
190s [5,]    1    1    1
190s [6,]    1    1    1
190s [7,]    1    1    1
190s [8,]    1    1    1
190s mode: integer
190s  int [1:8, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
190s   0% 50% 100%
190s a  1  17   33
190s b  2  18   34
190s c  3  19   35
190s d  4  20   36
190s e  5  21   37
190s f  6  22   38
190s g  7  23   39
190s h  8  24   40
190s   0% 50% 100%
190s a  1  17   33
190s b  2  18   34
190s c  3  19   35
190s d  4  20   36
190s e  5  21   37
190s f  6  22   38
190s g  7  23   39
190s h  8  24   40
190s      [,1] [,2] [,3]
190s [1,]    1   17   33
190s [2,]    2   18   34
190s [3,]    3   19   35
190s [4,]    4   20   36
190s [5,]    5   21   37
190s [6,]    6   22   38
190s [7,]    7   23   39
190s [8,]    8   24   40
190s      [,1] [,2] [,3]
190s [1,]    1   17   33
190s [2,]    2   18   34
190s [3,]    3   19   35
190s [4,]    4   20   36
190s [5,]    5   21   37
190s [6,]    6   22   38
190s [7,]    7   23   39
190s [8,]    8   24   40
190s      0% 50% 100%
190s [1,]  1  17   33
190s [2,]  2  18   34
190s [3,]  3  19   35
190s [4,]  4  20   36
190s [5,]  5  21   37
190s [6,]  6  22   38
190s [7,]  7  23   39
190s [8,]  8  24   40
190s      0% 50% 100%
190s [1,]  1  17   33
190s [2,]  2  18   34
190s [3,]  3  19   35
190s [4,]  4  20   36
190s [5,]  5  21   37
190s [6,]  6  22   38
190s [7,]  7  23   39
190s [8,]  8  24   40
190s      [,1] [,2] [,3]
190s [1,]    1   17   33
190s [2,]    2   18   34
190s [3,]    3   19   35
190s [4,]    4   20   36
190s [5,]    5   21   37
190s [6,]    6   22   38
190s [7,]    7   23   39
190s [8,]    8   24   40
190s      [,1] [,2] [,3]
190s [1,]    1   17   33
190s [2,]    2   18   34
190s [3,]    3   19   35
190s [4,]    4   20   36
190s [5,]    5   21   37
190s [6,]    6   22   38
190s [7,]    7   23   39
190s [8,]    8   24   40
190s mode: double
190s  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 ...
190s    0%  50% 100%
190s a 1.1 17.1 33.1
190s b 2.1 18.1 34.1
190s c 3.1 19.1 35.1
190s d 4.1 20.1 36.1
190s e 5.1 21.1 37.1
190s f 6.1 22.1 38.1
190s g 7.1 23.1 39.1
190s h 8.1 24.1 40.1
190s    0%  50% 100%
190s a 1.1 17.1 33.1
190s b 2.1 18.1 34.1
190s c 3.1 19.1 35.1
190s d 4.1 20.1 36.1
190s e 5.1 21.1 37.1
190s f 6.1 22.1 38.1
190s g 7.1 23.1 39.1
190s h 8.1 24.1 40.1
190s      [,1] [,2] [,3]
190s [1,]  1.1 17.1 33.1
190s [2,]  2.1 18.1 34.1
190s [3,]  3.1 19.1 35.1
190s [4,]  4.1 20.1 36.1
190s [5,]  5.1 21.1 37.1
190s [6,]  6.1 22.1 38.1
190s [7,]  7.1 23.1 39.1
190s [8,]  8.1 24.1 40.1
190s      [,1] [,2] [,3]
190s [1,]  1.1 17.1 33.1
190s [2,]  2.1 18.1 34.1
190s [3,]  3.1 19.1 35.1
190s [4,]  4.1 20.1 36.1
190s [5,]  5.1 21.1 37.1
190s [6,]  6.1 22.1 38.1
190s [7,]  7.1 23.1 39.1
190s [8,]  8.1 24.1 40.1
190s       0%  50% 100%
190s [1,] 1.1 17.1 33.1
190s [2,] 2.1 18.1 34.1
190s [3,] 3.1 19.1 35.1
190s [4,] 4.1 20.1 36.1
190s [5,] 5.1 21.1 37.1
190s [6,] 6.1 22.1 38.1
190s [7,] 7.1 23.1 39.1
190s [8,] 8.1 24.1 40.1
190s       0%  50% 100%
190s [1,] 1.1 17.1 33.1
190s [2,] 2.1 18.1 34.1
190s [3,] 3.1 19.1 35.1
190s [4,] 4.1 20.1 36.1
190s [5,] 5.1 21.1 37.1
190s [6,] 6.1 22.1 38.1
190s [7,] 7.1 23.1 39.1
190s [8,] 8.1 24.1 40.1
190s      [,1] [,2] [,3]
190s [1,]  1.1 17.1 33.1
190s [2,]  2.1 18.1 34.1
190s [3,]  3.1 19.1 35.1
190s [4,]  4.1 20.1 36.1
190s [5,]  5.1 21.1 37.1
190s [6,]  6.1 22.1 38.1
190s [7,]  7.1 23.1 39.1
190s [8,]  8.1 24.1 40.1
190s      [,1] [,2] [,3]
190s [1,]  1.1 17.1 33.1
190s [2,]  2.1 18.1 34.1
190s [3,]  3.1 19.1 35.1
190s [4,]  4.1 20.1 36.1
190s [5,]  5.1 21.1 37.1
190s [6,]  6.1 22.1 38.1
190s [7,]  7.1 23.1 39.1
190s [8,]  8.1 24.1 40.1
190s > 
190s > 
190s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
190s > # Test with a single quantile
190s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
190s > for (mode in c("logical", "integer", "double")) {
190s +   cat("mode: ", mode, "\n", sep = "")
190s +   x <- matrix(1:40, nrow = 8, ncol = 5)
190s +   storage.mode(x) <- mode
190s +   dimnames <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
190s +   str(x)
190s + 
190s +   probs <- c(0.5)
190s +   # Test with and without dimnames on x
190s +   for (setDimnames in c(TRUE, FALSE)) {
190s +     if (setDimnames) dimnames(x) <- dimnames
190s +     else dimnames(x) <- NULL    
190s +     # Check names attribute
190s +     for (useNames in c(TRUE, FALSE)) {
190s +       q0 <- rowQuantiles_R(x, probs = probs, useNames = useNames)
190s +       print(q0)
190s +       q1 <- rowQuantiles(x, probs = probs, useNames = useNames)
190s +       print(q1)
190s +       stopifnot(all.equal(q1, q0))
190s +       q2 <- colQuantiles(t(x), probs = probs, useNames = useNames)
190s +       stopifnot(all.equal(q2, q0))      
190s +     }
190s +   }
190s + } # for (mode ...)
190s mode: logical
190s  logi [1:8, 1:5] TRUE TRUE TRUE TRUE TRUE TRUE ...
190s a b c d e f g h 
190s 1 1 1 1 1 1 1 1 
190s a b c d e f g h 
190s 1 1 1 1 1 1 1 1 
190s [1] 1 1 1 1 1 1 1 1
190s [1] 1 1 1 1 1 1 1 1
190s [1] 1 1 1 1 1 1 1 1
190s [1] 1 1 1 1 1 1 1 1
190s [1] 1 1 1 1 1 1 1 1
190s [1] 1 1 1 1 1 1 1 1
190s mode: integer
190s  int [1:8, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
190s  a  b  c  d  e  f  g  h 
190s 17 18 19 20 21 22 23 24 
190s  a  b  c  d  e  f  g  h 
190s 17 18 19 20 21 22 23 24 
190s [1] 17 18 19 20 21 22 23 24
190s [1] 17 18 19 20 21 22 23 24
190s [1] 17 18 19 20 21 22 23 24
190s [1] 17 18 19 20 21 22 23 24
190s [1] 17 18 19 20 21 22 23 24
190s [1] 17 18 19 20 21 22 23 24
190s mode: double
190s  num [1:8, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
190s  a  b  c  d  e  f  g  h 
190s 17 18 19 20 21 22 23 24 
190s  a  b  c  d  e  f  g  h 
190s 17 18 19 20 21 22 23 24 
190s [1] 17 18 19 20 21 22 23 24
190s [1] 17 18 19 20 21 22 23 24
190s [1] 17 18 19 20 21 22 23 24
190s [1] 17 18 19 20 21 22 23 24
190s [1] 17 18 19 20 21 22 23 24
190s [1] 17 18 19 20 21 22 23 24
190s > 
190s > 
190s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
190s > # Consistency checks
190s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
190s > set.seed(1)
190s > 
190s > probs <- seq(from = 0, to = 1, by = 0.25)
190s > 
190s > cat("Consistency checks:\n")
190s Consistency checks:
190s > n_sims <- if (Sys.getenv("_R_CHECK_USE_VALGRIND_") != "") 6L else 24L
190s > for (kk in seq_len(n_sims)) {
190s +   cat("Random test #", kk, "\n", sep = "")
190s + 
190s +   # Simulate data in a matrix of any shape
190s +   dim <- sample(20:60, size = 2L)
190s +   n <- prod(dim)
190s +   x <- rnorm(n, sd = 100)
190s +   dim(x) <- dim
190s +   dimnames <- lapply(dim(x), FUN = function(n) rep(letters, length.out = n))
190s + 
190s +   # Add NAs?
190s +   has_na <- ((kk %% 2) == 0L)
190s +   if (has_na) {
190s +     cat("Adding NAs\n")
190s +     nna <- sample(n, size = 1)
190s +     na_values <- c(NA_real_, NaN)
190s +     t <- sample(na_values, size = nna, replace = TRUE)
190s +     x[sample(length(x), size = nna)] <- t
190s +   }
190s + 
190s +   # Logical, integer, or double?
190s +   mode <- "numeric"
190s +   if ((kk %% 6) %in% 1:2) {
190s +     cat("Coercing to logical\n")
190s +     mode <- "logical"
190s +   } else if ((kk %% 6) %in% 3:4) {
190s +     cat("Coercing to integers\n")
190s +     mode <- "integer"
190s +   }
190s +   storage.mode(x) <- mode
190s +   
190s +   str(x)
190s + 
190s +   # rowQuantiles():
190s +   for (type in 1:9) {
190s +     cat(sprintf("type=%d, has_na=%s:\n", type, has_na))
190s +     # Test with and without dimnames on x
190s +     for (setDimnames in c(TRUE, FALSE)) {
190s +       if (setDimnames) dimnames(x) <- dimnames
190s +       else dimnames(x) <- NULL    
190s +       # Check names attribute
190s +       for (useNames in c(TRUE, FALSE)) {
190s +         q0 <- rowQuantiles_R(x, probs = probs, na.rm = has_na, type = type, useNames = useNames)
190s +         q1 <- rowQuantiles(x, probs = probs, na.rm = has_na, type = type, useNames = useNames)
190s +         stopifnot(all.equal(q1, q0))
190s +         q2 <- colQuantiles(t(x), probs = probs, na.rm = has_na, type = type, useNames = useNames)
190s +         stopifnot(all.equal(q2, q0))
190s +       }
190s +     }
190s +   }
190s + } # for (kk ...)
190s Random test #1
190s Coercing to logical
190s  logi [1:23, 1:58] TRUE TRUE TRUE TRUE TRUE TRUE ...
190s type=1, has_na=FALSE:
190s type=2, has_na=FALSE:
190s type=3, has_na=FALSE:
190s type=4, has_na=FALSE:
190s type=5, has_na=FALSE:
190s type=6, has_na=FALSE:
190s type=7, has_na=FALSE:
190s type=8, has_na=FALSE:
190s type=9, has_na=FALSE:
190s Random test #2
190s Adding NAs
190s Coercing to logical
190s  logi [1:58, 1:33] TRUE TRUE TRUE TRUE TRUE NA ...
190s type=1, has_na=TRUE:
190s type=2, has_na=TRUE:
190s type=3, has_na=TRUE:
190s type=4, has_na=TRUE:
190s type=5, has_na=TRUE:
190s type=6, has_na=TRUE:
190s type=7, has_na=TRUE:
190s type=8, has_na=TRUE:
191s type=9, has_na=TRUE:
191s Random test #3
191s Coercing to integers
191s  int [1:28, 1:60] 119 -164 115 -129 209 -175 2 -32 120 -28 ...
191s type=1, has_na=FALSE:
191s type=2, has_na=FALSE:
191s type=3, has_na=FALSE:
191s type=4, has_na=FALSE:
191s type=5, has_na=FALSE:
191s type=6, has_na=FALSE:
191s type=7, has_na=FALSE:
191s type=8, has_na=FALSE:
191s type=9, has_na=FALSE:
191s Random test #4
191s Adding NAs
191s Coercing to integers
191s  int [1:54, 1:35] 147 11 116 -50 NA -69 132 NA 114 NA ...
191s type=1, has_na=TRUE:
191s type=2, has_na=TRUE:
191s type=3, has_na=TRUE:
191s type=4, has_na=TRUE:
191s type=5, has_na=TRUE:
191s type=6, has_na=TRUE:
191s type=7, has_na=TRUE:
191s type=8, has_na=TRUE:
191s type=9, has_na=TRUE:
191s Random test #5
191s  num [1:39, 1:53] 5.94 -27.16 -30.78 173 126.05 ...
191s type=1, has_na=FALSE:
191s type=2, has_na=FALSE:
191s type=3, has_na=FALSE:
191s type=4, has_na=FALSE:
191s type=5, has_na=FALSE:
191s type=6, has_na=FALSE:
191s type=7, has_na=FALSE:
191s type=8, has_na=FALSE:
191s type=9, has_na=FALSE:
191s Random test #6
191s Adding NAs
191s  num [1:46, 1:22] 197 -107 15 148 -110 ...
191s type=1, has_na=TRUE:
191s type=2, has_na=TRUE:
191s type=3, has_na=TRUE:
191s type=4, has_na=TRUE:
191s type=5, has_na=TRUE:
191s type=6, has_na=TRUE:
191s type=7, has_na=TRUE:
191s type=8, has_na=TRUE:
191s type=9, has_na=TRUE:
191s Random test #7
191s Coercing to logical
191s  logi [1:21, 1:51] TRUE TRUE TRUE TRUE TRUE TRUE ...
191s type=1, has_na=FALSE:
191s type=2, has_na=FALSE:
191s type=3, has_na=FALSE:
191s type=4, has_na=FALSE:
191s type=5, has_na=FALSE:
191s type=6, has_na=FALSE:
191s type=7, has_na=FALSE:
191s type=8, has_na=FALSE:
192s type=9, has_na=FALSE:
192s Random test #8
192s Adding NAs
192s Coercing to logical
192s  logi [1:33, 1:53] NA NA TRUE TRUE TRUE TRUE ...
192s type=1, has_na=TRUE:
192s type=2, has_na=TRUE:
192s type=3, has_na=TRUE:
192s type=4, has_na=TRUE:
192s type=5, has_na=TRUE:
192s type=6, has_na=TRUE:
192s type=7, has_na=TRUE:
192s type=8, has_na=TRUE:
192s type=9, has_na=TRUE:
192s Random test #9
192s Coercing to integers
192s  int [1:53, 1:24] -73 10 -73 -5 44 -107 -100 95 58 -50 ...
192s type=1, has_na=FALSE:
192s type=2, has_na=FALSE:
192s type=3, has_na=FALSE:
192s type=4, has_na=FALSE:
192s type=5, has_na=FALSE:
192s type=6, has_na=FALSE:
192s type=7, has_na=FALSE:
192s type=8, has_na=FALSE:
192s type=9, has_na=FALSE:
192s Random test #10
192s Adding NAs
192s Coercing to integers
192s  int [1:44, 1:20] NA -140 NA -57 -252 NA NA 20 NA NA ...
192s type=1, has_na=TRUE:
192s type=2, has_na=TRUE:
192s type=3, has_na=TRUE:
192s type=4, has_na=TRUE:
192s type=5, has_na=TRUE:
192s type=6, has_na=TRUE:
192s type=7, has_na=TRUE:
192s type=8, has_na=TRUE:
192s type=9, has_na=TRUE:
192s Random test #11
192s  num [1:54, 1:23] -160.87 74.13 196.08 7.27 4.92 ...
192s type=1, has_na=FALSE:
192s type=2, has_na=FALSE:
192s type=3, has_na=FALSE:
192s type=4, has_na=FALSE:
192s type=5, has_na=FALSE:
192s type=6, has_na=FALSE:
192s type=7, has_na=FALSE:
192s type=8, has_na=FALSE:
192s type=9, has_na=FALSE:
192s Random test #12
192s Adding NAs
192s  num [1:59, 1:27] -139.2 -86.3 NA -40.7 NA ...
192s type=1, has_na=TRUE:
192s type=2, has_na=TRUE:
193s type=3, has_na=TRUE:
193s type=4, has_na=TRUE:
193s type=5, has_na=TRUE:
193s type=6, has_na=TRUE:
193s type=7, has_na=TRUE:
193s type=8, has_na=TRUE:
193s type=9, has_na=TRUE:
193s Random test #13
193s Coercing to logical
193s  logi [1:53, 1:60] TRUE TRUE TRUE TRUE TRUE TRUE ...
193s type=1, has_na=FALSE:
193s type=2, has_na=FALSE:
193s type=3, has_na=FALSE:
193s type=4, has_na=FALSE:
193s type=5, has_na=FALSE:
193s type=6, has_na=FALSE:
193s type=7, has_na=FALSE:
193s type=8, has_na=FALSE:
193s type=9, has_na=FALSE:
193s Random test #14
193s Adding NAs
193s Coercing to logical
193s  logi [1:22, 1:57] TRUE TRUE TRUE TRUE TRUE TRUE ...
193s type=1, has_na=TRUE:
193s type=2, has_na=TRUE:
193s type=3, has_na=TRUE:
193s type=4, has_na=TRUE:
193s type=5, has_na=TRUE:
193s type=6, has_na=TRUE:
193s type=7, has_na=TRUE:
193s type=8, has_na=TRUE:
193s type=9, has_na=TRUE:
193s Random test #15
193s Coercing to integers
193s  int [1:20, 1:34] 78 -41 183 190 -71 37 0 -4 -86 27 ...
193s type=1, has_na=FALSE:
193s type=2, has_na=FALSE:
193s type=3, has_na=FALSE:
193s type=4, has_na=FALSE:
193s type=5, has_na=FALSE:
193s type=6, has_na=FALSE:
193s type=7, has_na=FALSE:
193s type=8, has_na=FALSE:
193s type=9, has_na=FALSE:
193s Random test #16
193s Adding NAs
193s Coercing to integers
193s  int [1:42, 1:37] NA 12 -15 41 -28 17 NA -74 NA NA ...
193s type=1, has_na=TRUE:
193s type=2, has_na=TRUE:
193s type=3, has_na=TRUE:
193s type=4, has_na=TRUE:
193s type=5, has_na=TRUE:
193s type=6, has_na=TRUE:
193s type=7, has_na=TRUE:
193s type=8, has_na=TRUE:
193s type=9, has_na=TRUE:
193s Random test #17
193s  num [1:42, 1:29] -50.51 -6.51 -117.59 135.58 226.87 ...
193s type=1, has_na=FALSE:
194s type=2, has_na=FALSE:
194s type=3, has_na=FALSE:
194s type=4, has_na=FALSE:
194s type=5, has_na=FALSE:
194s type=6, has_na=FALSE:
194s type=7, has_na=FALSE:
194s type=8, has_na=FALSE:
194s type=9, has_na=FALSE:
194s Random test #18
194s Adding NAs
194s  num [1:57, 1:39] 223 156.8 -44.6 -127.5 -147.7 ...
194s type=1, has_na=TRUE:
194s type=2, has_na=TRUE:
194s type=3, has_na=TRUE:
194s type=4, has_na=TRUE:
194s type=5, has_na=TRUE:
194s type=6, has_na=TRUE:
194s type=7, has_na=TRUE:
194s type=8, has_na=TRUE:
194s type=9, has_na=TRUE:
194s Random test #19
194s Coercing to logical
194s  logi [1:52, 1:57] TRUE TRUE TRUE TRUE TRUE TRUE ...
194s type=1, has_na=FALSE:
194s type=2, has_na=FALSE:
194s type=3, has_na=FALSE:
194s type=4, has_na=FALSE:
194s type=5, has_na=FALSE:
194s type=6, has_na=FALSE:
194s type=7, has_na=FALSE:
194s type=8, has_na=FALSE:
194s type=9, has_na=FALSE:
194s Random test #20
194s Adding NAs
194s Coercing to logical
194s  logi [1:25, 1:48] NA TRUE NA NA NA NA ...
194s type=1, has_na=TRUE:
194s type=2, has_na=TRUE:
194s type=3, has_na=TRUE:
194s type=4, has_na=TRUE:
194s type=5, has_na=TRUE:
194s type=6, has_na=TRUE:
194s type=7, has_na=TRUE:
194s type=8, has_na=TRUE:
194s type=9, has_na=TRUE:
194s Random test #21
194s Coercing to integers
194s  int [1:53, 1:27] 3 -30 203 -49 19 -45 -138 28 46 -44 ...
194s type=1, has_na=FALSE:
194s type=2, has_na=FALSE:
194s type=3, has_na=FALSE:
194s type=4, has_na=FALSE:
194s type=5, has_na=FALSE:
195s type=6, has_na=FALSE:
195s type=7, has_na=FALSE:
195s type=8, has_na=FALSE:
195s type=9, has_na=FALSE:
195s Random test #22
195s Adding NAs
195s Coercing to integers
195s  int [1:48, 1:36] -131 NA NA -201 45 -17 NA 57 NA NA ...
195s type=1, has_na=TRUE:
195s type=2, has_na=TRUE:
195s type=3, has_na=TRUE:
195s type=4, has_na=TRUE:
195s type=5, has_na=TRUE:
195s type=6, has_na=TRUE:
195s type=7, has_na=TRUE:
195s type=8, has_na=TRUE:
195s type=9, has_na=TRUE:
195s Random test #23
195s  num [1:23, 1:43] -99.2 -68.8 -86.7 -104.2 48 ...
195s type=1, has_na=FALSE:
195s type=2, has_na=FALSE:
195s type=3, has_na=FALSE:
195s type=4, has_na=FALSE:
195s type=5, has_na=FALSE:
195s type=6, has_na=FALSE:
195s type=7, has_na=FALSE:
195s type=8, has_na=FALSE:
195s type=9, has_na=FALSE:
195s Random test #24
195s Adding NAs
195s  num [1:53, 1:29] NaN -67.6 10.8 -88.4 130.1 ...
195s type=1, has_na=TRUE:
195s type=2, has_na=TRUE:
195s type=3, has_na=TRUE:
195s type=4, has_na=TRUE:
195s type=5, has_na=TRUE:
195s type=6, has_na=TRUE:
195s type=7, has_na=TRUE:
195s type=8, has_na=TRUE:
195s type=9, has_na=TRUE:
195s > 
195s > 
195s > 
195s > for (mode in c("logical", "integer", "double")) {
195s +   naValue <- NA_real_
195s +   storage.mode(naValue) <- mode
195s + 
195s +   someValue <- 1
195s +   storage.mode(someValue) <- mode
195s + 
195s +   for (type in 1:9) {
195s +     # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
195s +     # All NA
195s +     # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
195s +     x <- matrix(naValue, nrow = 3L, ncol = 4L)
195s +     dimnames <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
195s +     # Test with and without dimnames on x
195s +     for (setDimnames in c(TRUE, FALSE)) {
195s +       if (setDimnames) dimnames(x) <- dimnames
195s +       else dimnames(x) <- NULL    
195s +       # Check names attribute
195s +       for (useNames in c(TRUE, FALSE)) {
195s +         qr0 <- rowQuantiles_R(x, type = type, useNames = useNames)
195s +         
195s +         qr <- rowQuantiles(x, type = type, useNames = useNames)
195s +         stopifnot(identical(qr, qr0))
195s +         
195s +         # x <- matrix(naValue, nrow = 4L, ncol = 3L)
195s +         qc <- colQuantiles(t(x), type = type, useNames = useNames)
195s +         
195s +         stopifnot(identical(qc, qr))
195s +       }
195s +     }
195s + 
195s + 
195s +     # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
195s +     # Empty matrices
195s +     # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
195s +     probs <- c(0, 0.25, 0.75, 1)
195s +     x <- matrix(naValue, nrow = 0L, ncol = 0L)
195s +     dimnames(x) <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
195s +     q <- rowQuantiles(x, probs = probs, type = type, useNames = TRUE)
195s +     stopifnot(identical(dim(q), c(nrow(x), length(probs))))
195s +     q <- colQuantiles(x, probs = probs, type = type, useNames = TRUE)
195s +     stopifnot(identical(dim(q), c(ncol(x), length(probs))))
195s +     
195s +     x <- matrix(naValue, nrow = 2L, ncol = 0L)
195s +     dimnames(x) <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
195s +     q <- rowQuantiles(x, probs = probs, type = type, useNames = TRUE)
195s +     stopifnot(identical(dim(q), c(nrow(x), length(probs))))
195s +     
195s +     x <- matrix(naValue, nrow = 0L, ncol = 2L)
195s +     dimnames(x) <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
195s +     q <- colQuantiles(x, probs = probs, type = type, useNames = TRUE)
195s +     stopifnot(identical(dim(q), c(ncol(x), length(probs))))
195s + 
195s + 
195s +     # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
195s +     # Single column matrices
195s +     # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
195s +     probs <- c(0, 0.25, 0.75, 1)
195s +     x <- matrix(someValue, nrow = 2L, ncol = 1L)
195s +     dimnames(x) <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
195s +     qr <- rowQuantiles(x, probs = probs, type = type, useNames = TRUE)
195s +     print(qr)
195s +     
195s +     x <- matrix(someValue, nrow = 1L, ncol = 2L)
195s +     dimnames(x) <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
195s +     qc <- colQuantiles(x, probs = probs, type = type, useNames = TRUE)
195s +     print(qc)
195s +     
195s +     stopifnot(identical(qc, qr))
195s +   }
195s + }
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s   0% 25% 75% 100%
195s a  1   1   1    1
195s b  1   1   1    1
195s > 
195s 
195s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
195s Copyright (C) 2025 The R Foundation for Statistical Computing
195s Platform: x86_64-pc-linux-gnu
195s 
195s R is free software and comes with ABSOLUTELY NO WARRANTY.
195s You are welcome to redistribute it under certain conditions.
195s Type 'license()' or 'licence()' for distribution details.
195s 
195s R is a collaborative project with many contributors.
195s Type 'contributors()' for more information and
195s 'citation()' on how to cite R or R packages in publications.
195s 
195s Type 'demo()' for some demos, 'help()' for on-line help, or
195s 'help.start()' for an HTML browser interface to help.
195s Type 'q()' to quit R.
195s 
195s > library("matrixStats")
195s > 
195s > ## Create isFALSE() if running on an old version of R
195s > if (!exists("isFALSE", mode="function")) {
195s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
195s + }
195s > 
195s > rowQuantiles_R <- function(x, probs, na.rm = FALSE, drop = TRUE, ..., useNames = TRUE) {
195s +   q <- apply(x, MARGIN = 1L, FUN = function(x, probs, na.rm) {
195s +     if (!na.rm && any(is.na(x))) {
195s +       na_value <- NA_real_
195s +       storage.mode(na_value) <- storage.mode(x)
195s +       rep(na_value, times = length(probs))
195s + 
195s +     } else {
195s +       as.vector(quantile(x, probs = probs, na.rm = na.rm, names = FALSE, ...))
195s +     }
195s +   }, probs = probs, na.rm = na.rm)
195s + 
195s +   if (!is.null(dim(q))) q <- t(q)
195s +   else dim(q) <- c(nrow(x), length(probs))
195s + 
195s +   colnames(q) <- matrixStats:::quantile_probs_names(probs)
195s +   rownames(q) <- rownames(x)
195s +   if (isFALSE(useNames)) dimnames(q) <- NULL
195s + 
195s +   if (drop) q <- drop(q)
195s +   q
195s + }
195s > 
195s > 
195s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
195s > # Subsetted tests
195s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
195s > source("utils/validateIndicesFramework.R")
195s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
195s > dimnames <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
195s > probs <- c(0, 0.25, 0.75, 1)
195s > # Test with and without dimnames on x
195s > for (setDimnames in c(TRUE, FALSE)) {
195s +   if (setDimnames) dimnames(x) <- dimnames
195s +   else dimnames(x) <- NULL
195s +   
195s +   count <- 0L
195s +   for (rows in index_cases) {
195s +     for (cols in index_cases) {
195s +       count <- count + 1L
195s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
195s +       useNames <- c(TRUE, FALSE)
195s +       useNames <- useNames[count %% length(useNames) + 1]
195s + 
195s +       validateIndicesTestMatrix(x, rows, cols,
195s +                                 ftest = rowQuantiles, fsure = rowQuantiles_R,
195s +                                 probs = probs, na.rm = na.rm, drop = FALSE, useNames = useNames)
195s +       validateIndicesTestMatrix(x, rows, cols,
195s +                                 fcoltest = colQuantiles, fsure = rowQuantiles_R,
195s +                                 probs = probs, na.rm = na.rm, drop = FALSE, useNames = useNames)
195s +     }
195s +   }
195s + }
196s > 
196s > 
196s 
196s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
196s Copyright (C) 2025 The R Foundation for Statistical Computing
196s Platform: x86_64-pc-linux-gnu
196s 
196s R is free software and comes with ABSOLUTELY NO WARRANTY.
196s You are welcome to redistribute it under certain conditions.
196s Type 'license()' or 'licence()' for distribution details.
196s 
196s R is a collaborative project with many contributors.
196s Type 'contributors()' for more information and
196s 'citation()' on how to cite R or R packages in publications.
196s 
196s Type 'demo()' for some demos, 'help()' for on-line help, or
196s 'help.start()' for an HTML browser interface to help.
196s Type 'q()' to quit R.
196s 
196s > library("matrixStats")
196s > 
196s > rowMins_R <- function(x, ..., useNames = TRUE) {
196s +   suppressWarnings({
196s +     res <- apply(x, MARGIN = 1L, FUN = min, ...)
196s +   })
196s +   if (!useNames) names(res) <- NULL
196s +   res
196s + } # rowMins_R()
196s > 
196s > rowMaxs_R <- function(x, ..., useNames = TRUE) {
196s +   suppressWarnings({
196s +     res <- apply(x, MARGIN = 1L, FUN = max, ...)
196s +   })
196s +   if (!useNames) names(res) <- NULL
196s +   res
196s + } # rowMaxs_R()
196s > 
196s > rowRanges_R <- function(x, ..., useNames = TRUE) {
196s +   suppressWarnings({
196s +     ans <- t(apply(x, MARGIN = 1L, FUN = range, ...))
196s +   })
196s +   
196s +   # Preserve rownames attribute
196s +   dim <- c(dim(x)[1], 2L)
196s +   if (!isTRUE(all.equal(dim(ans), dim))) {
196s +     dim(ans) <- dim
196s +     rownames <- rownames(x)
196s +     if (!is.null(dimnames)) rownames(ans) <- rownames
196s +   }
196s +   if (!useNames) dimnames(ans) <- NULL
196s +   ans
196s + } # rowRanges_R()
196s > 
196s > 
196s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
196s > # With and without some NAs
196s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
196s > for (mode in c("integer", "double")) {
196s +   cat("mode: ", mode, "\n", sep = "")
196s + 
196s +   for (add_na in c(FALSE, TRUE)) {
196s +     cat("add_na = ", add_na, "\n", sep = "")
196s + 
196s +     x <- matrix(1:50 + 0.1, nrow = 10L, ncol = 5L)
196s +     if (add_na) {
196s +       x[3:7, c(2, 4)] <- NA_real_
196s +     }
196s +     storage.mode(x) <- mode
196s +     str(x)
196s +     
196s +     # To check names attribute
196s +     dimnames <- list(letters[1:10], LETTERS[1:5])
196s +     
196s +     # Test with and without dimnames on x
196s +     for (setDimnames in c(TRUE, FALSE)) {
196s +       if (setDimnames) dimnames(x) <- dimnames
196s +       else dimnames(x) <- NULL
196s +       # Row/column extremes
196s +       for (na.rm in c(FALSE, TRUE)) {
196s +         # Check names attribute
196s +         for (useNames in c(TRUE, FALSE)) {
196s +           cat("na.rm = ", na.rm, "\n", sep = "")
196s +           
196s +           # Ranges
196s +           cat("range:\n")
196s +           r0 <- rowRanges_R(x, na.rm = na.rm, useNames = useNames)
196s +           r1 <- rowRanges(x, na.rm = na.rm, useNames = useNames)
196s +           r2 <- colRanges(t(x), na.rm = na.rm, useNames = useNames)
196s +           stopifnot(all.equal(r1, r2))
196s +           stopifnot(all.equal(r1, r0))
196s +           
196s +           # Min
196s +           cat("min:\n")
196s +           m0 <- rowMins_R(x, na.rm = na.rm, useNames = useNames)
196s +           m1 <- rowMins(x, na.rm = na.rm, useNames = useNames)
196s +           m2 <- colMins(t(x), na.rm = na.rm, useNames = useNames)
196s +           stopifnot(all.equal(m1, m2))
196s +           stopifnot(all.equal(m1, m0))
196s +           
196s +           # Max
196s +           cat("max:\n")
196s +           m0 <- rowMaxs_R(x, na.rm = na.rm, useNames = useNames)
196s +           m1 <- rowMaxs(x, na.rm = na.rm, useNames = useNames)
196s +           m2 <- colMaxs(t(x), na.rm = na.rm, useNames = useNames)
196s +           stopifnot(all.equal(m1, m2))
196s +           stopifnot(all.equal(m1, m0))
196s +         }
196s +       }
196s +     }
196s +   } # for (add_na ...)
196s + } # for (mode ...)
196s mode: integer
196s add_na = FALSE
196s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
196s na.rm = FALSE
196s range:
196s min:
196s max:
196s na.rm = FALSE
196s range:
196s min:
196s max:
196s na.rm = TRUE
196s range:
196s min:
196s max:
196s na.rm = TRUE
196s range:
196s min:
196s max:
196s na.rm = FALSE
196s range:
196s min:
196s max:
196s na.rm = FALSE
196s range:
196s min:
196s max:
196s na.rm = TRUE
196s range:
196s min:
196s max:
196s na.rm = TRUE
196s range:
196s min:
196s max:
196s add_na = TRUE
196s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
196s na.rm = FALSE
196s range:
196s min:
196s max:
196s na.rm = FALSE
196s range:
196s min:
196s max:
196s na.rm = TRUE
196s range:
196s min:
196s max:
196s na.rm = TRUE
196s range:
196s min:
196s max:
196s na.rm = FALSE
196s range:
196s min:
196s max:
196s na.rm = FALSE
196s range:
196s min:
196s max:
196s na.rm = TRUE
196s range:
196s min:
196s max:
196s na.rm = TRUE
196s range:
196s min:
196s max:
196s mode: double
196s add_na = FALSE
196s  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 ...
196s na.rm = FALSE
196s range:
196s min:
196s max:
196s na.rm = FALSE
196s range:
196s min:
196s max:
196s na.rm = TRUE
196s range:
196s min:
196s max:
196s na.rm = TRUE
196s range:
196s min:
196s max:
196s na.rm = FALSE
196s range:
196s min:
196s max:
196s na.rm = FALSE
196s range:
196s min:
196s max:
196s na.rm = TRUE
196s range:
196s min:
196s max:
196s na.rm = TRUE
196s range:
196s min:
196s max:
196s add_na = TRUE
196s  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 ...
196s na.rm = FALSE
196s range:
196s min:
196s max:
196s na.rm = FALSE
196s range:
196s min:
196s max:
196s na.rm = TRUE
196s range:
196s min:
196s max:
196s na.rm = TRUE
196s range:
196s min:
196s max:
196s na.rm = FALSE
196s range:
196s min:
196s max:
196s na.rm = FALSE
196s range:
196s min:
196s max:
196s na.rm = TRUE
196s range:
196s min:
196s max:
196s na.rm = TRUE
196s range:
196s min:
196s max:
196s > 
196s > 
196s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
196s > # All NAs
196s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
196s > for (mode in c("integer", "double")) {
196s +   cat("mode: ", mode, "\n", sep = "")
196s +   x <- matrix(NA_real_, nrow = 10L, ncol = 5L)
196s +   storage.mode(x) <- mode
196s +   str(x)
196s +   
196s +   # Test with and without dimnames on x
196s +   for (setDimnames in c(TRUE, FALSE)) {
196s +     if (setDimnames) dimnames(x) <- dimnames
196s +     else dimnames(x) <- NULL
196s +     for (na.rm in c(FALSE, TRUE)) {
196s +       # Check names attribute
196s +       for (useNames in c(TRUE, FALSE)) {
196s +         cat("na.rm = ", na.rm, "\n", sep = "")
196s +         r0 <- rowRanges_R(x, na.rm = na.rm, useNames = useNames)
196s +         r1 <- rowRanges(x, na.rm = na.rm, useNames = useNames)
196s +         r2 <- colRanges(t(x), na.rm = na.rm, useNames = useNames)
196s +         stopifnot(all.equal(r1, r2))
196s +         stopifnot(all.equal(r1, r0))
196s +       }
196s +     }
196s +   }
196s + } # for (mode ...)
196s mode: integer
196s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
196s na.rm = FALSE
196s na.rm = FALSE
196s na.rm = TRUE
196s na.rm = TRUE
196s na.rm = FALSE
196s na.rm = FALSE
196s na.rm = TRUE
196s na.rm = TRUE
196s mode: double
196s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
196s na.rm = FALSE
196s na.rm = FALSE
196s na.rm = TRUE
196s na.rm = TRUE
196s na.rm = FALSE
196s na.rm = FALSE
196s na.rm = TRUE
196s na.rm = TRUE
196s > 
196s > 
196s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
196s > # Special cases
196s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
196s > # Nx0 matrix
196s > x <- matrix(double(0L), nrow = 5L, ncol = 0L)
196s > r0 <- rowRanges_R(x)
196s > #r1 <- rowRanges(x)
196s > #r_truth <- matrix(c(Inf, -Inf), nrow = nrow(x), ncol = 2L, byrow = TRUE)
196s > #stopifnot(all.equal(r1, r_truth))
196s > 
196s > # 0xN matrix
196s > x <- t(x)
196s > #r1 <- colRanges(x)
196s > #stopifnot(all.equal(r1, r_truth))
196s > 
196s > # Nx1 matrix
196s > x <- matrix(1:5, nrow = 5L, ncol = 1L)
196s > # To check names attribute
196s > dimnames <- list(letters[1:5], "A")
196s > r1 <- rowRanges(x)
196s > r_truth <- matrix(1:5, nrow = nrow(x), ncol = 2L, byrow = FALSE)
196s > stopifnot(all.equal(r1, r_truth))
196s > # Check names attribute
196s > dimnames(x) <- dimnames
196s > r0 <- rowRanges_R(x, useNames = TRUE)
196s > r1 <- rowRanges(x, useNames = TRUE)
196s > stopifnot(all.equal(r1, r0))
196s > dimnames(x) <- NULL
196s > 
196s > # 1xN matrix
196s > x <- t(x)
196s > r1 <- colRanges(x)
196s > stopifnot(all.equal(r1, r_truth))
196s > # Check names attribute
196s > dimnames(x) <- list("a", LETTERS[1:5])
196s > r1 <- colRanges(x, useNames = TRUE)
196s > stopifnot(identical(rownames(r1), colnames(x)))
196s > 
196s > 
196s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
196s > # Additional tests with NA_integer_, NA_real, NaN, -Inf, +Inf
196s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
196s > x <- matrix(1:12, nrow = 4L, ncol = 3L)
196s > 
196s > na_list <- list(
196s +   "integer"       = matrix(1:12, nrow = 4L, ncol = 3L),
196s +   "integer w/ NA" = matrix(NA_integer_, nrow = 4L, ncol = 3L),
196s +   "real"          = matrix(as.double(1:12), nrow = 4L, ncol = 3L),
196s +   "real w/ NA"    = matrix(NA_real_, nrow = 4L, ncol = 3L)
196s + )
196s > 
196s > na <- na_list[["real"]]
196s > na[2, 2] <- NA
196s > na_list[["real + NA cell"]] <- na
196s > 
196s > na <- na_list[["real"]]
196s > na[2, ] <- NA
196s > na_list[["real + NA row"]] <- na
196s > 
196s > na <- na_list[["real"]]
196s > na[2, ] <- NaN
196s > na_list[["real + NaN row"]] <- na
196s > 
196s > na <- na_list[["real"]]
196s > na[2, 2] <- Inf
196s > na_list[["real + Inf cell"]] <- na
196s > 
196s > na <- na_list[["real"]]
196s > na[2, ] <- Inf
196s > na_list[["real + Inf row"]] <- na
196s > 
196s > na <- na_list[["real"]]
196s > na[2, 2] <- NaN
196s > na_list[["real + NaN cell"]] <- na
196s > 
196s > na <- na_list[["real w/ NA"]]
196s > na[2, 2] <- NaN
196s > na_list[["real w/ NA + NaN cell"]] <- na
196s > 
196s > na <- na_list[["real w/ NA"]]
196s > na[2, ] <- NaN
196s > na_list[["real w/ NA + NaN row"]] <- na
196s > 
196s > # To check names attribute
196s > dimnames <- list(letters[1:4], LETTERS[1:3])
196s > 
196s > # Test with and without dimnames on x
196s > for (setDimnames in c(TRUE, FALSE)) {
196s +   if (setDimnames) dimnames(x) <- dimnames
196s +   else dimnames(x) <- NULL
196s +   for (na.rm in c(FALSE, TRUE)) {
196s +     for (name in names(na_list)) {
196s +       # Check names attribute
196s +       for (useNames in c(TRUE, FALSE)) {
196s +         na <- na_list[[name]]
196s +         cat(sprintf("%s (%s) w/ na.rm = %s:\n", name, typeof(na), na.rm))
196s +         print(na)
196s +         
196s +         cat("  min:\n")
196s +         y0 <- rowMins_R(na, na.rm = na.rm, useNames = useNames)
196s +         str(y0)
196s +         y1 <- rowMins(na, na.rm = na.rm, useNames = useNames)
196s +         str(y1)
196s +         stopifnot(all.equal(y1, y0))
196s +         y1c <- colMins(t(na), na.rm = na.rm, useNames = useNames)
196s +         str(y1c)
196s +         stopifnot(all.equal(y1c, y1))
196s +         
196s +         cat("  max:\n")
196s +         y0 <- rowMaxs_R(na, na.rm = na.rm, useNames = useNames)
196s +         str(y0)
196s +         y1 <- rowMaxs(na, na.rm = na.rm, useNames = useNames)
196s +         str(y1)
196s +         stopifnot(all.equal(y1, y0))
196s +         y1c <- colMaxs(t(na), na.rm = na.rm, useNames = useNames)
196s +         str(y1c)
196s +         stopifnot(all.equal(y1c, y1))
196s +         
196s +         cat("  range:\n")
196s +         y0 <- rowRanges_R(na, na.rm = na.rm, useNames = useNames)
196s +         str(y0)
196s +         y1 <- rowRanges(na, na.rm = na.rm, useNames = useNames)
196s +         str(y1)
196s +         stopifnot(all.equal(y1, y0))
196s +         y1c <- colRanges(t(na), na.rm = na.rm, useNames = useNames)
196s +         str(y1c)
196s +         stopifnot(all.equal(y1c, y1))
196s +       }
196s +     } # for (name ...)
196s +   } # for (na.rm ...)
196s + }
196s integer (integer) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2    6   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  int [1:4] 1 2 3 4
196s  int [1:4] 1 2 3 4
196s  int [1:4] 1 2 3 4
196s   max:
196s  int [1:4] 9 10 11 12
196s  int [1:4] 9 10 11 12
196s  int [1:4] 9 10 11 12
196s   range:
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s integer (integer) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2    6   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  int [1:4] 1 2 3 4
196s  int [1:4] 1 2 3 4
196s  int [1:4] 1 2 3 4
196s   max:
196s  int [1:4] 9 10 11 12
196s  int [1:4] 9 10 11 12
196s  int [1:4] 9 10 11 12
196s   range:
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s integer w/ NA (integer) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA   NA   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  int [1:4] NA NA NA NA
196s  int [1:4] NA NA NA NA
196s  int [1:4] NA NA NA NA
196s   max:
196s  int [1:4] NA NA NA NA
196s  int [1:4] NA NA NA NA
196s  int [1:4] NA NA NA NA
196s   range:
196s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
196s integer w/ NA (integer) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA   NA   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  int [1:4] NA NA NA NA
196s  int [1:4] NA NA NA NA
196s  int [1:4] NA NA NA NA
196s   max:
196s  int [1:4] NA NA NA NA
196s  int [1:4] NA NA NA NA
196s  int [1:4] NA NA NA NA
196s   range:
196s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
196s real (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2    6   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s   max:
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s   range:
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s real (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2    6   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s   max:
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s   range:
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s real w/ NA (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA   NA   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s   max:
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s   range:
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s real w/ NA (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA   NA   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s   max:
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s   range:
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s real + NA cell (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2   NA   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 NA 3 4
196s  num [1:4] 1 NA 3 4
196s  num [1:4] 1 NA 3 4
196s   max:
196s  num [1:4] 9 NA 11 12
196s  num [1:4] 9 NA 11 12
196s  num [1:4] 9 NA 11 12
196s   range:
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s real + NA cell (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2   NA   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 NA 3 4
196s  num [1:4] 1 NA 3 4
196s  num [1:4] 1 NA 3 4
196s   max:
196s  num [1:4] 9 NA 11 12
196s  num [1:4] 9 NA 11 12
196s  num [1:4] 9 NA 11 12
196s   range:
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s real + NA row (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]   NA   NA   NA
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 NA 3 4
196s  num [1:4] 1 NA 3 4
196s  num [1:4] 1 NA 3 4
196s   max:
196s  num [1:4] 9 NA 11 12
196s  num [1:4] 9 NA 11 12
196s  num [1:4] 9 NA 11 12
196s   range:
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s real + NA row (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]   NA   NA   NA
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 NA 3 4
196s  num [1:4] 1 NA 3 4
196s  num [1:4] 1 NA 3 4
196s   max:
196s  num [1:4] 9 NA 11 12
196s  num [1:4] 9 NA 11 12
196s  num [1:4] 9 NA 11 12
196s   range:
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s real + NaN row (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]  NaN  NaN  NaN
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 NaN 3 4
196s  num [1:4] 1 NaN 3 4
196s  num [1:4] 1 NaN 3 4
196s   max:
196s  num [1:4] 9 NaN 11 12
196s  num [1:4] 9 NaN 11 12
196s  num [1:4] 9 NaN 11 12
196s   range:
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s real + NaN row (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]  NaN  NaN  NaN
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 NaN 3 4
196s  num [1:4] 1 NaN 3 4
196s  num [1:4] 1 NaN 3 4
196s   max:
196s  num [1:4] 9 NaN 11 12
196s  num [1:4] 9 NaN 11 12
196s  num [1:4] 9 NaN 11 12
196s   range:
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s real + Inf cell (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2  Inf   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s   max:
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s   range:
196s  num [1:4, 1:2] 1 2 3 4 9 ...
196s  num [1:4, 1:2] 1 2 3 4 9 ...
196s  num [1:4, 1:2] 1 2 3 4 9 ...
196s real + Inf cell (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2  Inf   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s   max:
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s   range:
196s  num [1:4, 1:2] 1 2 3 4 9 ...
196s  num [1:4, 1:2] 1 2 3 4 9 ...
196s  num [1:4, 1:2] 1 2 3 4 9 ...
196s real + Inf row (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]  Inf  Inf  Inf
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 Inf 3 4
196s  num [1:4] 1 Inf 3 4
196s  num [1:4] 1 Inf 3 4
196s   max:
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s   range:
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s real + Inf row (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]  Inf  Inf  Inf
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 Inf 3 4
196s  num [1:4] 1 Inf 3 4
196s  num [1:4] 1 Inf 3 4
196s   max:
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s   range:
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s real + NaN cell (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2  NaN   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 NaN 3 4
196s  num [1:4] 1 NaN 3 4
196s  num [1:4] 1 NaN 3 4
196s   max:
196s  num [1:4] 9 NaN 11 12
196s  num [1:4] 9 NaN 11 12
196s  num [1:4] 9 NaN 11 12
196s   range:
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s real + NaN cell (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2  NaN   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 NaN 3 4
196s  num [1:4] 1 NaN 3 4
196s  num [1:4] 1 NaN 3 4
196s   max:
196s  num [1:4] 9 NaN 11 12
196s  num [1:4] 9 NaN 11 12
196s  num [1:4] 9 NaN 11 12
196s   range:
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s real w/ NA + NaN cell (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA  NaN   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s   max:
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s   range:
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s real w/ NA + NaN cell (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA  NaN   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s   max:
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s   range:
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s real w/ NA + NaN row (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]  NaN  NaN  NaN
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] NA NaN NA NA
196s  num [1:4] NA NaN NA NA
196s  num [1:4] NA NaN NA NA
196s   max:
196s  num [1:4] NA NaN NA NA
196s  num [1:4] NA NaN NA NA
196s  num [1:4] NA NaN NA NA
196s   range:
196s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
196s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
196s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
196s real w/ NA + NaN row (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]  NaN  NaN  NaN
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] NA NaN NA NA
196s  num [1:4] NA NaN NA NA
196s  num [1:4] NA NaN NA NA
196s   max:
196s  num [1:4] NA NaN NA NA
196s  num [1:4] NA NaN NA NA
196s  num [1:4] NA NaN NA NA
196s   range:
196s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
196s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
196s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
196s integer (integer) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2    6   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  int [1:4] 1 2 3 4
196s  int [1:4] 1 2 3 4
196s  int [1:4] 1 2 3 4
196s   max:
196s  int [1:4] 9 10 11 12
196s  int [1:4] 9 10 11 12
196s  int [1:4] 9 10 11 12
196s   range:
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s integer (integer) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2    6   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  int [1:4] 1 2 3 4
196s  int [1:4] 1 2 3 4
196s  int [1:4] 1 2 3 4
196s   max:
196s  int [1:4] 9 10 11 12
196s  int [1:4] 9 10 11 12
196s  int [1:4] 9 10 11 12
196s   range:
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s integer w/ NA (integer) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA   NA   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s   max:
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s   range:
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s integer w/ NA (integer) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA   NA   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s   max:
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s   range:
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s real (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2    6   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s   max:
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s   range:
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s real (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2    6   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s   max:
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s   range:
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s real w/ NA (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA   NA   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s   max:
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s   range:
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s real w/ NA (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA   NA   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s   max:
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s   range:
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s real + NA cell (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2   NA   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s   max:
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s   range:
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s real + NA cell (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2   NA   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s   max:
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s   range:
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s real + NA row (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]   NA   NA   NA
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 Inf 3 4
196s  num [1:4] 1 Inf 3 4
196s  num [1:4] 1 Inf 3 4
196s   max:
196s  num [1:4] 9 -Inf 11 12
196s  num [1:4] 9 -Inf 11 12
196s  num [1:4] 9 -Inf 11 12
196s   range:
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s real + NA row (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]   NA   NA   NA
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 Inf 3 4
196s  num [1:4] 1 Inf 3 4
196s  num [1:4] 1 Inf 3 4
196s   max:
196s  num [1:4] 9 -Inf 11 12
196s  num [1:4] 9 -Inf 11 12
196s  num [1:4] 9 -Inf 11 12
196s   range:
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s real + NaN row (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]  NaN  NaN  NaN
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 Inf 3 4
196s  num [1:4] 1 Inf 3 4
196s  num [1:4] 1 Inf 3 4
196s   max:
196s  num [1:4] 9 -Inf 11 12
196s  num [1:4] 9 -Inf 11 12
196s  num [1:4] 9 -Inf 11 12
196s   range:
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s real + NaN row (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]  NaN  NaN  NaN
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 Inf 3 4
196s  num [1:4] 1 Inf 3 4
196s  num [1:4] 1 Inf 3 4
196s   max:
196s  num [1:4] 9 -Inf 11 12
196s  num [1:4] 9 -Inf 11 12
196s  num [1:4] 9 -Inf 11 12
196s   range:
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s real + Inf cell (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2  Inf   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s   max:
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s   range:
196s  num [1:4, 1:2] 1 2 3 4 9 ...
196s  num [1:4, 1:2] 1 2 3 4 9 ...
196s  num [1:4, 1:2] 1 2 3 4 9 ...
196s real + Inf cell (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2  Inf   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s   max:
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s   range:
196s  num [1:4, 1:2] 1 2 3 4 9 ...
196s  num [1:4, 1:2] 1 2 3 4 9 ...
196s  num [1:4, 1:2] 1 2 3 4 9 ...
196s real + Inf row (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]  Inf  Inf  Inf
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 Inf 3 4
196s  num [1:4] 1 Inf 3 4
196s  num [1:4] 1 Inf 3 4
196s   max:
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s   range:
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s real + Inf row (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]  Inf  Inf  Inf
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 Inf 3 4
196s  num [1:4] 1 Inf 3 4
196s  num [1:4] 1 Inf 3 4
196s   max:
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s   range:
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s real + NaN cell (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2  NaN   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s   max:
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s   range:
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s real + NaN cell (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2  NaN   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s   max:
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s   range:
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s real w/ NA + NaN cell (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA  NaN   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s   max:
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s   range:
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s real w/ NA + NaN cell (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA  NaN   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s   max:
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s   range:
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s real w/ NA + NaN row (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]  NaN  NaN  NaN
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s   max:
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s   range:
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s real w/ NA + NaN row (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]  NaN  NaN  NaN
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s   max:
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s   range:
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s integer (integer) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2    6   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  int [1:4] 1 2 3 4
196s  int [1:4] 1 2 3 4
196s  int [1:4] 1 2 3 4
196s   max:
196s  int [1:4] 9 10 11 12
196s  int [1:4] 9 10 11 12
196s  int [1:4] 9 10 11 12
196s   range:
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s integer (integer) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2    6   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  int [1:4] 1 2 3 4
196s  int [1:4] 1 2 3 4
196s  int [1:4] 1 2 3 4
196s   max:
196s  int [1:4] 9 10 11 12
196s  int [1:4] 9 10 11 12
196s  int [1:4] 9 10 11 12
196s   range:
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s integer w/ NA (integer) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA   NA   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  int [1:4] NA NA NA NA
196s  int [1:4] NA NA NA NA
196s  int [1:4] NA NA NA NA
196s   max:
196s  int [1:4] NA NA NA NA
196s  int [1:4] NA NA NA NA
196s  int [1:4] NA NA NA NA
196s   range:
196s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
196s integer w/ NA (integer) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA   NA   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  int [1:4] NA NA NA NA
196s  int [1:4] NA NA NA NA
196s  int [1:4] NA NA NA NA
196s   max:
196s  int [1:4] NA NA NA NA
196s  int [1:4] NA NA NA NA
196s  int [1:4] NA NA NA NA
196s   range:
196s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  int [1:4, 1:2] NA NA NA NA NA NA NA NA
196s real (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2    6   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s   max:
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s   range:
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s real (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2    6   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s   max:
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s   range:
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s real w/ NA (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA   NA   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s   max:
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s   range:
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s real w/ NA (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA   NA   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s   max:
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s   range:
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s real + NA cell (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2   NA   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 NA 3 4
196s  num [1:4] 1 NA 3 4
196s  num [1:4] 1 NA 3 4
196s   max:
196s  num [1:4] 9 NA 11 12
196s  num [1:4] 9 NA 11 12
196s  num [1:4] 9 NA 11 12
196s   range:
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s real + NA cell (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2   NA   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 NA 3 4
196s  num [1:4] 1 NA 3 4
196s  num [1:4] 1 NA 3 4
196s   max:
196s  num [1:4] 9 NA 11 12
196s  num [1:4] 9 NA 11 12
196s  num [1:4] 9 NA 11 12
196s   range:
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s real + NA row (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]   NA   NA   NA
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 NA 3 4
196s  num [1:4] 1 NA 3 4
196s  num [1:4] 1 NA 3 4
196s   max:
196s  num [1:4] 9 NA 11 12
196s  num [1:4] 9 NA 11 12
196s  num [1:4] 9 NA 11 12
196s   range:
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s real + NA row (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]   NA   NA   NA
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 NA 3 4
196s  num [1:4] 1 NA 3 4
196s  num [1:4] 1 NA 3 4
196s   max:
196s  num [1:4] 9 NA 11 12
196s  num [1:4] 9 NA 11 12
196s  num [1:4] 9 NA 11 12
196s   range:
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s  num [1:4, 1:2] 1 NA 3 4 9 NA 11 12
196s real + NaN row (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]  NaN  NaN  NaN
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 NaN 3 4
196s  num [1:4] 1 NaN 3 4
196s  num [1:4] 1 NaN 3 4
196s   max:
196s  num [1:4] 9 NaN 11 12
196s  num [1:4] 9 NaN 11 12
196s  num [1:4] 9 NaN 11 12
196s   range:
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s real + NaN row (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]  NaN  NaN  NaN
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 NaN 3 4
196s  num [1:4] 1 NaN 3 4
196s  num [1:4] 1 NaN 3 4
196s   max:
196s  num [1:4] 9 NaN 11 12
196s  num [1:4] 9 NaN 11 12
196s  num [1:4] 9 NaN 11 12
196s   range:
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s real + Inf cell (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2  Inf   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s   max:
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s   range:
196s  num [1:4, 1:2] 1 2 3 4 9 ...
196s  num [1:4, 1:2] 1 2 3 4 9 ...
196s  num [1:4, 1:2] 1 2 3 4 9 ...
196s real + Inf cell (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2  Inf   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s   max:
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s   range:
196s  num [1:4, 1:2] 1 2 3 4 9 ...
196s  num [1:4, 1:2] 1 2 3 4 9 ...
196s  num [1:4, 1:2] 1 2 3 4 9 ...
196s real + Inf row (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]  Inf  Inf  Inf
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 Inf 3 4
196s  num [1:4] 1 Inf 3 4
196s  num [1:4] 1 Inf 3 4
196s   max:
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s   range:
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s real + Inf row (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]  Inf  Inf  Inf
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 Inf 3 4
196s  num [1:4] 1 Inf 3 4
196s  num [1:4] 1 Inf 3 4
196s   max:
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s  num [1:4] 9 Inf 11 12
196s   range:
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s  num [1:4, 1:2] 1 Inf 3 4 9 ...
196s real + NaN cell (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2  NaN   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 NaN 3 4
196s  num [1:4] 1 NaN 3 4
196s  num [1:4] 1 NaN 3 4
196s   max:
196s  num [1:4] 9 NaN 11 12
196s  num [1:4] 9 NaN 11 12
196s  num [1:4] 9 NaN 11 12
196s   range:
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s real + NaN cell (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2  NaN   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 NaN 3 4
196s  num [1:4] 1 NaN 3 4
196s  num [1:4] 1 NaN 3 4
196s   max:
196s  num [1:4] 9 NaN 11 12
196s  num [1:4] 9 NaN 11 12
196s  num [1:4] 9 NaN 11 12
196s   range:
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s  num [1:4, 1:2] 1 NaN 3 4 9 NaN 11 12
196s real w/ NA + NaN cell (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA  NaN   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s   max:
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s   range:
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s real w/ NA + NaN cell (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA  NaN   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s   max:
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s  num [1:4] NA NA NA NA
196s   range:
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s  num [1:4, 1:2] NA NA NA NA NA NA NA NA
196s real w/ NA + NaN row (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]  NaN  NaN  NaN
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] NA NaN NA NA
196s  num [1:4] NA NaN NA NA
196s  num [1:4] NA NaN NA NA
196s   max:
196s  num [1:4] NA NaN NA NA
196s  num [1:4] NA NaN NA NA
196s  num [1:4] NA NaN NA NA
196s   range:
196s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
196s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
196s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
196s real w/ NA + NaN row (double) w/ na.rm = FALSE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]  NaN  NaN  NaN
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] NA NaN NA NA
196s  num [1:4] NA NaN NA NA
196s  num [1:4] NA NaN NA NA
196s   max:
196s  num [1:4] NA NaN NA NA
196s  num [1:4] NA NaN NA NA
196s  num [1:4] NA NaN NA NA
196s   range:
196s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
196s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
196s  num [1:4, 1:2] NA NaN NA NA NA NaN NA NA
196s integer (integer) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2    6   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  int [1:4] 1 2 3 4
196s  int [1:4] 1 2 3 4
196s  int [1:4] 1 2 3 4
196s   max:
196s  int [1:4] 9 10 11 12
196s  int [1:4] 9 10 11 12
196s  int [1:4] 9 10 11 12
196s   range:
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s integer (integer) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2    6   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  int [1:4] 1 2 3 4
196s  int [1:4] 1 2 3 4
196s  int [1:4] 1 2 3 4
196s   max:
196s  int [1:4] 9 10 11 12
196s  int [1:4] 9 10 11 12
196s  int [1:4] 9 10 11 12
196s   range:
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  int [1:4, 1:2] 1 2 3 4 9 10 11 12
196s integer w/ NA (integer) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA   NA   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s   max:
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s   range:
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s integer w/ NA (integer) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA   NA   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s   max:
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s   range:
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s real (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2    6   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s   max:
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s   range:
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s real (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]    1    5    9
196s [2,]    2    6   10
196s [3,]    3    7   11
196s [4,]    4    8   12
196s   min:
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s  num [1:4] 1 2 3 4
196s   max:
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s  num [1:4] 9 10 11 12
196s   range:
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
196s real w/ NA (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA   NA   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s   max:
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s   range:
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s real w/ NA (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
196s [1,]   NA   NA   NA
196s [2,]   NA   NA   NA
196s [3,]   NA   NA   NA
196s [4,]   NA   NA   NA
196s   min:
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s  num [1:4] Inf Inf Inf Inf
196s   max:
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s  num [1:4] -Inf -Inf -Inf -Inf
196s   range:
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
196s real + NA cell (double) w/ na.rm = TRUE:
196s      [,1] [,2] [,3]
197s [1,]    1    5    9
197s [2,]    2   NA   10
197s [3,]    3    7   11
197s [4,]    4    8   12
197s   min:
197s  num [1:4] 1 2 3 4
197s  num [1:4] 1 2 3 4
197s  num [1:4] 1 2 3 4
197s   max:
197s  num [1:4] 9 10 11 12
197s  num [1:4] 9 10 11 12
197s  num [1:4] 9 10 11 12
197s   range:
197s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
197s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
197s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
197s real + NA cell (double) w/ na.rm = TRUE:
197s      [,1] [,2] [,3]
197s [1,]    1    5    9
197s [2,]    2   NA   10
197s [3,]    3    7   11
197s [4,]    4    8   12
197s   min:
197s  num [1:4] 1 2 3 4
197s  num [1:4] 1 2 3 4
197s  num [1:4] 1 2 3 4
197s   max:
197s  num [1:4] 9 10 11 12
197s  num [1:4] 9 10 11 12
197s  num [1:4] 9 10 11 12
197s   range:
197s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
197s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
197s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
197s real + NA row (double) w/ na.rm = TRUE:
197s      [,1] [,2] [,3]
197s [1,]    1    5    9
197s [2,]   NA   NA   NA
197s [3,]    3    7   11
197s [4,]    4    8   12
197s   min:
197s  num [1:4] 1 Inf 3 4
197s  num [1:4] 1 Inf 3 4
197s  num [1:4] 1 Inf 3 4
197s   max:
197s  num [1:4] 9 -Inf 11 12
197s  num [1:4] 9 -Inf 11 12
197s  num [1:4] 9 -Inf 11 12
197s   range:
197s  num [1:4, 1:2] 1 Inf 3 4 9 ...
197s  num [1:4, 1:2] 1 Inf 3 4 9 ...
197s  num [1:4, 1:2] 1 Inf 3 4 9 ...
197s real + NA row (double) w/ na.rm = TRUE:
197s      [,1] [,2] [,3]
197s [1,]    1    5    9
197s [2,]   NA   NA   NA
197s [3,]    3    7   11
197s [4,]    4    8   12
197s   min:
197s  num [1:4] 1 Inf 3 4
197s  num [1:4] 1 Inf 3 4
197s  num [1:4] 1 Inf 3 4
197s   max:
197s  num [1:4] 9 -Inf 11 12
197s  num [1:4] 9 -Inf 11 12
197s  num [1:4] 9 -Inf 11 12
197s   range:
197s  num [1:4, 1:2] 1 Inf 3 4 9 ...
197s  num [1:4, 1:2] 1 Inf 3 4 9 ...
197s  num [1:4, 1:2] 1 Inf 3 4 9 ...
197s real + NaN row (double) w/ na.rm = TRUE:
197s      [,1] [,2] [,3]
197s [1,]    1    5    9
197s [2,]  NaN  NaN  NaN
197s [3,]    3    7   11
197s [4,]    4    8   12
197s   min:
197s  num [1:4] 1 Inf 3 4
197s  num [1:4] 1 Inf 3 4
197s  num [1:4] 1 Inf 3 4
197s   max:
197s  num [1:4] 9 -Inf 11 12
197s  num [1:4] 9 -Inf 11 12
197s  num [1:4] 9 -Inf 11 12
197s   range:
197s  num [1:4, 1:2] 1 Inf 3 4 9 ...
197s  num [1:4, 1:2] 1 Inf 3 4 9 ...
197s  num [1:4, 1:2] 1 Inf 3 4 9 ...
197s real + NaN row (double) w/ na.rm = TRUE:
197s      [,1] [,2] [,3]
197s [1,]    1    5    9
197s [2,]  NaN  NaN  NaN
197s [3,]    3    7   11
197s [4,]    4    8   12
197s   min:
197s  num [1:4] 1 Inf 3 4
197s  num [1:4] 1 Inf 3 4
197s  num [1:4] 1 Inf 3 4
197s   max:
197s  num [1:4] 9 -Inf 11 12
197s  num [1:4] 9 -Inf 11 12
197s  num [1:4] 9 -Inf 11 12
197s   range:
197s  num [1:4, 1:2] 1 Inf 3 4 9 ...
197s  num [1:4, 1:2] 1 Inf 3 4 9 ...
197s  num [1:4, 1:2] 1 Inf 3 4 9 ...
197s real + Inf cell (double) w/ na.rm = TRUE:
197s      [,1] [,2] [,3]
197s [1,]    1    5    9
197s [2,]    2  Inf   10
197s [3,]    3    7   11
197s [4,]    4    8   12
197s   min:
197s  num [1:4] 1 2 3 4
197s  num [1:4] 1 2 3 4
197s  num [1:4] 1 2 3 4
197s   max:
197s  num [1:4] 9 Inf 11 12
197s  num [1:4] 9 Inf 11 12
197s  num [1:4] 9 Inf 11 12
197s   range:
197s  num [1:4, 1:2] 1 2 3 4 9 ...
197s  num [1:4, 1:2] 1 2 3 4 9 ...
197s  num [1:4, 1:2] 1 2 3 4 9 ...
197s real + Inf cell (double) w/ na.rm = TRUE:
197s      [,1] [,2] [,3]
197s [1,]    1    5    9
197s [2,]    2  Inf   10
197s [3,]    3    7   11
197s [4,]    4    8   12
197s   min:
197s  num [1:4] 1 2 3 4
197s  num [1:4] 1 2 3 4
197s  num [1:4] 1 2 3 4
197s   max:
197s  num [1:4] 9 Inf 11 12
197s  num [1:4] 9 Inf 11 12
197s  num [1:4] 9 Inf 11 12
197s   range:
197s  num [1:4, 1:2] 1 2 3 4 9 ...
197s  num [1:4, 1:2] 1 2 3 4 9 ...
197s  num [1:4, 1:2] 1 2 3 4 9 ...
197s real + Inf row (double) w/ na.rm = TRUE:
197s      [,1] [,2] [,3]
197s [1,]    1    5    9
197s [2,]  Inf  Inf  Inf
197s [3,]    3    7   11
197s [4,]    4    8   12
197s   min:
197s  num [1:4] 1 Inf 3 4
197s  num [1:4] 1 Inf 3 4
197s  num [1:4] 1 Inf 3 4
197s   max:
197s  num [1:4] 9 Inf 11 12
197s  num [1:4] 9 Inf 11 12
197s  num [1:4] 9 Inf 11 12
197s   range:
197s  num [1:4, 1:2] 1 Inf 3 4 9 ...
197s  num [1:4, 1:2] 1 Inf 3 4 9 ...
197s  num [1:4, 1:2] 1 Inf 3 4 9 ...
197s real + Inf row (double) w/ na.rm = TRUE:
197s      [,1] [,2] [,3]
197s [1,]    1    5    9
197s [2,]  Inf  Inf  Inf
197s [3,]    3    7   11
197s [4,]    4    8   12
197s   min:
197s  num [1:4] 1 Inf 3 4
197s  num [1:4] 1 Inf 3 4
197s  num [1:4] 1 Inf 3 4
197s   max:
197s  num [1:4] 9 Inf 11 12
197s  num [1:4] 9 Inf 11 12
197s  num [1:4] 9 Inf 11 12
197s   range:
197s  num [1:4, 1:2] 1 Inf 3 4 9 ...
197s  num [1:4, 1:2] 1 Inf 3 4 9 ...
197s  num [1:4, 1:2] 1 Inf 3 4 9 ...
197s real + NaN cell (double) w/ na.rm = TRUE:
197s      [,1] [,2] [,3]
197s [1,]    1    5    9
197s [2,]    2  NaN   10
197s [3,]    3    7   11
197s [4,]    4    8   12
197s   min:
197s  num [1:4] 1 2 3 4
197s  num [1:4] 1 2 3 4
197s  num [1:4] 1 2 3 4
197s   max:
197s  num [1:4] 9 10 11 12
197s  num [1:4] 9 10 11 12
197s  num [1:4] 9 10 11 12
197s   range:
197s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
197s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
197s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
197s real + NaN cell (double) w/ na.rm = TRUE:
197s      [,1] [,2] [,3]
197s [1,]    1    5    9
197s [2,]    2  NaN   10
197s [3,]    3    7   11
197s [4,]    4    8   12
197s   min:
197s  num [1:4] 1 2 3 4
197s  num [1:4] 1 2 3 4
197s  num [1:4] 1 2 3 4
197s   max:
197s  num [1:4] 9 10 11 12
197s  num [1:4] 9 10 11 12
197s  num [1:4] 9 10 11 12
197s   range:
197s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
197s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
197s  num [1:4, 1:2] 1 2 3 4 9 10 11 12
197s real w/ NA + NaN cell (double) w/ na.rm = TRUE:
197s      [,1] [,2] [,3]
197s [1,]   NA   NA   NA
197s [2,]   NA  NaN   NA
197s [3,]   NA   NA   NA
197s [4,]   NA   NA   NA
197s   min:
197s  num [1:4] Inf Inf Inf Inf
197s  num [1:4] Inf Inf Inf Inf
197s  num [1:4] Inf Inf Inf Inf
197s   max:
197s  num [1:4] -Inf -Inf -Inf -Inf
197s  num [1:4] -Inf -Inf -Inf -Inf
197s  num [1:4] -Inf -Inf -Inf -Inf
197s   range:
197s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
197s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
197s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
197s real w/ NA + NaN cell (double) w/ na.rm = TRUE:
197s      [,1] [,2] [,3]
197s [1,]   NA   NA   NA
197s [2,]   NA  NaN   NA
197s [3,]   NA   NA   NA
197s [4,]   NA   NA   NA
197s   min:
197s  num [1:4] Inf Inf Inf Inf
197s  num [1:4] Inf Inf Inf Inf
197s  num [1:4] Inf Inf Inf Inf
197s   max:
197s  num [1:4] -Inf -Inf -Inf -Inf
197s  num [1:4] -Inf -Inf -Inf -Inf
197s  num [1:4] -Inf -Inf -Inf -Inf
197s   range:
197s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
197s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
197s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
197s real w/ NA + NaN row (double) w/ na.rm = TRUE:
197s      [,1] [,2] [,3]
197s [1,]   NA   NA   NA
197s [2,]  NaN  NaN  NaN
197s [3,]   NA   NA   NA
197s [4,]   NA   NA   NA
197s   min:
197s  num [1:4] Inf Inf Inf Inf
197s  num [1:4] Inf Inf Inf Inf
197s  num [1:4] Inf Inf Inf Inf
197s   max:
197s  num [1:4] -Inf -Inf -Inf -Inf
197s  num [1:4] -Inf -Inf -Inf -Inf
197s  num [1:4] -Inf -Inf -Inf -Inf
197s   range:
197s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
197s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
197s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
197s real w/ NA + NaN row (double) w/ na.rm = TRUE:
197s      [,1] [,2] [,3]
197s [1,]   NA   NA   NA
197s [2,]  NaN  NaN  NaN
197s [3,]   NA   NA   NA
197s [4,]   NA   NA   NA
197s   min:
197s  num [1:4] Inf Inf Inf Inf
197s  num [1:4] Inf Inf Inf Inf
197s  num [1:4] Inf Inf Inf Inf
197s   max:
197s  num [1:4] -Inf -Inf -Inf -Inf
197s  num [1:4] -Inf -Inf -Inf -Inf
197s  num [1:4] -Inf -Inf -Inf -Inf
197s   range:
197s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
197s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
197s  num [1:4, 1:2] Inf Inf Inf Inf -Inf ...
197s > 
197s 
197s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
197s Copyright (C) 2025 The R Foundation for Statistical Computing
197s Platform: x86_64-pc-linux-gnu
197s 
197s R is free software and comes with ABSOLUTELY NO WARRANTY.
197s You are welcome to redistribute it under certain conditions.
197s Type 'license()' or 'licence()' for distribution details.
197s 
197s R is a collaborative project with many contributors.
197s Type 'contributors()' for more information and
197s 'citation()' on how to cite R or R packages in publications.
197s 
197s Type 'demo()' for some demos, 'help()' for on-line help, or
197s 'help.start()' for an HTML browser interface to help.
197s Type 'q()' to quit R.
197s 
197s > library("matrixStats")
197s > 
197s > rowMins_R <- function(x, ..., useNames = TRUE) {
197s +   suppressWarnings({
197s +     res <- apply(x, MARGIN = 1L, FUN = min, ...)
197s +   })
197s +   if (!useNames) names(res) <- NULL
197s +   res
197s + } # rowMins_R()
197s > 
197s > rowMaxs_R <- function(x, ..., useNames = TRUE) {
197s +   suppressWarnings({
197s +     res <- apply(x, MARGIN = 1L, FUN = max, ...)
197s +   })
197s +   if (!useNames) names(res) <- NULL
197s +   res
197s + } # rowMaxs_R()
197s > 
197s > rowRanges_R <- function(x, ..., useNames = TRUE) {
197s +   suppressWarnings({
197s +     ans <- t(apply(x, MARGIN = 1L, FUN = range, ...))
197s +   })
197s + 
197s +   # Preserve rownames attribute
197s +   dim <- c(dim(x)[1], 2L)
197s +   if (!isTRUE(all.equal(dim(ans), dim))) {
197s +     dim(ans) <- dim
197s +     rownames <- rownames(x)
197s +     if (!is.null(dimnames)) rownames(ans) <- rownames
197s +   }
197s +   if (!useNames) dimnames(ans) <- NULL
197s +   ans
197s + } # rowRanges_R()
197s > 
197s > 
197s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
197s > # Subsetted tests
197s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
197s > source("utils/validateIndicesFramework.R")
197s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
197s > storage.mode(x) <- "integer"
197s > 
197s > # To check rownames/names attributes
197s > dimnames <- list(letters[1:6], LETTERS[1:6])
197s > 
197s > # Test with and without dimnames on x
197s > for (setDimnames in c(TRUE, FALSE)) {
197s +   if (setDimnames) dimnames(x) <- dimnames
197s +   else dimnames(x) <- NULL
197s +   
197s +   count <- 0L
197s +   for (rows in index_cases) {
197s +     for (cols in index_cases) {
197s +       count <- count + 1L
197s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
197s +       useNames <- c(TRUE, FALSE)
197s +       useNames <- useNames[count %% length(useNames) + 1]
197s + 
197s +       validateIndicesTestMatrix(x, rows, cols,
197s +                                 ftest = rowRanges, fsure = rowRanges_R,
197s +                                 na.rm = na.rm, useNames = useNames)
197s +       validateIndicesTestMatrix(x, rows, cols,
197s +                                 ftest = rowMins, fsure = rowMins_R,
197s +                                 na.rm = na.rm, useNames = useNames)
197s +       validateIndicesTestMatrix(x, rows, cols,
197s +                                 ftest = rowMaxs, fsure = rowMaxs_R,
197s +                                 na.rm = na.rm, useNames = useNames)
197s + 
197s +       validateIndicesTestMatrix(x, rows, cols,
197s +                                 fcoltest = colRanges, fsure = rowRanges_R,
197s +                                 na.rm = na.rm, useNames = useNames)
197s +       validateIndicesTestMatrix(x, rows, cols,
197s +                                 fcoltest = colMins, fsure = rowMins_R,
197s +                                 na.rm = na.rm, useNames = useNames)
197s +       validateIndicesTestMatrix(x, rows, cols,
197s +                                 fcoltest = colMaxs, fsure = rowMaxs_R,
197s +                                 na.rm = na.rm, useNames = useNames)
197s +     }
197s +   }
197s + }
197s > 
197s 
197s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
197s Copyright (C) 2025 The R Foundation for Statistical Computing
197s Platform: x86_64-pc-linux-gnu
197s 
197s R is free software and comes with ABSOLUTELY NO WARRANTY.
197s You are welcome to redistribute it under certain conditions.
197s Type 'license()' or 'licence()' for distribution details.
197s 
197s R is a collaborative project with many contributors.
197s Type 'contributors()' for more information and
197s 'citation()' on how to cite R or R packages in publications.
197s 
197s Type 'demo()' for some demos, 'help()' for on-line help, or
197s 'help.start()' for an HTML browser interface to help.
197s Type 'q()' to quit R.
197s 
197s > library("matrixStats")
197s > 
197s > dense_rank <- function(x) match(x, table = sort(unique(x)))
197s > 
197s > rowRanks_R <- function(x, ties.method, ..., useNames = TRUE) {
197s +   if (ties.method == "dense") {
197s +     res <- t(apply(x, MARGIN = 1L, FUN = dense_rank))
197s +   } else {
197s +     res <- t(apply(x, MARGIN = 1L, FUN = rank, na.last = "keep", ties.method = ties.method))
197s +   }
197s +   
197s +   # Preserve dimnames attribute?
197s +   dim(res) <- dim(x)
197s +   dimnames(res) <- if (useNames) dimnames(x) else NULL
197s +   
197s +   res
197s + }
197s > 
197s > colRanks_R <- function(x, ties.method, preserveShape = FALSE, ..., useNames = TRUE) {
197s +   if (ties.method == "dense") {
197s +     res <- t(apply(x, MARGIN = 2L, FUN = dense_rank))
197s +   } else {
197s +     res <- t(apply(x, MARGIN = 2L, FUN = rank, na.last = "keep", ties.method = ties.method))
197s +   }
197s +   
197s +   # Preserve dimnames attribute?
197s +   tx <- t(x)
197s +   dim(res) <- dim(tx)
197s +   dimnames(res) <- if (useNames) dimnames(tx) else NULL
197s +   
197s +   if (preserveShape) res <- t(res)
197s +   res
197s + }
197s > 
197s > set.seed(1)
197s > 
197s > cat("Consistency checks:\n")
197s Consistency checks:
197s > xs <- vector("list", length = 4L)
197s > for (kk in 1:4) {
197s +   
197s +   # Simulate data in a matrix of any shape
197s +   dim <- sample(40:80, size = 2L)
197s +   n <- prod(dim)
197s +   x <- rnorm(n, sd = 10)
197s +   dim(x) <- dim
197s +   
197s +   # Add NAs?
197s +   if ((kk %% 4) %in% c(3, 0)) {
197s +     cat("Adding NAs\n")
197s +     nna <- sample(n, size = 1L)
197s +     x[sample(length(x), size = nna)] <- NA_real_
197s +   }
197s +   
197s +   # Integer or double?
197s +   if ((kk %% 4) %in% c(2, 0)) {
197s +     cat("Coercing to integers\n")
197s +     storage.mode(x) <- "integer"
197s +   }
197s + 
197s +   xs[[kk]] <- x
197s + } # for (kk ...)
197s Coercing to integers
197s Adding NAs
197s Adding NAs
197s Coercing to integers
197s > str(xs)
197s List of 4
197s  $ : num [1:43, 1:78] 13.3 12.72 4.15 -15.4 -9.29 ...
197s  $ : int [1:46, 1:61] 2 11 -16 -5 19 5 26 -13 1 -9 ...
197s  $ : num [1:42, 1:47] NA -22.3 NA NA NA ...
197s  $ : int [1:42, 1:78] NA NA NA NA NA NA NA NA NA NA ...
197s > 
197s > for (kk in 1:4) {
197s +   cat("Random test #", kk, "\n", sep = "")
197s +   x <- xs[[kk]]
197s +   tx <- t(x)
197s +   
197s +   for (ties in c("max", "min", "average", "first", "last", "dense")) {
197s +     cat(sprintf("ties.method = %s\n", ties))
197s +     # rowRanks():
197s +     y1 <- matrixStats::rowRanks(x, ties.method = ties)
197s +     y2 <- rowRanks_R(x, ties.method = ties)
197s +     stopifnot(identical(y1, y2))
197s +     
197s +     y3 <- matrixStats::colRanks(tx, ties.method = ties)
197s +     stopifnot(identical(y1, y3))
197s +     
197s +     # colRanks():
197s +     y1 <- matrixStats::colRanks(x, ties.method = ties)
197s +     y2 <- colRanks_R(x, ties.method = ties)
197s +     stopifnot(identical(y1, y2))
197s +     
197s +     y3 <- matrixStats::rowRanks(tx, ties.method = ties)
197s +     stopifnot(identical(y1, y3))
197s +   }
197s + } # for (kk ...)
197s Random test #1
197s ties.method = max
197s ties.method = min
197s ties.method = average
197s ties.method = first
197s ties.method = last
197s ties.method = dense
197s Random test #2
197s ties.method = max
197s ties.method = min
197s ties.method = average
197s ties.method = first
197s ties.method = last
197s ties.method = dense
197s Random test #3
197s ties.method = max
197s ties.method = min
197s ties.method = average
197s ties.method = first
197s ties.method = last
197s ties.method = dense
197s Random test #4
197s ties.method = max
197s ties.method = min
197s ties.method = average
197s ties.method = first
197s ties.method = last
197s ties.method = dense
198s > 
198s > # Note, below we know ties.method %in% c("min", "max", "average") is correct
198s > 
198s > cat("Consistency checks for random:\n")
198s Consistency checks for random:
198s > tolerance <- 0.1
198s > nsamples <- 10000
198s > for (kk in 1:4) {
198s +   cat("Random test #", kk, "\n", sep = "")
198s +   x <- xs[[kk]]
198s +   tx <- t(x)
198s + 
198s +   for (ties in c("random")) {
198s +     cat(sprintf("ties.method = %s\n", ties))
198s +     
198s +     ## rowRanks():
198s +     y0 <- rowRanks_R(x, ties.method = ties)
198s +     y1 <- matrixStats::rowRanks(x, ties.method = ties)
198s +     
198s +     ## Assert symmetric rank differences
198s +     d <- y1 - y0
198s +     stopifnot(all(rowSums(d) == 0, na.rm = TRUE))
198s +     
198s +     ## Assert within [min, max]
198s +     y2min <- matrixStats::rowRanks(x, ties.method = "min")
198s +     y2max <- matrixStats::rowRanks(x, ties.method = "max")
198s +     stopifnot(all(y1 >= y2min, na.rm = TRUE) && all(y1 <= y2max, na.rm = TRUE))
198s +     ## Assert near average
198s +     y1list <- replicate(nsamples, matrixStats::rowRanks(x, ties.method = ties), simplify = FALSE)
198s +     y1mean <- Reduce(`+`, y1list) / nsamples
198s +     y2avg <- matrixStats::rowRanks(x, ties.method = "average")
198s +     stopifnot(all(abs(y1mean - y2avg) < tolerance, na.rm = TRUE))
198s + 
198s +     ## colRanks():
198s +     y0 <- colRanks_R(x, ties.method = ties)
198s +     y1 <- matrixStats::colRanks(x, ties.method = ties)
198s + 
198s +     ## Assert symmetric rank differences
198s +     d <- y1 - y0
198s +     stopifnot(all(rowSums(d) == 0, na.rm = TRUE))
198s + 
198s +     ## Assert within [min, max]
198s +     y2min <- matrixStats::colRanks(x, ties.method = "min")
198s +     y2max <- matrixStats::colRanks(x, ties.method = "max")
198s +     stopifnot(all(y1 >= y2min, na.rm = TRUE) && all(y1 <= y2max, na.rm = TRUE))
198s +     y1list <- replicate(nsamples, matrixStats::colRanks(x, ties.method = ties), simplify = FALSE)
198s +     y1mean <- Reduce(`+`, y1list) / nsamples
198s +     ## Assert near average
198s +     y2avg <- matrixStats::colRanks(x, ties.method = "average")
198s +     stopifnot(all(abs(y1mean - y2avg) < tolerance, na.rm = TRUE))
198s +   }
198s + } # for (kk ...)
198s Random test #1
198s ties.method = random
199s Random test #2
199s ties.method = random
200s Random test #3
200s ties.method = random
200s Random test #4
200s ties.method = random
201s > 
201s > 
201s > ## Exception handling
201s > x <- matrix(1:12, nrow = 3L, ncol = 4L)
201s > y <- try(rowRanks(x, ties.method = "unknown"), silent = TRUE)
201s > stopifnot(inherits(y, "try-error"))
201s > 
201s > y <- try(colRanks(x, ties.method = "unknown"), silent = TRUE)
201s > stopifnot(inherits(y, "try-error"))
201s > 
201s > dimnames <- list(letters[1:3], LETTERS[1:4])
201s > for (mode in c("integer", "double")){
201s +   storage.mode(x) <- mode
201s +   # Test with and without dimnames on x
201s +   for (setDimnames in c(TRUE, FALSE)) {
201s +     if (setDimnames) dimnames(x) <- dimnames
201s +     else dimnames(x) <- NULL
201s +     # Check names attribute
201s +     for (useNames in c(TRUE, FALSE)) {
201s +       for (ties in c("max", "min", "average", "first", "last", "dense", "random")) {
201s +         cat(sprintf("ties.method = %s\n", ties))
201s +         # rowRanks():
201s +         y1 <- matrixStats::rowRanks(x, ties.method = ties, useNames = useNames)
201s +         y2 <- rowRanks_R(x, ties.method = ties, useNames = useNames)
201s +         stopifnot(identical(y1, y2))
201s +         
201s +         y3 <- matrixStats::colRanks(t(x), ties.method = ties, useNames = useNames)
201s +         stopifnot(identical(y1, y3))
201s +         
201s +         # colRanks():
201s +         y1 <- matrixStats::colRanks(x, ties.method = ties, useNames = useNames)
201s +         y2 <- colRanks_R(x, ties.method = ties, useNames = useNames)
201s +         stopifnot(identical(y1, y2))
201s +         
201s +         y3 <- matrixStats::rowRanks(t(x), ties.method = ties, useNames = useNames)
201s +         stopifnot(identical(y1, y3))
201s +         
201s +         # Check preserveShape
201s +         y1 <- matrixStats::colRanks(x, ties.method = ties, preserveShape = TRUE, useNames = useNames)
201s +         y2 <- colRanks_R(x, ties.method = ties, preserveShape = TRUE, useNames = useNames)
201s +         stopifnot(identical(y1, y2))
201s +       }
201s +     }
201s +   }
201s + }
201s ties.method = max
201s ties.method = min
201s ties.method = average
201s ties.method = first
201s ties.method = last
201s ties.method = dense
201s ties.method = random
201s ties.method = max
201s ties.method = min
201s ties.method = average
201s ties.method = first
201s ties.method = last
201s ties.method = dense
201s ties.method = random
201s ties.method = max
201s ties.method = min
201s ties.method = average
201s ties.method = first
201s ties.method = last
201s ties.method = dense
201s ties.method = random
201s ties.method = max
201s ties.method = min
201s ties.method = average
201s ties.method = first
201s ties.method = last
201s ties.method = dense
201s ties.method = random
201s ties.method = max
201s ties.method = min
201s ties.method = average
201s ties.method = first
201s ties.method = last
201s ties.method = dense
201s ties.method = random
201s ties.method = max
201s ties.method = min
201s ties.method = average
201s ties.method = first
201s ties.method = last
201s ties.method = dense
201s ties.method = random
201s ties.method = max
201s ties.method = min
201s ties.method = average
201s ties.method = first
201s ties.method = last
201s ties.method = dense
201s ties.method = random
201s ties.method = max
201s ties.method = min
201s ties.method = average
201s ties.method = first
201s ties.method = last
201s ties.method = dense
201s ties.method = random
201s > 
201s 
201s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
201s Copyright (C) 2025 The R Foundation for Statistical Computing
201s Platform: x86_64-pc-linux-gnu
201s 
201s R is free software and comes with ABSOLUTELY NO WARRANTY.
201s You are welcome to redistribute it under certain conditions.
201s Type 'license()' or 'licence()' for distribution details.
201s 
201s R is a collaborative project with many contributors.
201s Type 'contributors()' for more information and
201s 'citation()' on how to cite R or R packages in publications.
201s 
201s Type 'demo()' for some demos, 'help()' for on-line help, or
201s 'help.start()' for an HTML browser interface to help.
201s Type 'q()' to quit R.
201s 
201s > library("matrixStats")
201s > 
201s > rowRanks_R <- function(x, ties.method = "average", ..., useNames = TRUE) {
201s +   ans <- t(apply(x, MARGIN = 1L, FUN = rank, na.last = "keep",
201s +                  ties.method = ties.method))
201s +   
201s +   # Preserve dimnames attribute?
201s +   dim(ans) <- dim(x)
201s +   dimnames(ans) <- if (useNames) dimnames(x) else NULL
201s + 
201s +   ans
201s + }
201s > 
201s > colRanks_R <- function(x, ties.method, preserveShape = FALSE, ..., useNames = TRUE) {
201s +   ans <- t(apply(x, MARGIN = 2L, FUN = rank, na.last = "keep", ties.method = ties.method))
201s +   
201s +   # Preserve dimnames attribute?
201s +   tx <- t(x)
201s +   dim(ans) <- dim(tx)
201s +   dimnames(ans) <- if (useNames) dimnames(tx) else NULL
201s +   
201s +   if (preserveShape) ans <- t(ans)
201s +   ans
201s + }
201s > 
201s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
201s > # Subsetted tests
201s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
201s > source("utils/validateIndicesFramework.R")
201s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
201s > storage.mode(x) <- "integer"
201s > 
201s > # To check dimnames attribute
201s > dimnames <- list(letters[1:6], LETTERS[1:6])
201s > 
201s > colRanks_R_t <- function(x, rows, cols, ..., useNames = TRUE) {
201s +   t(colRanks(t(x), rows = cols, cols = rows, preserveShape = TRUE, ..., useNames = useNames))
201s + }
201s > 
201s > # Test with and without dimnames on x
201s > for (setDimnames in c(TRUE, FALSE)) {
201s +   if (setDimnames) dimnames(x) <- dimnames
201s +   else dimnames(x) <- NULL
201s + 
201s +   count <- 0L
201s +   for (rows in index_cases) {
201s +     for (cols in index_cases) {
201s +       count <- count + 1L
201s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
201s +       useNames <- c(TRUE, FALSE)
201s +       useNames <- useNames[count %% length(useNames) + 1]
201s + 
201s +       validateIndicesTestMatrix(x, rows, cols,
201s +                                 ftest = rowRanks, fsure = rowRanks_R,
201s +                                 ties.method = "average", useNames = useNames)
201s +       
201s +       validateIndicesTestMatrix(x, rows, cols,
201s +                                 ftest = colRanks_R_t, fsure = rowRanks_R,
201s +                                 ties.method = "average", useNames = useNames)
201s +       
201s +       for (perserveShape in c(TRUE, FALSE)) {
201s +         validateIndicesTestMatrix(x, rows, cols,
201s +                                   ftest = colRanks, fsure = colRanks_R,
201s +                                   ties.method = "average", perserveShape = perserveShape,
201s +                                   useNames = useNames)          
201s +       }
201s +     }
201s +   }
201s + }
201s > 
201s 
201s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
201s Copyright (C) 2025 The R Foundation for Statistical Computing
201s Platform: x86_64-pc-linux-gnu
201s 
201s R is free software and comes with ABSOLUTELY NO WARRANTY.
201s You are welcome to redistribute it under certain conditions.
201s Type 'license()' or 'licence()' for distribution details.
201s 
201s R is a collaborative project with many contributors.
201s Type 'contributors()' for more information and
201s 'citation()' on how to cite R or R packages in publications.
201s 
201s Type 'demo()' for some demos, 'help()' for on-line help, or
201s 'help.start()' for an HTML browser interface to help.
201s Type 'q()' to quit R.
201s 
201s > library("matrixStats")
201s > 
201s > ## Always allow testing of the 'center' argument (as long as it's not defunct)
201s > options(matrixStats.center.onUse = "ignore")
201s > 
201s > ## Create isFALSE() if running on an old version of R
201s > if (!exists("isFALSE", mode="function")) {
201s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
201s + }
201s > 
201s > rowSds_R <- function(x, na.rm = FALSE, center = NULL, ..., useNames = TRUE) {
201s +   suppressWarnings({
201s +     sigma <- apply(x, MARGIN = 1L, FUN = sd, na.rm = na.rm)
201s +   })
201s +   stopifnot(!any(is.infinite(sigma)))
201s +   
201s +   # Keep naming support consistency same as rowSds()
201s +   if (is.null(center) || ncol(x) <= 1L) {
201s +     if (isFALSE(useNames)) names(sigma) <- NULL
201s +   }
201s +   else if (isFALSE(useNames)) names(sigma) <- NULL
201s +   sigma
201s + }
201s > 
201s > colSds_R <- function(x, na.rm = FALSE, center = NULL, ..., useNames = TRUE) {
201s +   suppressWarnings({
201s +     sigma <- apply(x, MARGIN = 2L, FUN = sd, na.rm = na.rm)
201s +   })
201s +   stopifnot(!any(is.infinite(sigma)))
201s +   
201s +   # Keep naming support consistency same as colSds()
201s +   if (is.null(center) || nrow(x) <= 1L) {
201s +     if (isFALSE(useNames)) names(sigma) <- NULL
201s +   }
201s +   if (isFALSE(useNames)) names(sigma) <- NULL
201s +   sigma
201s + }
201s > 
201s > 
201s > rowSds_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = TRUE) {
201s +   center <- rowWeightedMeans(x, cols = cols, na.rm = na.rm, useNames = FALSE)
201s +   sigma <- rowSds(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
201s +   stopifnot(!any(is.infinite(sigma)))
201s +   sigma
201s + }
201s > 
201s > colSds_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = TRUE) {
201s +   center <- colWeightedMeans(x, rows = rows, na.rm = na.rm, useNames = FALSE)
201s +   sigma <- colSds(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
201s +   stopifnot(!any(is.infinite(sigma)))
201s +   sigma
201s + }
201s > 
201s > 
201s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
201s > # With and without some NAs
201s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
201s > for (mode in c("integer", "double")) {
201s +   for (add_na in c(FALSE, TRUE)) {
201s +     cat("add_na = ", add_na, "\n", sep = "")
201s + 
201s +     x <- matrix(1:50 + 0.1, nrow = 10L, ncol = 5L)
201s +     if (add_na) {
201s +       x[3:7, c(2, 4)] <- NA_real_
201s +     }
201s +     cat("mode: ", mode, "\n", sep = "")
201s +     storage.mode(x) <- mode
201s +     str(x)
201s +     
201s +     # To check names attribute
201s +     dimnames <- list(letters[1:10], LETTERS[1:5])
201s +     
201s +     # Test with and without dimnames on x
201s +     for (setDimnames in c(TRUE, FALSE)) {
201s +       if (setDimnames) dimnames(x) <- dimnames
201s +       else dimnames(x) <- NULL
201s +       # Row/column ranges
201s +       for (na.rm in c(FALSE, TRUE)) {
201s +         # Check names attribute
201s +         for (useNames in c(TRUE, FALSE)) {
201s +           r0 <- rowSds_R(x, na.rm = na.rm, useNames = useNames)
201s +           r1 <- rowSds(x, na.rm = na.rm, useNames = useNames)
201s +           r1b <- rowSds_center(x, na.rm = na.rm, useNames = useNames)
201s +           r2 <- colSds(t(x), na.rm = na.rm, useNames = useNames)
201s +           r2b <- colSds_center(t(x), na.rm = na.rm, useNames = useNames)
201s +           stopifnot(all.equal(r1, r2))
201s +           stopifnot(all.equal(r1, r0))
201s +           stopifnot(all.equal(r2, r0))
201s +           stopifnot(all.equal(r1b, r2b))
201s +           stopifnot(
201s +             !any(is.infinite(r1)),
201s +             !any(is.infinite(r2)),
201s +             !any(is.infinite(r1b)),
201s +             !any(is.infinite(r2b))
201s +           )
201s +         }
201s +       }
201s +     }
201s +   } # for (add_na ...)
201s + }
201s add_na = FALSE
201s mode: integer
201s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
201s add_na = TRUE
201s mode: integer
201s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
201s add_na = FALSE
201s mode: double
201s  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 ...
201s add_na = TRUE
201s mode: double
201s  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 ...
201s > 
201s > 
201s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
201s > # All NAs
201s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
201s > for (mode in c("integer", "double")) {
201s +   x <- matrix(NA_real_, nrow = 10L, ncol = 5L)
201s +   cat("mode: ", mode, "\n", sep = "")
201s +   storage.mode(x) <- mode
201s +   str(x)
201s +   
201s +   # Test with and without dimnames on x
201s +   for (setDimnames in c(TRUE, FALSE)) {
201s +     if (setDimnames) dimnames(x) <- dimnames
201s +     else dimnames(x) <- NULL
201s +     # Row/column ranges
201s +     for (na.rm in c(FALSE, TRUE)) {
201s +       # Check names attribute
201s +       for (useNames in c(TRUE, FALSE)) {
201s +         r0 <- rowSds_R(x, na.rm = na.rm, useNames = useNames)
201s +         r1 <- rowSds(x, na.rm = na.rm, useNames = useNames)
201s +         r1b <- rowSds_center(x, na.rm = na.rm, useNames = useNames)
201s +         r2 <- colSds(t(x), na.rm = na.rm, useNames = useNames)
201s +         r2b <- colSds_center(t(x), na.rm = na.rm, useNames = useNames)
201s +         stopifnot(all.equal(r1, r2))
201s +         stopifnot(all.equal(r1, r0))
201s +         stopifnot(all.equal(r2, r0))
201s +         stopifnot(all.equal(r1b, r2b))
201s +         stopifnot(
201s +           !any(is.infinite(r1)),
201s +           !any(is.infinite(r2)),
201s +           !any(is.infinite(r1b)),
201s +           !any(is.infinite(r2b))
201s +         )
201s +       }
201s +     }
201s +   }
201s + }
201s mode: integer
201s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
201s mode: double
201s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
201s > 
201s > 
201s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
201s > # A 1x1 matrix
201s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
201s > x <- matrix(0, nrow = 1L, ncol = 1L)
201s > dimnames <- list("a", "A")
201s > for (na.rm in c(FALSE, TRUE)) {
201s +   cat("na.rm = ", na.rm, "\n", sep = "")
201s +   
201s +   # Test with and without dimnames on x
201s +   for (setDimnames in c(TRUE, FALSE)) {
201s +     if (setDimnames) dimnames(x) <- dimnames
201s +     else dimnames(x) <- NULL
201s +     # Row/column ranges
201s +     for (na.rm in c(FALSE, TRUE)) {
201s +       # Check names attribute
201s +       for (useNames in c(TRUE, FALSE)) {
201s +         r0 <- rowSds_R(x, na.rm = na.rm, useNames = useNames)
201s +         r1 <- rowSds(x, na.rm = na.rm, useNames = useNames)
201s +         r1b <- rowSds_center(x, na.rm = na.rm, useNames = useNames)
201s +         r2 <- colSds(t(x), na.rm = na.rm, useNames = useNames)
201s +         r2b <- colSds_center(t(x), na.rm = na.rm, useNames = useNames)
201s +         stopifnot(all.equal(r1, r2))
201s +         stopifnot(all.equal(r1, r0))
201s +         stopifnot(all.equal(r2, r0))
201s +         stopifnot(all.equal(r1b, r2b))
201s +         stopifnot(
201s +           !any(is.infinite(r1)),
201s +           !any(is.infinite(r2)),
201s +           !any(is.infinite(r1b)),
201s +           !any(is.infinite(r2b))
201s +         )
201s +       }
201s +     }
201s +   }
201s + }
201s na.rm = FALSE
201s na.rm = TRUE
201s > 
201s 
201s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
201s Copyright (C) 2025 The R Foundation for Statistical Computing
201s Platform: x86_64-pc-linux-gnu
201s 
201s R is free software and comes with ABSOLUTELY NO WARRANTY.
201s You are welcome to redistribute it under certain conditions.
201s Type 'license()' or 'licence()' for distribution details.
201s 
201s R is a collaborative project with many contributors.
201s Type 'contributors()' for more information and
201s 'citation()' on how to cite R or R packages in publications.
201s 
201s Type 'demo()' for some demos, 'help()' for on-line help, or
201s 'help.start()' for an HTML browser interface to help.
201s Type 'q()' to quit R.
201s 
202s > library("matrixStats")
202s > 
202s > ## Always allow testing of the 'center' argument (as long as it's not defunct)
202s > options(matrixStats.center.onUse = "ignore")
202s > 
202s > ## Create isFALSE() if running on an old version of R
202s > if (!exists("isFALSE", mode="function")) {
202s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
202s + }
202s > 
202s > rowSds_R <- function(x, na.rm = FALSE, center = NULL, ..., useNames = TRUE) {
202s +   suppressWarnings({
202s +     sigma <- apply(x, MARGIN = 1L, FUN = sd, na.rm = na.rm)
202s +   })
202s +   stopifnot(!any(is.infinite(sigma)))
202s +   
202s +   # Keep naming support consistency same as rowSds()
202s +   if (is.null(center) || ncol(x) <= 1L) {
202s +     if (isFALSE(useNames)) names(sigma) <- NULL
202s +   }
202s +   else if (isFALSE(useNames)) names(sigma) <- NULL
202s +   sigma
202s + }
202s > 
202s > colSds_R <- function(x, na.rm = FALSE, center = NULL, ..., useNames = TRUE) {
202s +   suppressWarnings({
202s +     sigma <- apply(x, MARGIN = 2L, FUN = sd, na.rm = na.rm)
202s +   })
202s +   stopifnot(!any(is.infinite(sigma)))
202s +   
202s +   # Keep naming support consistency same as colSds()
202s +   if (is.null(center) || nrow(x) <= 1L) {
202s +     if (isFALSE(useNames)) names(sigma) <- NULL
202s +   }
202s +   else if (isFALSE(useNames)) names(sigma) <- NULL
202s +   sigma
202s + }
202s > 
202s > 
202s > rowSds_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = TRUE) {
202s +   center <- rowWeightedMeans(x, cols = cols, na.rm = na.rm, useNames = FALSE)
202s +   sigma <- rowSds(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
202s +   stopifnot(!any(is.infinite(sigma)))
202s +   sigma
202s + }
202s > 
202s > colSds_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = TRUE) {
202s +   center <- colWeightedMeans(x, rows = rows, na.rm = na.rm, useNames = FALSE)
202s +   sigma <- colSds(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
202s +   stopifnot(!any(is.infinite(sigma)))
202s +   sigma
202s + }
202s > 
202s > 
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > # Subsetted tests
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > source("utils/validateIndicesFramework.R")
202s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
202s > storage.mode(x) <- "integer"
202s > 
202s > # To check names attribute
202s > dimnames <- list(letters[1:6], LETTERS[1:6])
202s > 
202s > # Test with and without dimnames on x
202s > for (setDimnames in c(TRUE, FALSE)) {
202s +   if (setDimnames) dimnames(x) <- dimnames
202s +   else dimnames(x) <- NULL
202s + 
202s +   count <- 0L
202s +   for (rows in index_cases) {
202s +     for (cols in index_cases) {
202s +       count <- count + 1L
202s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
202s +       useNames <- c(TRUE, FALSE)
202s +       useNames <- useNames[count %% length(useNames) + 1]
202s +       
202s +       validateIndicesTestMatrix(x, rows, cols,
202s +                                 ftest = rowSds, fsure = rowSds_R,
202s +                                 na.rm = na.rm, useNames = useNames)
202s +       validateIndicesTestMatrix(x, rows, cols,
202s +                                 ftest = rowSds_center, fsure = rowSds_R,
202s +                                 na.rm = na.rm, center = TRUE, useNames = useNames)
202s + 
202s +       validateIndicesTestMatrix(x, rows, cols,
202s +                                 fcoltest = colSds, fsure = rowSds_R,
202s +                                 na.rm = na.rm, useNames = useNames)
202s +       validateIndicesTestMatrix(x, rows, cols,
202s +                                 fcoltest = colSds_center, fsure = rowSds_R,
202s +                                 na.rm = na.rm, center = TRUE, useNames = useNames)
202s +     }
202s +   }
202s + }
202s > 
202s 
202s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
202s Copyright (C) 2025 The R Foundation for Statistical Computing
202s Platform: x86_64-pc-linux-gnu
202s 
202s R is free software and comes with ABSOLUTELY NO WARRANTY.
202s You are welcome to redistribute it under certain conditions.
202s Type 'license()' or 'licence()' for distribution details.
202s 
202s R is a collaborative project with many contributors.
202s Type 'contributors()' for more information and
202s 'citation()' on how to cite R or R packages in publications.
202s 
202s Type 'demo()' for some demos, 'help()' for on-line help, or
202s 'help.start()' for an HTML browser interface to help.
202s Type 'q()' to quit R.
202s 
202s > library("matrixStats")
202s > 
202s > rowSums2_R <- function(x, na.rm = FALSE, ..., useNames = TRUE) {
202s +   ## FIXME: sum() may overflow for integers, whereas
202s +   ## base::rowSums() doesn't.  What should rowSums2() do?
202s +   ## apply(x, MARGIN = 1L, FUN = sum, na.rm = na.rm)
202s +   res <- rowSums(x, na.rm = na.rm)
202s +   if (!useNames) names(res) <- NULL
202s +   res
202s + }
202s > 
202s > colSums2_R <- function(x, na.rm = FALSE, ..., useNames = TRUE) {
202s +   ## FIXME: sum() may overflow for integers, whereas
202s +   ## base::colSums() doesn't.  What should colSums2() do?
202s +   ## apply(x, MARGIN = 2L, FUN = sum, na.rm = na.rm)
202s +   res <- colSums(x, na.rm = na.rm)
202s +   if (!useNames) names(res) <- NULL
202s +   res
202s + }
202s > 
202s > for (mode in c("integer", "logical", "double")) {
202s +   x <- matrix(-4:4, nrow = 3, ncol = 3)
202s +   storage.mode(x) <- mode
202s +   if (mode == "double") x <- x + 0.1
202s +   
202s +   # To check names attribute
202s +   dimnames <- list(letters[1:3], LETTERS[1:3])
202s +   
202s +   # Test with and without dimnames on x
202s +   for (setDimnames in c(TRUE, FALSE)) {
202s +     if (setDimnames) dimnames(x) <- dimnames
202s +     else dimnames(x) <- NULL
202s +     # Check names attribute
202s +     for (useNames in c(TRUE, FALSE)) {
202s +       y0 <- rowSums2_R(x, na.rm = FALSE, useNames = useNames)
202s +       y1 <- rowSums2(x, na.rm = FALSE, useNames = useNames)
202s +       stopifnot(all.equal(y1, y0))
202s +       
202s +       y0 <- colSums2_R(x, na.rm = FALSE, useNames = useNames)
202s +       y1 <- colSums2(x, na.rm = FALSE, useNames = useNames)
202s +       stopifnot(all.equal(y1, y0))
202s +     }
202s +   }
202s + }
202s > 
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > # Special case: Single-element matrix
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > cat("Special case: Single-element matrix:\n")
202s Special case: Single-element matrix:
202s > for (mode in c("integer", "logical", "double")) {
202s +   x <- matrix(1, nrow = 1, ncol = 1)
202s +   storage.mode(x) <- mode
202s +   
202s +   # To check names attribute
202s +   dimnames <- list("a", "A")
202s +   
202s +   # Test with and without dimnames on x
202s +   for (setDimnames in c(TRUE, FALSE)) {
202s +     if (setDimnames) dimnames(x) <- dimnames
202s +     else dimnames(x) <- NULL
202s +     # Check names attribute
202s +     for (useNames in c(TRUE, FALSE)) {
202s +       y0 <- rowSums2_R(x, na.rm = FALSE, useNames = useNames)
202s +       y1 <- rowSums2(x, na.rm = FALSE, useNames = useNames)
202s +       stopifnot(all.equal(y1, y0))
202s +       
202s +       y0 <- colSums2_R(x, na.rm = FALSE, useNames = useNames)
202s +       y1 <- colSums2(x, na.rm = FALSE, useNames = useNames)
202s +       stopifnot(all.equal(y1, y0))
202s +     }
202s +   }
202s + }
202s > 
202s > 
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > # Special case: Empty matrix
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > cat("Special case: Empty matrix:\n")
202s Special case: Empty matrix:
202s > for (mode in c("integer", "logical", "double")) {
202s +   x <- matrix(integer(0), nrow = 0, ncol = 0)
202s +   storage.mode(x) <- mode
202s + 
202s +   y0 <- rowSums2_R(x, na.rm = FALSE)
202s +   y1 <- rowSums2(x, na.rm = FALSE)
202s +   stopifnot(all.equal(y1, y0))
202s + 
202s +   y0 <- colSums2_R(x, na.rm = FALSE)
202s +   y1 <- colSums2(x, na.rm = FALSE)
202s +   stopifnot(all.equal(y1, y0))
202s + }
202s > 
202s > 
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > # Special case: All NAs
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > cat("Special case: All NAs:\n")
202s Special case: All NAs:
202s > for (mode in c("integer", "logical", "double")) {
202s +   x <- matrix(NA_integer_, nrow = 3, ncol = 3)
202s +   storage.mode(x) <- mode
202s +   
202s +   # To check names attribute
202s +   dimnames <- list(letters[1:3], LETTERS[1:3])
202s +   
202s +   # Test with and without dimnames on x
202s +   for (setDimnames in c(TRUE, FALSE)) {
202s +     if (setDimnames) dimnames(x) <- dimnames
202s +     else dimnames(x) <- NULL
202s +     # Check names attribute
202s +     for (useNames in c(TRUE, FALSE)) {
202s +       y0 <- rowSums2_R(x, na.rm = TRUE, useNames = useNames)
202s +       y1 <- rowSums2(x, na.rm = TRUE, useNames = useNames)
202s +       stopifnot(all.equal(y1, y0))
202s +       
202s +       y0 <- colSums2_R(x, na.rm = TRUE, useNames = useNames)
202s +       y1 <- colSums2(x, na.rm = TRUE, useNames = useNames)
202s +       stopifnot(all.equal(y1, y0))
202s +     }
202s +   }
202s + }
202s > 
202s > 
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > # Special case: All NaNs
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > cat("Special case: All NaNs:\n")
202s Special case: All NaNs:
202s > x <- matrix(NA_real_, nrow = 3, ncol = 3)
202s > 
202s > # Test with and without dimnames on x
202s > for (setDimnames in c(TRUE, FALSE)) {
202s +   if (setDimnames) dimnames(x) <- dimnames
202s +   else dimnames(x) <- NULL
202s +   # Check names attribute
202s +   for (useNames in c(TRUE, FALSE)) {
202s +     y0 <- rowSums2_R(x, na.rm = TRUE, useNames = useNames)
202s +     y1 <- rowSums2(x, na.rm = TRUE, useNames = useNames)
202s +     stopifnot(all.equal(y1, y0))
202s +     
202s +     y0 <- colSums2_R(x, na.rm = TRUE, useNames = useNames)
202s +     y1 <- colSums2(x, na.rm = TRUE, useNames = useNames)
202s +     stopifnot(all.equal(y1, y0))
202s +   }
202s + }
202s > 
202s > 
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > # Special case: All Infs
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > cat("Special case: All Infs:\n")
202s Special case: All Infs:
202s > x <- matrix(Inf, nrow = 3, ncol = 3)
202s > 
202s > # Test with and without dimnames on x
202s > for (setDimnames in c(TRUE, FALSE)) {
202s +   if (setDimnames) dimnames(x) <- dimnames
202s +   else dimnames(x) <- NULL
202s +   # Check names attribute
202s +   for (useNames in c(TRUE, FALSE)) {
202s +     y0 <- rowSums2_R(x, na.rm = FALSE, useNames = useNames)
202s +     y1 <- rowSums2(x, na.rm = FALSE, useNames = useNames)
202s +     stopifnot(all.equal(y1, y0))
202s +     
202s +     y0 <- colSums2_R(x, na.rm = FALSE, useNames = useNames)
202s +     y1 <- colSums2(x, na.rm = FALSE, useNames = useNames)
202s +     stopifnot(all.equal(y1, y0))
202s +   }
202s + }
202s > 
202s > 
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > # Special case: All -Infs
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > cat("Special case: All -Infs:\n")
202s Special case: All -Infs:
202s > x <- matrix(-Inf, nrow = 3, ncol = 3)
202s > 
202s > # Test with and without dimnames on x
202s > for (setDimnames in c(TRUE, FALSE)) {
202s +   if (setDimnames) dimnames(x) <- dimnames
202s +   else dimnames(x) <- NULL
202s +   # Check names attribute
202s +   for (useNames in c(TRUE, FALSE)) {
202s +     y0 <- rowSums2_R(x, na.rm = FALSE, useNames = useNames)
202s +     y1 <- rowSums2(x, na.rm = FALSE, useNames = useNames)
202s +     stopifnot(all.equal(y1, y0))
202s +     
202s +     y0 <- colSums2_R(x, na.rm = FALSE, useNames = useNames)
202s +     y1 <- colSums2(x, na.rm = FALSE, useNames = useNames)
202s +     stopifnot(all.equal(y1, y0))
202s +   }
202s + }
202s > 
202s > 
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > # Special case: Infs and -Infs
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > cat("Special case: Infs and -Infs:\n")
202s Special case: Infs and -Infs:
202s > x <- matrix(c(-Inf, +Inf), nrow = 4, ncol = 4)
202s > 
202s > # To check names attribute
202s > dimnames <- list(letters[1:4], LETTERS[1:4])
202s > 
202s > # Test with and without dimnames on x
202s > for (setDimnames in c(TRUE, FALSE)) {
202s +   if (setDimnames) dimnames(x) <- dimnames
202s +   else dimnames(x) <- NULL
202s +   # Check names attribute
202s +   for (useNames in c(TRUE, FALSE)) {
202s +     y0 <- rowSums2_R(x, na.rm = FALSE, useNames = useNames)
202s +     y1 <- rowSums2(x, na.rm = FALSE, useNames = useNames)
202s +     stopifnot(all.equal(y1, y0))
202s +     
202s +     y0 <- colSums2_R(x, na.rm = FALSE, useNames = useNames)
202s +     y1 <- colSums2(x, na.rm = FALSE, useNames = useNames)
202s +     stopifnot(all.equal(y1, y0))
202s +   }
202s + }
202s > 
202s > 
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > # Special case: NaNs and NAs
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > cat("Special case: Infs and -Infs:\n")
202s Special case: Infs and -Infs:
202s > x <- matrix(c(NaN, NA_real_), nrow = 4, ncol = 4)
202s > 
202s > y0 <- rowSums(x, na.rm = FALSE)
202s > str(y0)
202s  num [1:4] NaN NA NaN NA
202s > stopifnot(all(is.na(y0)), length(unique(y0)) >= 1L)
202s > y1 <- rowSums2(x, na.rm = FALSE)
202s > str(y0)
202s  num [1:4] NaN NA NaN NA
202s > stopifnot(all(is.na(y1)), length(unique(y1)) >= 1L)
202s > stopifnot(all.equal(y1, y0))
202s > 
202s > y0 <- colSums(x, na.rm = FALSE)
202s > stopifnot(all(is.na(y0)), length(unique(y0)) == 1L)
202s > y1 <- colSums2(x, na.rm = FALSE)
202s > stopifnot(all(is.na(y1)), length(unique(y1)) == 1L)
202s > ## NOTE, due to compiler optimization, it is not guaranteed that NA is
202s > ## returned here (as one would expect). NaN might very well be returned,
202s > ## when both NA and NaN are involved.  This is an accepted feature in R,
202s > ## which is documented in help("is.nan").  See also
202s > ## https://stat.ethz.ch/pipermail/r-devel/2017-April/074009.html.
202s > ## Thus, we cannot guarantee that y1 is identical to y0.
202s > 
202s > 
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > # Special case: Integer overflow with ties
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > cat("Special case: Integer overflow with ties:\n")
202s Special case: Integer overflow with ties:
202s > x <- matrix(.Machine$integer.max, nrow = 4, ncol = 4)
202s > 
202s > # Test with and without dimnames on x
202s > for (setDimnames in c(TRUE, FALSE)) {
202s +   if (setDimnames) dimnames(x) <- dimnames
202s +   else dimnames(x) <- NULL
202s +   # Check names attribute
202s +   for (useNames in c(TRUE, FALSE)) {
202s +     y0 <- rowSums2_R(x, na.rm = FALSE, useNames = useNames)
202s +     y1 <- rowSums2(x, na.rm = FALSE, useNames = useNames)
202s +     stopifnot(all.equal(y1, y0))
202s +     
202s +     y0 <- colSums2_R(x, na.rm = FALSE, useNames = useNames)
202s +     y1 <- colSums2(x, na.rm = FALSE, useNames = useNames)
202s +     stopifnot(all.equal(y1, y0))
202s +   }
202s + }
202s > 
202s > 
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > # Consistency checks
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > set.seed(1)
202s > 
202s > cat("Consistency checks:\n")
202s Consistency checks:
202s > n_sims <- if (Sys.getenv("_R_CHECK_USE_VALGRIND_") != "") 4L else 20L
202s > for (kk in seq_len(n_sims)) {
202s +   cat("Random test #", kk, "\n", sep = "")
202s + 
202s +   # Simulate data in a matrix of any shape
202s +   dim <- sample(50:200, size = 2)
202s +   n <- prod(dim)
202s +   x <- rnorm(n, sd = 100)
202s +   dim(x) <- dim
202s + 
202s +   # Add NAs?
202s +   if ((kk %% 4) %in% c(3, 0)) {
202s +     cat("Adding NAs\n")
202s +     nna <- sample(n, size = 1)
202s +     na_values <- c(NA_real_, NaN)
202s +     t <- sample(na_values, size = nna, replace = TRUE)
202s +     x[sample(length(x), size = nna)] <- t
202s +   }
202s + 
202s +   # Mode?
202s +   modes <- "double"
202s +   if ((kk %% 4) %in% c(2, 0)) {
202s +     modes <- c("integer", "logical")
202s +   }
202s + 
202s +   for (mode in modes) {
202s +     if (mode != "double") {
202s +       cat(sprintf("Coercing from %s to %s\n", storage.mode(x), mode))
202s +       storage.mode(x) <- mode
202s +     }
202s + 
202s +     na.rm <- sample(c(TRUE, FALSE), size = 1)
202s +   
202s +     # rowSums2():
202s +     y0 <- rowSums2_R(x, na.rm = na.rm)
202s +     y1 <- rowSums2(x, na.rm = na.rm)
202s +     stopifnot(all.equal(y1, y0))
202s +     y2 <- colSums2(t(x), na.rm = na.rm)
202s +     stopifnot(all.equal(y2, y0))
202s +   
202s +     # colSums2():
202s +     y0 <- colSums2_R(x, na.rm = na.rm)
202s +     y1 <- colSums2(x, na.rm = na.rm)
202s +     stopifnot(all.equal(y1, y0))
202s +     y2 <- rowSums2(t(x), na.rm = na.rm)
202s +     stopifnot(all.equal(y2, y0))
202s +   }
202s + } # for (kk ...)
202s Random test #1
202s Random test #2
202s Coercing from double to integer
202s Coercing from integer to logical
202s Random test #3
202s Adding NAs
202s Random test #4
202s Adding NAs
202s Coercing from double to integer
202s Coercing from integer to logical
202s Random test #5
202s Random test #6
202s Coercing from double to integer
202s Coercing from integer to logical
202s Random test #7
202s Adding NAs
202s Random test #8
202s Adding NAs
202s Coercing from double to integer
202s Coercing from integer to logical
202s Random test #9
202s Random test #10
202s Coercing from double to integer
202s Coercing from integer to logical
202s Random test #11
202s Adding NAs
202s Random test #12
202s Adding NAs
202s Coercing from double to integer
202s Coercing from integer to logical
202s Random test #13
202s Random test #14
202s Coercing from double to integer
202s Coercing from integer to logical
202s Random test #15
202s Adding NAs
202s Random test #16
202s Adding NAs
202s Coercing from double to integer
202s Coercing from integer to logical
202s Random test #17
202s Random test #18
202s Coercing from double to integer
202s Coercing from integer to logical
202s Random test #19
202s Adding NAs
202s Random test #20
202s Adding NAs
202s Coercing from double to integer
202s Coercing from integer to logical
202s > 
202s 
202s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
202s Copyright (C) 2025 The R Foundation for Statistical Computing
202s Platform: x86_64-pc-linux-gnu
202s 
202s R is free software and comes with ABSOLUTELY NO WARRANTY.
202s You are welcome to redistribute it under certain conditions.
202s Type 'license()' or 'licence()' for distribution details.
202s 
202s R is a collaborative project with many contributors.
202s Type 'contributors()' for more information and
202s 'citation()' on how to cite R or R packages in publications.
202s 
202s Type 'demo()' for some demos, 'help()' for on-line help, or
202s 'help.start()' for an HTML browser interface to help.
202s Type 'q()' to quit R.
202s 
202s > library("matrixStats")
202s > 
202s > rowSums2_R <- function(x, na.rm = FALSE, ..., useNames = TRUE) {
202s +   ## FIXME: sum() may overflow for integers, whereas
202s +   ## base::rowSums() doesn't.  What should rowSums2() do?
202s +   ## apply(x, MARGIN = 1L, FUN = sum, na.rm = na.rm)
202s +   res <- rowSums(x, na.rm = na.rm)
202s +   if (!useNames) names(res) <- NULL
202s +   res
202s + }
202s > 
202s > colSums2_R <- function(x, na.rm = FALSE, ..., useNames = TRUE) {
202s +   ## FIXME: sum() may overflow for integers, whereas
202s +   ## base::colSums() doesn't.  What should colSums2() do?
202s +   ## apply(x, MARGIN = 2L, FUN = sum, na.rm = na.rm)
202s +   res <- colSums(x, na.rm = na.rm)
202s +   if (!useNames) names(res) <- NULL
202s +   res
202s + }
202s > 
202s > 
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > # Subsetted tests
202s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
202s > source("utils/validateIndicesFramework.R")
202s > x <- matrix(runif(6 * 6, min = -3, max = 3), nrow = 6, ncol = 6)
202s > storage.mode(x) <- "integer"
202s > 
202s > # To check names attribute
202s > dimnames <- list(letters[1:6], LETTERS[1:6])
202s > 
202s > # Test with and without dimnames on x
202s > for (setDimnames in c(TRUE, FALSE)) {
202s +   if (setDimnames) dimnames(x) <- dimnames
202s +   else dimnames(x) <- NULL
202s +   for (rows in index_cases) {
202s +     for (cols in index_cases) {
202s +       for (na.rm in c(TRUE, FALSE)) {
202s +         for (useNames in c(TRUE, FALSE)) {
202s +           validateIndicesTestMatrix(x, rows, cols,
202s +                                     ftest = rowSums2, fsure = rowSums2_R,
202s +                                     na.rm = na.rm, useNames = useNames)
202s +           validateIndicesTestMatrix(x, rows, cols,
202s +                                     fcoltest = colSums2, fsure = rowSums2_R,
202s +                                     na.rm = na.rm, useNames = useNames)
202s +         }
202s +       }
202s +     }
202s +   }
202s + }
203s > 
203s 
203s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
203s Copyright (C) 2025 The R Foundation for Statistical Computing
203s Platform: x86_64-pc-linux-gnu
203s 
203s R is free software and comes with ABSOLUTELY NO WARRANTY.
203s You are welcome to redistribute it under certain conditions.
203s Type 'license()' or 'licence()' for distribution details.
203s 
203s R is a collaborative project with many contributors.
203s Type 'contributors()' for more information and
203s 'citation()' on how to cite R or R packages in publications.
203s 
203s Type 'demo()' for some demos, 'help()' for on-line help, or
203s 'help.start()' for an HTML browser interface to help.
203s Type 'q()' to quit R.
203s 
203s > library("matrixStats")
203s > 
203s > nrow <- 6L
203s > ncol <- 5L
203s > data <- matrix(0:4, nrow = nrow, ncol = ncol)
203s > 
203s > # To check names attribute
203s > dimnames <- list(letters[1:6], LETTERS[1:5])
203s > 
203s > modes <- c("integer", "logical", "raw")
203s > for (mode in modes) {
203s +   cat(sprintf("Mode: %s...\n", mode))
203s + 
203s +   x <- data
203s +   if (mode == "logical") x <- x - 2L
203s +   if (mode != "raw") x[c(2,5,7)] <- NA_integer_
203s +   storage.mode(x) <- mode
203s +   print(x)
203s + 
203s +   unique_values <- unique(as.vector(x))
203s +   nbr_of_unique_values <- length(unique_values)
203s + 
203s +   y <- rowTabulates(x)
203s +   print(y)
203s +   stopifnot(
203s +     identical(dim(y), c(nrow, nbr_of_unique_values)),
203s +     all(y >= 0)
203s +   )
203s +   if (mode != "raw") {
203s +     y0 <- t(table(x, row(x), useNA = "always")[, seq_len(nrow(x))])
203s +     stopifnot(all(y == y0))
203s +   }
203s +   # Check names attribute
203s +   dimnames(x) <- dimnames
203s +   y1 <- rowTabulates(x, useNames = FALSE)
203s +   stopifnot(all.equal(y1, y))
203s +   y <- rowTabulates(x, useNames = TRUE)
203s +   stopifnot(identical(rownames(y), rownames(x)))
203s +   dimnames(x) <- NULL
203s + 
203s +   y <- colTabulates(x)
203s +   print(y)
203s +   stopifnot(
203s +     identical(dim(y), c(ncol, nbr_of_unique_values)),
203s +     all(y >= 0)
203s +   )
203s +   if (mode != "raw") {
203s +     y0 <- t(table(x, col(x), useNA = "always")[, seq_len(ncol(x))])
203s +     stopifnot(all(y == y0))
203s +   }
203s +   # Check names attribute
203s +   dimnames(x) <- dimnames
203s +   y1 <- colTabulates(x, useNames = FALSE)
203s +   stopifnot(all.equal(y1, y))
203s +   y <- colTabulates(x, useNames = TRUE)
203s +   stopifnot(identical(rownames(y), colnames(x)))
203s +   dimnames(x) <- NULL
203s + 
203s +   # Count only certain values
203s +   if (mode == "integer") {
203s +     subset <- c(0:2, NA_integer_)
203s +   } else if (mode == "logical") {
203s +     subset <- c(TRUE, FALSE, NA)
203s +   } else {
203s +     subset <- c(0:2)
203s +   }
203s +   y <- rowTabulates(x, values = subset)
203s +   print(y)
203s +   stopifnot(identical(dim(y), c(nrow, length(subset))))
203s +   # Check names attribute
203s +   dimnames(x) <- dimnames
203s +   y1 <- rowTabulates(x, values = subset, useNames = FALSE)
203s +   stopifnot(all.equal(y1, y))
203s +   y <- rowTabulates(x, values = subset, useNames = TRUE)
203s +   stopifnot(identical(rownames(y), rownames(x)))
203s +   dimnames(x) <- NULL
203s + 
203s +   y <- colTabulates(x, values = subset)
203s +   print(y)
203s +   stopifnot(identical(dim(y), c(ncol, length(subset))))
203s +   # Check names attribute
203s +   dimnames(x) <- dimnames
203s +   y1 <- colTabulates(x, values = subset, useNames = FALSE)
203s +   stopifnot(all.equal(y1, y))
203s +   y <- colTabulates(x, values = subset, useNames = TRUE)
203s +   stopifnot(identical(rownames(y), colnames(x)))
203s +   dimnames(x) <- NULL
203s + 
203s +   # Raw
203s +   if (mode %in% c("integer", "raw")) {
203s +     subset <- c(0:2)
203s +     
203s +     y <- rowTabulates(x, values = as.raw(subset))
203s +     print(y)
203s +     stopifnot(identical(dim(y), c(nrow, length(subset))))
203s +     # Check names attribute
203s +     dimnames(x) <- dimnames
203s +     y1 <- rowTabulates(x, values = as.raw(subset), useNames = FALSE)
203s +     stopifnot(all.equal(y1, y))
203s +     y3 <- rowTabulates(x, values = as.raw(subset), useNames = TRUE)
203s +     stopifnot(identical(rownames(y3), rownames(x)))
203s +     dimnames(x) <- NULL
203s +     
203s +     y2 <- colTabulates(t(x), values = as.raw(subset))
203s +     print(y2)
203s +     stopifnot(
203s +       identical(dim(y2), c(nrow, length(subset))),
203s +       identical(y2, y)
203s +     )
203s +     # Check names attribute
203s +     dimnames(x) <- dimnames
203s +     y1 <- colTabulates(t(x), values = as.raw(subset), useNames = FALSE)
203s +     stopifnot(all.equal(y1, y))
203s +     y <- colTabulates(t(x), values = as.raw(subset), useNames = TRUE)
203s +     stopifnot(identical(rownames(y), colnames(t(x))))
203s +     dimnames(x) <- NULL
203s +   }
203s + 
203s +   cat(sprintf("Mode: %s...done\n", mode))
203s + } # for (mode ...)
203s Mode: integer...
203s      [,1] [,2] [,3] [,4] [,5]
203s [1,]    0   NA    2    3    4
203s [2,]   NA    2    3    4    0
203s [3,]    2    3    4    0    1
203s [4,]    3    4    0    1    2
203s [5,]   NA    0    1    2    3
203s [6,]    0    1    2    3    4
203s      0 1 2 3 4 <NA>
203s [1,] 1 0 1 1 1    1
203s [2,] 1 0 1 1 1    1
203s [3,] 1 1 1 1 1    0
203s [4,] 1 1 1 1 1    0
203s [5,] 1 1 1 1 0    1
203s [6,] 1 1 1 1 1    0
203s      0 1 2 3 4 <NA>
203s [1,] 2 0 1 1 0    2
203s [2,] 1 1 1 1 1    1
203s [3,] 1 1 2 1 1    0
203s [4,] 1 1 1 2 1    0
203s [5,] 1 1 1 1 2    0
203s      0 1 2 <NA>
203s [1,] 1 0 1    1
203s [2,] 1 0 1    1
203s [3,] 1 1 1    0
203s [4,] 1 1 1    0
203s [5,] 1 1 1    1
203s [6,] 1 1 1    0
203s      0 1 2 <NA>
203s [1,] 2 0 1    2
203s [2,] 1 1 1    1
203s [3,] 1 1 2    0
203s [4,] 1 1 1    0
203s [5,] 1 1 1    0
203s      0x0 0x1 0x2
203s [1,]   1   0   1
203s [2,]   1   0   1
203s [3,]   1   1   1
203s [4,]   1   1   1
203s [5,]   1   1   1
203s [6,]   1   1   1
203s      0x0 0x1 0x2
203s [1,]   1   0   1
203s [2,]   1   0   1
203s [3,]   1   1   1
203s [4,]   1   1   1
203s [5,]   1   1   1
203s [6,]   1   1   1
203s Mode: integer...done
203s Mode: logical...
203s       [,1]  [,2]  [,3]  [,4]  [,5]
203s [1,]  TRUE    NA FALSE  TRUE  TRUE
203s [2,]    NA FALSE  TRUE  TRUE  TRUE
203s [3,] FALSE  TRUE  TRUE  TRUE  TRUE
203s [4,]  TRUE  TRUE  TRUE  TRUE FALSE
203s [5,]    NA  TRUE  TRUE FALSE  TRUE
203s [6,]  TRUE  TRUE FALSE  TRUE  TRUE
203s      FALSE TRUE <NA>
203s [1,]     1    3    1
203s [2,]     1    3    1
203s [3,]     1    4    0
203s [4,]     1    4    0
203s [5,]     1    3    1
203s [6,]     1    4    0
203s      FALSE TRUE <NA>
203s [1,]     1    3    2
203s [2,]     1    4    1
203s [3,]     2    4    0
203s [4,]     1    5    0
203s [5,]     1    5    0
203s      TRUE FALSE <NA>
203s [1,]    3     1    1
203s [2,]    3     1    1
203s [3,]    4     1    0
203s [4,]    4     1    0
203s [5,]    3     1    1
203s [6,]    4     1    0
203s      TRUE FALSE <NA>
203s [1,]    3     1    2
203s [2,]    4     1    1
203s [3,]    4     2    0
203s [4,]    5     1    0
203s [5,]    5     1    0
203s Mode: logical...done
203s Mode: raw...
203s      [,1] [,2] [,3] [,4] [,5]
203s [1,]   00   01   02   03   04
203s [2,]   01   02   03   04   00
203s [3,]   02   03   04   00   01
203s [4,]   03   04   00   01   02
203s [5,]   04   00   01   02   03
203s [6,]   00   01   02   03   04
203s      0x0 0x1 0x2 0x3 0x4
203s [1,]   1   1   1   1   1
203s [2,]   1   1   1   1   1
203s [3,]   1   1   1   1   1
203s [4,]   1   1   1   1   1
203s [5,]   1   1   1   1   1
203s [6,]   1   1   1   1   1
203s      0x0 0x1 0x2 0x3 0x4
203s [1,]   2   1   1   1   1
203s [2,]   1   2   1   1   1
203s [3,]   1   1   2   1   1
203s [4,]   1   1   1   2   1
203s [5,]   1   1   1   1   2
203s      0 1 2
203s [1,] 1 1 1
203s [2,] 1 1 1
203s [3,] 1 1 1
203s [4,] 1 1 1
203s [5,] 1 1 1
203s [6,] 1 1 1
203s      0 1 2
203s [1,] 2 1 1
203s [2,] 1 2 1
203s [3,] 1 1 2
203s [4,] 1 1 1
203s [5,] 1 1 1
203s      0x0 0x1 0x2
203s [1,]   1   1   1
203s [2,]   1   1   1
203s [3,]   1   1   1
203s [4,]   1   1   1
203s [5,]   1   1   1
203s [6,]   1   1   1
203s      0x0 0x1 0x2
203s [1,]   1   1   1
203s [2,]   1   1   1
203s [3,]   1   1   1
203s [4,]   1   1   1
203s [5,]   1   1   1
203s [6,]   1   1   1
203s Mode: raw...done
203s > 
203s 
203s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
203s Copyright (C) 2025 The R Foundation for Statistical Computing
203s Platform: x86_64-pc-linux-gnu
203s 
203s R is free software and comes with ABSOLUTELY NO WARRANTY.
203s You are welcome to redistribute it under certain conditions.
203s Type 'license()' or 'licence()' for distribution details.
203s 
203s R is a collaborative project with many contributors.
203s Type 'contributors()' for more information and
203s 'citation()' on how to cite R or R packages in publications.
203s 
203s Type 'demo()' for some demos, 'help()' for on-line help, or
203s 'help.start()' for an HTML browser interface to help.
203s Type 'q()' to quit R.
203s 
203s > library("matrixStats")
203s > 
203s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
203s > # Subsetted tests
203s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
203s > source("utils/validateIndicesFramework.R")
203s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
203s > storage.mode(x) <- "integer"
203s > 
203s > # To check names attribute
203s > dimnames <- list(letters[1:6], LETTERS[1:6])
203s > 
203s > # Test with and without dimnames on x
203s > for (setDimnames in c(TRUE, FALSE)) {
203s +   if (setDimnames) dimnames(x) <- dimnames
203s +   else dimnames(x) <- NULL
203s +   
203s +   count <- 0L
203s +   for (rows in index_cases) {
203s +     for (cols in index_cases) {
203s +       count <- count + 1L
203s +       useNames <- c(TRUE, FALSE)
203s +       useNames <- useNames[count %% length(useNames) + 1]
203s +       
203s +       validateIndicesTestMatrix(x, rows, cols,
203s +                                 ftest = rowTabulates, fsure = rowTabulates, useNames = useNames)
203s +       validateIndicesTestMatrix(x, rows, cols,
203s +                                 ftest = rowTabulates, fsure = rowTabulates,
203s +                                 values = 1:3, useNames = useNames)
203s +   
203s +       validateIndicesTestMatrix(x, rows, cols,
203s +                                 ftest = colTabulates, fsure = colTabulates, useNames = useNames)
203s +       validateIndicesTestMatrix(x, rows, cols,
203s +                                 ftest = colTabulates, fsure = colTabulates,
203s +                                 values = 1:3, useNames = useNames)
203s +     }
203s +   }
203s + }
203s > 
204s 
204s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
204s Copyright (C) 2025 The R Foundation for Statistical Computing
204s Platform: x86_64-pc-linux-gnu
204s 
204s R is free software and comes with ABSOLUTELY NO WARRANTY.
204s You are welcome to redistribute it under certain conditions.
204s Type 'license()' or 'licence()' for distribution details.
204s 
204s R is a collaborative project with many contributors.
204s Type 'contributors()' for more information and
204s 'citation()' on how to cite R or R packages in publications.
204s 
204s Type 'demo()' for some demos, 'help()' for on-line help, or
204s 'help.start()' for an HTML browser interface to help.
204s Type 'q()' to quit R.
204s 
204s > library("matrixStats")
204s > 
204s > fcns <- list(
204s +   rowVarDiffs = list(rowVarDiffs, colVarDiffs),
204s +   rowSdDiffs  = list(rowSdDiffs, colSdDiffs),
204s +   rowMadDiffs = list(rowMadDiffs, colMadDiffs),
204s +   rowIQRDiffs = list(rowIQRDiffs, colIQRDiffs)
204s + )
204s > 
204s > for (fcn in names(fcns)) {
204s +   cat(sprintf("%s()...\n", fcn))
204s +   row_fcn <- fcns[[fcn]][[1L]]
204s +   col_fcn <- fcns[[fcn]][[2L]]
204s + 
204s +   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
204s +   # With and without some NAs
204s +   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
204s +   for (mode in c("integer", "double")) {
204s +     for (add_na in c(FALSE, TRUE)) {
204s +       cat("add_na = ", add_na, "\n", sep = "")
204s + 
204s +       x <- matrix(1:50 + 0.1, nrow = 10L, ncol = 5L)
204s +       if (add_na) {
204s +         x[3:7, c(2, 4)] <- NA_real_
204s +       }
204s +       cat("mode: ", mode, "\n", sep = "")
204s +       storage.mode(x) <- mode
204s +       str(x)
204s +       
204s +       # To check names attribute
204s +       dimnames <- list(letters[1:10], LETTERS[1:5])
204s + 
204s +       # Test with and without dimnames on x
204s +       for (setDimnames in c(TRUE, FALSE)) {
204s +         if (setDimnames) dimnames(x) <- dimnames
204s +         else dimnames(x) <- NULL
204s +         # Row/column ranges
204s +         for (na.rm in c(FALSE, TRUE)) {
204s +           # Check names attribute
204s +           for (useNames in c(TRUE, FALSE)) {
204s +             cat("na.rm = ", na.rm, "\n", sep = "")
204s +             r1 <- row_fcn(x, na.rm = na.rm, useNames = useNames)
204s +             r2 <- col_fcn(t(x), na.rm = na.rm, useNames = useNames)
204s +             stopifnot(all.equal(r1, r2))
204s +           }
204s +         }
204s +       }
204s +     } # for (add_na ...)
204s +   }
204s + 
204s + 
204s +   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
204s +   # All NAs
204s +   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
204s +   for (mode in c("integer", "double")) {
204s +     x <- matrix(NA_real_, nrow = 10L, ncol = 5L)
204s +     cat("mode: ", mode, "\n", sep = "")
204s +     storage.mode(x) <- mode
204s +     str(x)
204s + 
204s +     # Test with and without dimnames on x
204s +     for (setDimnames in c(TRUE, FALSE)) {
204s +       if (setDimnames) dimnames(x) <- dimnames
204s +       else dimnames(x) <- NULL
204s +       # Row/column ranges
204s +       for (na.rm in c(FALSE, TRUE)) {
204s +         # Check names attribute
204s +         for (useNames in c(TRUE, FALSE)) {
204s +           cat("na.rm = ", na.rm, "\n", sep = "")
204s +           r1 <- row_fcn(x, na.rm = na.rm, useNames = useNames)
204s +           r2 <- col_fcn(t(x), na.rm = na.rm, useNames = useNames)
204s +           stopifnot(all.equal(r1, r2))
204s +         }
204s +       }
204s +     }
204s +   }
204s + 
204s + 
204s +   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
204s +   # A 1x1 matrix
204s +   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
204s +   x <- matrix(0, nrow = 1L, ncol = 1L)
204s +   dimnames <- list("a", "A")
204s +   # Test with and without dimnames on x
204s +   for (setDimnames in c(TRUE, FALSE)) {
204s +     if (setDimnames) dimnames(x) <- dimnames
204s +     else dimnames(x) <- NULL
204s +     # Row/column ranges
204s +     for (na.rm in c(FALSE, TRUE)) {
204s +       # Check names attribute
204s +       for (useNames in c(TRUE, FALSE)) {
204s +         cat("na.rm = ", na.rm, "\n", sep = "")
204s +         r1 <- row_fcn(x, na.rm = na.rm, useNames = useNames)
204s +         r2 <- col_fcn(t(x), na.rm = na.rm, useNames = useNames)
204s +         stopifnot(all.equal(r1, r2))
204s +       }
204s +     }
204s +   }
204s + 
204s +   cat(sprintf("%s()...DONE\n", fcn))
204s + } # for (fcn ...)
204s rowVarDiffs()...
204s add_na = FALSE
204s mode: integer
204s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s add_na = TRUE
204s mode: integer
204s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s add_na = FALSE
204s mode: double
204s  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 ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s add_na = TRUE
204s mode: double
204s  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 ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s mode: integer
204s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s mode: double
204s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s rowVarDiffs()...DONE
204s rowSdDiffs()...
204s add_na = FALSE
204s mode: integer
204s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s add_na = TRUE
204s mode: integer
204s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s add_na = FALSE
204s mode: double
204s  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 ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s add_na = TRUE
204s mode: double
204s  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 ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s mode: integer
204s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s mode: double
204s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s rowSdDiffs()...DONE
204s rowMadDiffs()...
204s add_na = FALSE
204s mode: integer
204s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s add_na = TRUE
204s mode: integer
204s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s add_na = FALSE
204s mode: double
204s  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 ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s add_na = TRUE
204s mode: double
204s  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 ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s mode: integer
204s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s mode: double
204s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s rowMadDiffs()...DONE
204s rowIQRDiffs()...
204s add_na = FALSE
204s mode: integer
204s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s add_na = TRUE
204s mode: integer
204s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s add_na = FALSE
204s mode: double
204s  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 ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s add_na = TRUE
204s mode: double
204s  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 ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s mode: integer
204s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s mode: double
204s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s na.rm = FALSE
204s na.rm = FALSE
204s na.rm = TRUE
204s na.rm = TRUE
204s rowIQRDiffs()...DONE
204s > 
204s 
204s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
204s Copyright (C) 2025 The R Foundation for Statistical Computing
204s Platform: x86_64-pc-linux-gnu
204s 
204s R is free software and comes with ABSOLUTELY NO WARRANTY.
204s You are welcome to redistribute it under certain conditions.
204s Type 'license()' or 'licence()' for distribution details.
204s 
204s R is a collaborative project with many contributors.
204s Type 'contributors()' for more information and
204s 'citation()' on how to cite R or R packages in publications.
204s 
204s Type 'demo()' for some demos, 'help()' for on-line help, or
204s 'help.start()' for an HTML browser interface to help.
204s Type 'q()' to quit R.
204s 
204s > library("matrixStats")
204s > 
204s > fcns <- list(
204s +   madDiff = c(rowMadDiffs, colMadDiffs),
204s +   iqrDiff = c(rowIQRDiffs, colIQRDiffs)
204s + )
204s > 
204s > 
204s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
204s > # Subsetted tests
204s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
204s > source("utils/validateIndicesFramework.R")
204s > # To check names attribute
204s > dimnames <- list(letters[1:6], LETTERS[1:6])
204s > trim <- runif(1, min = 0, max = 0.5)
204s > for (fcn in names(fcns)) {
204s +   cat(sprintf("subsetted tests on %s()...\n", fcn))
204s +   row_fcn <- fcns[[fcn]][[1L]]
204s +   col_fcn <- fcns[[fcn]][[2L]]
204s + 
204s +   for (mode in c("numeric", "integer")) {
204s +     x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6L, ncol = 6L)
204s +     storage.mode(x) <- mode
204s +     if (mode == "numeric") x[1:2, 3:4] <- Inf
204s + 
204s +     # Test with and without dimnames on x
204s +     for (setDimnames in c(TRUE, FALSE)) {
204s +       if (setDimnames) dimnames(x) <- dimnames
204s +       else dimnames(x) <- NULL
204s +       
204s +       count <- 0L
204s +       for (diff in 1:2) {
204s +         for (rows in index_cases) {
204s +           for (cols in index_cases) {
204s +             count <- count + 1L
204s +             na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
204s +             useNames <- c(TRUE, FALSE)
204s +             useNames <- useNames[count %% length(useNames) + 1]
204s +             validateIndicesTestMatrix(x, rows, cols,
204s +                                       ftest = row_fcn, fsure = row_fcn,
204s +                                       na.rm = na.rm, diff = diff, trim = trim, useNames = useNames)
204s +             validateIndicesTestMatrix(x, rows, cols,
204s +                                       fcoltest = col_fcn, fsure = row_fcn,
204s +                                       na.rm = na.rm, diff = diff, trim = trim, useNames = useNames)
204s +           }
204s +         }
204s +       }
204s +     }
204s +   }
204s +   cat(sprintf("%s()...DONE\n", fcn))
204s + }
204s subsetted tests on madDiff()...
205s madDiff()...DONE
205s subsetted tests on iqrDiff()...
206s iqrDiff()...DONE
206s > 
206s 
206s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
206s Copyright (C) 2025 The R Foundation for Statistical Computing
206s Platform: x86_64-pc-linux-gnu
206s 
206s R is free software and comes with ABSOLUTELY NO WARRANTY.
206s You are welcome to redistribute it under certain conditions.
206s Type 'license()' or 'licence()' for distribution details.
206s 
206s R is a collaborative project with many contributors.
206s Type 'contributors()' for more information and
206s 'citation()' on how to cite R or R packages in publications.
206s 
206s Type 'demo()' for some demos, 'help()' for on-line help, or
206s 'help.start()' for an HTML browser interface to help.
206s Type 'q()' to quit R.
206s 
206s > library("matrixStats")
206s > 
206s > fcns <- list(
206s +   varDiff  = c(rowVarDiffs, colVarDiffs),
206s +   sdDiff   = c(rowSdDiffs, colSdDiffs)
206s + )
206s > 
206s > 
206s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
206s > # Subsetted tests
206s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
206s > source("utils/validateIndicesFramework.R")
206s > # To check names attribute
206s > dimnames <- list(letters[1:6], LETTERS[1:6])
206s > trim <- runif(1, min = 0, max = 0.5)
206s > for (fcn in names(fcns)) {
206s +   cat(sprintf("subsetted tests on %s()...\n", fcn))
206s +   row_fcn <- fcns[[fcn]][[1L]]
206s +   col_fcn <- fcns[[fcn]][[2L]]
206s + 
206s +   for (mode in c("numeric", "integer")) {
206s +     x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6L, ncol = 6L)
206s +     storage.mode(x) <- mode
206s +     if (mode == "numeric") x[1:2, 3:4] <- Inf
206s +   
206s +     # Test with and without dimnames on x
206s +     for (setDimnames in c(TRUE, FALSE)) {
206s +       if (setDimnames) dimnames(x) <- dimnames
206s +       else dimnames(x) <- NULL
206s + 
206s +       count <- 0L
206s +       for (diff in 1:2) {
206s +         for (rows in index_cases) {
206s +           for (cols in index_cases) {
206s +             count <- count + 1L
206s +             na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
206s +             useNames <- c(TRUE, FALSE)
206s +             useNames <- useNames[count %% length(useNames) + 1]
206s +             
206s +             validateIndicesTestMatrix(x, rows, cols,
206s +                                       ftest = row_fcn, fsure = row_fcn,
206s +                                       na.rm = na.rm, diff = diff, trim = trim, useNames = useNames)
206s +             validateIndicesTestMatrix(x, rows, cols,
206s +                                       fcoltest = col_fcn, fsure = row_fcn,
206s +                                       na.rm = na.rm, diff = diff, trim = trim, useNames = useNames)
206s +           }
206s +         }
206s +       }
206s +     }
206s +   }
206s +   cat(sprintf("%s()...DONE\n", fcn))
206s + }
206s subsetted tests on varDiff()...
207s varDiff()...DONE
207s subsetted tests on sdDiff()...
208s sdDiff()...DONE
208s > 
208s 
208s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
208s Copyright (C) 2025 The R Foundation for Statistical Computing
208s Platform: x86_64-pc-linux-gnu
208s 
208s R is free software and comes with ABSOLUTELY NO WARRANTY.
208s You are welcome to redistribute it under certain conditions.
208s Type 'license()' or 'licence()' for distribution details.
208s 
208s R is a collaborative project with many contributors.
208s Type 'contributors()' for more information and
208s 'citation()' on how to cite R or R packages in publications.
208s 
208s Type 'demo()' for some demos, 'help()' for on-line help, or
208s 'help.start()' for an HTML browser interface to help.
208s Type 'q()' to quit R.
208s 
208s > library("matrixStats")
208s > 
208s > ## Always allow testing of the 'center' argument (as long as it's not defunct)
208s > options(matrixStats.center.onUse = "ignore")
208s > options(matrixStats.vars.formula.freq = Inf)
208s > 
208s > ## Create isFALSE() if running on an old version of R
208s > if (!exists("isFALSE", mode="function")) {
208s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
208s + }
208s > 
208s > rowVars_R <- function(x, na.rm = FALSE, center = NULL, ..., useNames = TRUE) {
208s +   suppressWarnings({
208s +     res <- apply(x, MARGIN = 1L, FUN = var, na.rm = na.rm)
208s +   })
208s +   stopifnot(!any(is.infinite(res)))
208s +   
208s +   # Keep naming support consistency same as rowVars()
208s +   if (is.null(center) || ncol(x) <= 1L) {
208s +     if (isFALSE(useNames)) names(res) <- NULL
208s +   }
208s +   else if (isFALSE(useNames)) names(res) <- NULL
208s +   res
208s + }
208s > 
208s > colVars_R <- function(x, na.rm = FALSE, center = NULL, ..., useNames = TRUE) {
208s +   suppressWarnings({
208s +     res <- apply(x, MARGIN = 2L, FUN = var, na.rm = na.rm)
208s +   })
208s +   stopifnot(!any(is.infinite(res)))
208s +   
208s +   # Keep naming support consistency same as colVars()
208s +   if (is.null(center) || ncol(x) <= 1L) {
208s +     if (isFALSE(useNames)) names(res) <- NULL
208s +   }
208s +   else if (isFALSE(useNames)) names(res) <- NULL
208s +   res
208s + }
208s > 
208s > 
208s > rowVars_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = TRUE) {
208s +   center <- rowWeightedMeans(x, cols = cols, na.rm = na.rm, useNames = FALSE)
208s +   res <- rowVars(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
208s +   stopifnot(!any(is.infinite(res)))
208s +   res
208s + }
208s > 
208s > colVars_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = TRUE) {
208s +   center <- colWeightedMeans(x, rows = rows, na.rm = na.rm, useNames = FALSE)
208s +   res <- colVars(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
208s +   stopifnot(!any(is.infinite(res)))
208s +   res
208s + }
208s > 
208s > rowVars_center_naive <- function(x, rows = NULL, cols = NULL, center = NULL, na.rm = FALSE, ..., useNames = TRUE) {
208s +   x <- sweep(x, MARGIN = 1, STATS = as.array(center), FUN = "-")
208s +   x[is.infinite(center), ] <- NaN
208s +   res <- rowVars(x, rows = rows, cols = cols, center = rep(0, times = nrow(x)), na.rm = na.rm, useNames = useNames)
208s +   stopifnot(!any(is.infinite(res)))
208s +   res
208s + }
208s > 
208s > colVars_center_naive <- function(x, rows = NULL, cols = NULL, center = NULL, na.rm = FALSE, ..., useNames = TRUE) {
208s +   x <- sweep(x, MARGIN = 2, STATS = as.array(center), FUN = "-")
208s +   x[, is.infinite(center)] <- NaN
208s +   res <- colVars(x, rows = rows, cols = cols, center = rep(0, times = ncol(x)), na.rm = na.rm, useNames = useNames)
208s +   stopifnot(!any(is.infinite(res)))
208s +   res
208s + }
208s > 
208s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
208s > # With and without some NAs or Infs
208s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
208s > for (mode in c("integer", "double")) {
208s +   if (mode == "integer") {
208s +     specials <- c(0L, NA_integer_)
208s +     delta <- 0L
208s +   } else {
208s +     specials <- c(0, NA_real_, Inf)
208s +     delta <- 0.1
208s +   }
208s +   
208s +   for (special in specials) {
208s +     cat("special = ", special, "\n", sep = "")
208s +     x <- matrix(1:50 + delta, nrow = 10L, ncol = 5L)
208s +     x[3:7, c(2, 4)] <- special
208s +     cat("mode: ", mode, "\n", sep = "")
208s +     str(x)
208s +     stopifnot(storage.mode(x) == mode)
208s +     
208s +     # To check names attribute
208s +     dimnames <- list(letters[1:10], LETTERS[1:5])
208s +     
208s +     # Test with and without dimnames on x
208s +     for (setDimnames in c(TRUE, FALSE)) {
208s +       if (setDimnames) dimnames(x) <- dimnames
208s +       else dimnames(x) <- NULL
208s +       # Row/column variance
208s +       for (na.rm in c(FALSE, TRUE)) {
208s +         # Check names attribute
208s +         for (useNames in c(TRUE, FALSE)) {
208s +           cat("na.rm = ", na.rm, "\n", sep = "")
208s +           center <- rowMeans(x, na.rm = na.rm)
208s +           
208s +           r0 <- rowVars_R(x, na.rm = na.rm, useNames = useNames)
208s +           r1 <- rowVars(x, na.rm = na.rm, useNames = useNames)
208s +           r1b <- rowVars_center(x, na.rm = na.rm, useNames = useNames)
208s +           r1c <- rowVars(x, center = center, na.rm = na.rm, useNames = useNames)
208s +           
208s +           tx <- t(x)
208s +           r2 <- colVars(tx, na.rm = na.rm, useNames = useNames)
208s +           r2b <- colVars_center(tx, na.rm = na.rm, useNames = useNames)
208s +           r2c <- colVars(tx, center = center, na.rm = na.rm, useNames = useNames)
208s +           tx <- NULL
208s +           
208s +           stopifnot(all.equal(r1, r2))
208s +           stopifnot(all.equal(r1, r0))
208s +           stopifnot(all.equal(r1b, r1c))
208s +           stopifnot(all.equal(r2, r0))
208s +           stopifnot(all.equal(r2b, r2c))
208s +           
208s +           center <- colMeans(x, na.rm = na.rm)
208s + 
208s +           r3 <- colVars(x, center = center, na.rm = na.rm, useNames = useNames)
208s +           r3b <- colVars_center_naive(x, center = center, na.rm = na.rm, useNames = useNames)
208s +           r3c <- rowVars(t(x), center = center, na.rm = na.rm, useNames = useNames)
208s +           r3d <- rowVars_center_naive(t(x), center = center, na.rm = na.rm, useNames = useNames)
208s +           stopifnot(all.equal(r3b, r3))
208s +           stopifnot(all.equal(r3c, r3))
208s +           stopifnot(all.equal(r3d, r3))
208s +           
208s +           stopifnot(
208s +             !any(is.infinite(r0)),
208s +             !any(is.infinite(r1)),
208s +             !any(is.infinite(r2)),
208s +             !any(is.infinite(r3)),
208s +             !any(is.infinite(r1b)),
208s +             !any(is.infinite(r1c)),
208s +             !any(is.infinite(r2b)),
208s +             !any(is.infinite(r2c)),
208s +             !any(is.infinite(r3b)),
208s +             !any(is.infinite(r3c)),
208s +             !any(is.infinite(r3d))
208s +           )
208s +         }
208s +       }
208s +     }
208s +   } # for (special ...)
208s + }
208s special = 0
208s mode: integer
208s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
208s na.rm = FALSE
208s na.rm = FALSE
208s na.rm = TRUE
208s na.rm = TRUE
208s na.rm = FALSE
208s na.rm = FALSE
208s na.rm = TRUE
208s na.rm = TRUE
208s special = NA
208s mode: integer
208s  int [1:10, 1:5] 1 2 3 4 5 6 7 8 9 10 ...
208s na.rm = FALSE
208s na.rm = FALSE
208s na.rm = TRUE
208s na.rm = TRUE
208s na.rm = FALSE
208s na.rm = FALSE
208s na.rm = TRUE
208s na.rm = TRUE
208s special = 0
208s mode: double
208s  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 ...
208s na.rm = FALSE
208s na.rm = FALSE
208s na.rm = TRUE
208s na.rm = TRUE
208s na.rm = FALSE
208s na.rm = FALSE
208s na.rm = TRUE
208s na.rm = TRUE
208s special = NA
208s mode: double
208s  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 ...
208s na.rm = FALSE
208s na.rm = FALSE
208s na.rm = TRUE
208s na.rm = TRUE
208s na.rm = FALSE
208s na.rm = FALSE
208s na.rm = TRUE
208s na.rm = TRUE
208s special = Inf
208s mode: double
208s  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 ...
208s na.rm = FALSE
208s na.rm = FALSE
208s na.rm = TRUE
208s na.rm = TRUE
208s na.rm = FALSE
208s na.rm = FALSE
208s na.rm = TRUE
208s na.rm = TRUE
208s > 
208s > 
208s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
208s > # All NAs
208s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
208s > for (mode in c("integer", "double")) {
208s +   x <- matrix(NA_real_, nrow = 10L, ncol = 5L)
208s +   cat("mode: ", mode, "\n", sep = "")
208s +   storage.mode(x) <- mode
208s +   str(x)
208s +   
208s +   # Test with and without dimnames on x
208s +   for (setDimnames in c(TRUE, FALSE)) {
208s +     if (setDimnames) dimnames(x) <- dimnames
208s +     else dimnames(x) <- NULL
208s +     # Row/column variance
208s +     for (na.rm in c(FALSE, TRUE)) {
208s +       # Check names attribute
208s +       for (useNames in c(TRUE, FALSE)) {
208s +         cat("na.rm = ", na.rm, "\n", sep = "")
208s +         
208s +         r0 <- rowVars_R(x, na.rm = na.rm, useNames = useNames)
208s +         r1 <- rowVars(x, na.rm = na.rm, useNames = useNames)
208s +         r1b <- rowVars_center(x, na.rm = na.rm, useNames = useNames)
208s +         r2 <- colVars(t(x), na.rm = na.rm, useNames = useNames)
208s +         r2b <- colVars_center(t(x), na.rm = na.rm, useNames = useNames)
208s +         stopifnot(all.equal(r1, r2))
208s +         stopifnot(all.equal(r1, r0))
208s +         stopifnot(all.equal(r2, r0))
208s +         stopifnot(all.equal(r1b, r2b))
208s +         stopifnot(
208s +           !any(is.infinite(r0)),
208s +           !any(is.infinite(r1)),
208s +           !any(is.infinite(r2)),
208s +           !any(is.infinite(r1b)),
208s +           !any(is.infinite(r2b))
208s +         )
208s +       }
208s +     }
208s +   }
208s + }
208s mode: integer
208s  int [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
208s na.rm = FALSE
208s na.rm = FALSE
208s na.rm = TRUE
208s na.rm = TRUE
208s na.rm = FALSE
208s na.rm = FALSE
208s na.rm = TRUE
208s na.rm = TRUE
208s mode: double
208s  num [1:10, 1:5] NA NA NA NA NA NA NA NA NA NA ...
208s na.rm = FALSE
208s na.rm = FALSE
208s na.rm = TRUE
208s na.rm = TRUE
208s na.rm = FALSE
208s na.rm = FALSE
208s na.rm = TRUE
208s na.rm = TRUE
208s > 
208s > 
208s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
208s > # A 1x1 matrix
208s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
208s > x <- matrix(0, nrow = 1L, ncol = 1L)
208s > dimnames <- list("a", "A")
208s > # Test with and without dimnames on x
208s > for (setDimnames in c(TRUE, FALSE)) {
208s +   if (setDimnames) dimnames(x) <- dimnames
208s +   else dimnames(x) <- NULL
208s +   # Row/column variance
208s +   for (na.rm in c(FALSE, TRUE)) {
208s +     # Check names attribute
208s +     for (useNames in c(TRUE, FALSE)) {
208s +       cat("na.rm = ", na.rm, "\n", sep = "")
208s +       
208s +       r0 <- rowVars_R(x, na.rm = na.rm, useNames = useNames)
208s +       r1 <- rowVars(x, na.rm = na.rm, useNames = useNames)
208s +       r1b <- rowVars_center(x, na.rm = na.rm, useNames = useNames)
208s +       r2 <- colVars(t(x), na.rm = na.rm, useNames = useNames)
208s +       r2b <- colVars_center(t(x), na.rm = na.rm, useNames = useNames)
208s +       stopifnot(all.equal(r1, r2))
208s +       stopifnot(all.equal(r1, r0))
208s +       stopifnot(all.equal(r2, r0))
208s +       stopifnot(all.equal(r1b, r2b))
208s +       stopifnot(
208s +         !any(is.infinite(r0)),
208s +         !any(is.infinite(r1)),
208s +         !any(is.infinite(r2)),
208s +         !any(is.infinite(r1b)),
208s +         !any(is.infinite(r2b))
208s +       )
208s +     }
208s +   }
208s + }
208s na.rm = FALSE
208s na.rm = FALSE
208s na.rm = TRUE
208s na.rm = TRUE
208s na.rm = FALSE
208s na.rm = FALSE
208s na.rm = TRUE
208s na.rm = TRUE
208s > 
208s > 
208s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
208s > # center and .dim
208s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
208s > m <- matrix(1:12, nrow = 3L, ncol = 4L)
208s > a <- array(m, dim = c(3, 2, 2))
208s > stopifnot(prod(dim(a)) == prod(dim(m)))
208s > 
208s > y0 <- rowVars(m, dim. = dim(m))
208s > print(y0)
208s [1] 15 15 15
208s > y1 <- rowVars(a, dim. = dim(m))
208s > print(y1)
208s [1] 15 15 15
208s > stopifnot(identical(y1, y0))
208s > stopifnot(
208s +   !any(is.infinite(y0)),
208s +   !any(is.infinite(y1))
208s + )
208s > 
208s > mu <- rowMeans(m)
208s > y0 <- rowVars(m, center = mu, dim. = dim(m))
208s > print(y0)
208s [1] 15 15 15
208s > y1 <- rowVars(a, center = mu, dim. = dim(m))
208s > print(y1)
208s [1] 15 15 15
208s > stopifnot(identical(y1, y0))
208s > stopifnot(
208s +   !any(is.infinite(y0)),
208s +   !any(is.infinite(y1))
208s + )
208s > 
208s > 
208s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
208s > # Corner cases
208s > # https://github.com/HenrikBengtsson/matrixStats/issues/195
208s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
208s > x <- matrix(c(1,2,3,4), nrow = 2L, ncol = 2L)
208s > x[1,1] <- NA_real_
208s > x[1,2] <- Inf
208s > 
208s > center <- colMeans2(x, na.rm = TRUE)
208s > y <- colVars(x, center = center, na.rm = TRUE)
208s > stopifnot(!any(is.infinite(y)))
208s > 
208s > x <- t(x)
208s > center <- rowMeans2(x, na.rm = TRUE)
208s > y <- rowVars(x, center = center, na.rm = TRUE)
208s > stopifnot(!any(is.infinite(y)))
208s > 
208s 
208s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
208s Copyright (C) 2025 The R Foundation for Statistical Computing
208s Platform: x86_64-pc-linux-gnu
208s 
208s R is free software and comes with ABSOLUTELY NO WARRANTY.
208s You are welcome to redistribute it under certain conditions.
208s Type 'license()' or 'licence()' for distribution details.
208s 
208s R is a collaborative project with many contributors.
208s Type 'contributors()' for more information and
208s 'citation()' on how to cite R or R packages in publications.
208s 
208s Type 'demo()' for some demos, 'help()' for on-line help, or
208s 'help.start()' for an HTML browser interface to help.
208s Type 'q()' to quit R.
208s 
208s > library("matrixStats")
208s > 
208s > ## Always allow testing of the 'center' argument (as long as it's not defunct)
208s > options(matrixStats.center.onUse = "ignore")
208s > 
208s > ## Create isFALSE() if running on an old version of R
208s > if (!exists("isFALSE", mode="function")) {
208s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
208s + }
208s > 
208s > rowVars_R <- function(x, na.rm = FALSE, center = NULL, ..., useNames = TRUE) {
208s +   suppressWarnings({
208s +     res <- apply(x, MARGIN = 1L, FUN = var, na.rm = na.rm)
208s +   })
208s +   stopifnot(!any(is.infinite(res)))
208s +   
208s +   # Keep naming support consistency same as rowVars()
208s +   if (is.null(center) || ncol(x) <= 1L) {
208s +     if (isFALSE(useNames)) names(res) <- NULL
208s +   }
208s +   else if (isFALSE(useNames)) names(res) <- NULL
208s +   res
208s + }
208s > 
208s > colVars_R <- function(x, na.rm = FALSE, center = NULL, ..., useNames = TRUE) {
208s +   suppressWarnings({
208s +     res <- apply(x, MARGIN = 2L, FUN = var, na.rm = na.rm)
208s +   })
208s +   stopifnot(!any(is.infinite(res)))
208s +   
208s +   # Keep naming support consistency same as colVars()
208s +   if (is.null(center) || nrow(x) <= 1L) {
208s +     if (isFALSE(useNames)) names(res) <- NULL
208s +   }
208s +   else if (isFALSE(useNames)) names(res) <- NULL
208s +   res
208s + }
208s > 
208s > 
208s > rowVars_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = TRUE) {
208s +   center <- rowWeightedMeans(x, cols = cols, na.rm = na.rm, useNames = FALSE)
208s +   res <- rowVars(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
208s +   stopifnot(!any(is.infinite(res)))
208s +   res
208s + }
208s > 
208s > colVars_center <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = TRUE) {
208s +   center <- colWeightedMeans(x, rows = rows, na.rm = na.rm, useNames = FALSE)
208s +   res <- colVars(x, rows = rows, cols = cols, center = center, na.rm = na.rm, useNames = useNames)
208s +   stopifnot(!any(is.infinite(res)))
208s +   res
208s + }
208s > 
208s > 
208s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
208s > # Subsetted tests
208s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
208s > source("utils/validateIndicesFramework.R")
208s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
208s > storage.mode(x) <- "integer"
208s > 
208s > # To check names attribute
208s > dimnames <- list(letters[1:6], LETTERS[1:6])
208s > 
208s > # Test with and without dimnames on x
208s > for (setDimnames in c(TRUE, FALSE)) {
208s +   if (setDimnames) dimnames(x) <- dimnames
208s +   else dimnames(x) <- NULL
208s + 
208s +   count <- 0L
208s +   for (rows in index_cases) {
208s +     for (cols in index_cases) {
208s +       count <- count + 1L
208s +       na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
208s +       useNames <- c(TRUE, FALSE)
208s +       useNames <- useNames[count %% length(useNames) + 1]
208s +       
208s +       validateIndicesTestMatrix(x, rows, cols,
208s +                                 ftest = rowVars, fsure = rowVars_R,
208s +                                 na.rm = na.rm, useNames = useNames)
208s +       validateIndicesTestMatrix(x, rows, cols,
208s +                                 ftest = rowVars_center, fsure = rowVars_R,
208s +                                 na.rm = na.rm, center = TRUE, useNames = useNames)
208s + 
208s +       validateIndicesTestMatrix(x, rows, cols,
208s +                                 fcoltest = colVars, fsure = rowVars_R,
208s +                                 na.rm = na.rm, useNames = useNames)
208s +       validateIndicesTestMatrix(x, rows, cols,
208s +                                 fcoltest = colVars_center, fsure = rowVars_R,
208s +                                 na.rm = na.rm, center = TRUE, useNames = useNames)
208s +     }
208s +   }
208s + }
208s > 
209s 
209s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
209s Copyright (C) 2025 The R Foundation for Statistical Computing
209s Platform: x86_64-pc-linux-gnu
209s 
209s R is free software and comes with ABSOLUTELY NO WARRANTY.
209s You are welcome to redistribute it under certain conditions.
209s Type 'license()' or 'licence()' for distribution details.
209s 
209s R is a collaborative project with many contributors.
209s Type 'contributors()' for more information and
209s 'citation()' on how to cite R or R packages in publications.
209s 
209s Type 'demo()' for some demos, 'help()' for on-line help, or
209s 'help.start()' for an HTML browser interface to help.
209s Type 'q()' to quit R.
209s 
209s > library("matrixStats")
209s > 
209s > ## Create isFALSE() if running on an old version of R
209s > if (!exists("isFALSE", mode="function")) {
209s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
209s + }
209s > 
209s > rowWeightedMeans_R <- function(x, w, na.rm = FALSE, ..., useNames = TRUE) {
209s +   res <- apply(x, MARGIN = 1L, FUN = weighted.mean, w = w, na.rm = na.rm, ...)
209s +   
209s +   # Keep naming support consistency same as rowWeightedMeans()
209s +   idxs <- which(is.na(w) | w != 0)
209s +   nw <- length(idxs)
209s +   if (na.rm) na.rm <- anyMissing(x)
209s +   if ((!is.null(w) && nw == 0L) || isFALSE(na.rm)) {
209s +     if (!useNames) names(res) <- NULL
209s +   }
209s +   else if (isFALSE(useNames)) names(res) <- NULL
209s +   
209s +   res
209s + }
209s > 
209s > colWeightedMeans_R <- function(x, w, na.rm = FALSE, ..., useNames = TRUE) {
209s +   res <- apply(x, MARGIN = 2L, FUN = weighted.mean, w = w, na.rm = na.rm, ...)
209s +   
209s +   # Keep naming support consistency same as colWeightedMeans()
209s +   idxs <- which(is.na(w) | w != 0)
209s +   nw <- length(idxs)
209s +   if (!is.null(w) && nw == 0L) {
209s +     if (!useNames) names(res) <- NULL
209s +   }
209s +   else if (isFALSE(useNames)) names(res) <- NULL
209s +   
209s +   res
209s + }
209s > 
209s > set.seed(1)
209s > 
209s > x <- matrix(rnorm(20), nrow = 5, ncol = 4)
209s > print(x)
209s            [,1]       [,2]       [,3]        [,4]
209s [1,] -0.6264538 -0.8204684  1.5117812 -0.04493361
209s [2,]  0.1836433  0.4874291  0.3898432 -0.01619026
209s [3,] -0.8356286  0.7383247 -0.6212406  0.94383621
209s [4,]  1.5952808  0.5757814 -2.2146999  0.82122120
209s [5,]  0.3295078 -0.3053884  1.1249309  0.59390132
209s > 
209s > # To check names attribute
209s > dimnames <- list(letters[1:5], LETTERS[1:4])
209s > 
209s > # Non-weighted row averages
209s > x_est0 <- rowMeans(x)
209s > x_est1 <- rowWeightedMeans(x)
209s > print(x_est1)
209s [1] 0.004981341 0.261181337 0.056322931 0.194395865 0.435737906
209s > stopifnot(all.equal(x_est1, x_est0))
209s > x_est2 <- colWeightedMeans(t(x))
209s > stopifnot(all.equal(x_est2, x_est0))
209s > # Check names attribute
209s > dimnames(x) <- dimnames
209s > x_est1 <- rowWeightedMeans(x, useNames = FALSE)
209s > x_est2 <- colWeightedMeans(t(x), useNames = FALSE)
209s > stopifnot(all.equal(x_est1, x_est0))
209s > stopifnot(all.equal(x_est2, x_est0))
209s > x_est0 <- rowMeans(x)
209s > x_est1 <- rowWeightedMeans(x, useNames = TRUE)
209s > x_est2 <- colWeightedMeans(t(x), useNames = TRUE)
209s > stopifnot(all.equal(x_est1, x_est0))
209s > stopifnot(all.equal(x_est2, x_est0))
209s > dimnames(x) <- NULL
209s > 
209s > 
209s > # Weighted row averages (uniform weights)
209s > w <- rep(2.5, times = ncol(x))
209s > x_est0 <- rowMeans(x)
209s > x_est1 <- rowWeightedMeans(x, w = w)
209s > print(x_est1)
209s [1] 0.004981341 0.261181337 0.056322931 0.194395865 0.435737906
209s > stopifnot(all.equal(x_est1, x_est0))
209s > x_est2 <- colWeightedMeans(t(x), w = w)
209s > stopifnot(all.equal(x_est2, x_est0))
209s > # Test with and without dimnames on x
209s > for (setDimnames in c(TRUE, FALSE)) {
209s +   if (setDimnames) dimnames(x) <- dimnames
209s +   else dimnames(x) <- NULL    
209s +   # Check names attribute
209s +   for (useNames in c(TRUE, FALSE)) {
209s +     x_est0 <- rowWeightedMeans_R(x, w = w, useNames = useNames)
209s +     x_est1 <- rowWeightedMeans(x, w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +     x_est0 <- colWeightedMeans_R(t(x), w = w, useNames = useNames)
209s +     x_est1 <- colWeightedMeans(t(x), w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +   }
209s + }
209s > 
209s > 
209s > # Weighted row averages (excluding some columns)
209s > w <- c(1, 1, 0, 1)
209s > x_est0 <- rowMeans(x[, (w == 1), drop = FALSE])
209s > x_est1 <- rowWeightedMeans(x, w = w)
209s > print(x_est1)
209s [1] -0.4972853  0.2182940  0.2821774  0.9974278  0.2060069
209s > stopifnot(all.equal(x_est1, x_est0))
209s > x_est2 <- colWeightedMeans(t(x), w = w)
209s > stopifnot(all.equal(x_est2, x_est0))
209s > # Test with and without dimnames on x
209s > for (setDimnames in c(TRUE, FALSE)) {
209s +   if (setDimnames) dimnames(x) <- dimnames
209s +   else dimnames(x) <- NULL    
209s +   # Check names attribute
209s +   for (useNames in c(TRUE, FALSE)) {
209s +     x_est0 <- rowWeightedMeans_R(x, w = w, useNames = useNames)
209s +     x_est1 <- rowWeightedMeans(x, w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +     x_est0 <- colWeightedMeans_R(t(x), w = w, useNames = useNames)
209s +     x_est1 <- colWeightedMeans(t(x), w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +   }
209s + }
209s > 
209s > 
209s > # Weighted row averages (excluding some columns)
209s > w <- c(0, 1, 0, 0)
209s > x_est0 <- rowMeans(x[, (w == 1), drop = FALSE])
209s > x_est1 <- rowWeightedMeans(x, w = w)
209s > stopifnot(all.equal(x_est1, x_est0))
209s > x_est2 <- colWeightedMeans(t(x), w = w)
209s > stopifnot(all.equal(x_est2, x_est0))
209s > # Test with and without dimnames on x
209s > for (setDimnames in c(TRUE, FALSE)) {
209s +   if (setDimnames) dimnames(x) <- dimnames
209s +   else dimnames(x) <- NULL    
209s +   # Check names attribute
209s +   for (useNames in c(TRUE, FALSE)) {
209s +     x_est0 <- rowWeightedMeans_R(x, w = w, useNames = useNames)
209s +     x_est1 <- rowWeightedMeans(x, w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +     x_est0 <- colWeightedMeans_R(t(x), w = w, useNames = useNames)
209s +     x_est1 <- colWeightedMeans(t(x), w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +   }
209s + }
209s > 
209s > 
209s > # Weighted row averages (all zero weights)
209s > w <- c(0, 0, 0, 0)
209s > x_est0 <- rowMeans(x[, (w == 1), drop = FALSE])
209s > x_est1 <- rowWeightedMeans(x, w = w)
209s > stopifnot(all.equal(x_est1, x_est0))
209s > x_est2 <- colWeightedMeans(t(x), w = w)
209s > stopifnot(all.equal(x_est2, x_est0))
209s > # Test with and without dimnames on x
209s > for (setDimnames in c(TRUE, FALSE)) {
209s +   if (setDimnames) dimnames(x) <- dimnames
209s +   else dimnames(x) <- NULL    
209s +   # Check names attribute
209s +   for (useNames in c(TRUE, FALSE)) {
209s +     x_est0 <- rowWeightedMeans_R(x, w = w, useNames = useNames)
209s +     x_est1 <- rowWeightedMeans(x, w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +     x_est0 <- colWeightedMeans_R(t(x), w = w, useNames = useNames)
209s +     x_est1 <- colWeightedMeans(t(x), w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +   }
209s + }
209s > 
209s > 
209s > # Weighted averages by rows and columns
209s > w <- 1:4
209s > x_est1 <- rowWeightedMeans(x, w = w)
209s > print(x_est1)
209s [1]  0.20882185  0.22632701  0.25526439 -0.06123714  0.54691290
209s > x_est2 <- colWeightedMeans(t(x), w = w)
209s > stopifnot(all.equal(x_est2, x_est1))
209s > # Test with and without dimnames on x
209s > for (setDimnames in c(TRUE, FALSE)) {
209s +   if (setDimnames) dimnames(x) <- dimnames
209s +   else dimnames(x) <- NULL    
209s +   # Check names attribute
209s +   for (useNames in c(TRUE, FALSE)) {
209s +     x_est0 <- rowWeightedMeans_R(x, w = w, useNames = useNames)
209s +     x_est1 <- rowWeightedMeans(x, w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +     x_est0 <- colWeightedMeans_R(t(x), w = w, useNames = useNames)
209s +     x_est1 <- colWeightedMeans(t(x), w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +   }
209s + }
209s > 
209s > 
209s > x[sample(length(x), size = 0.3 * length(x))] <- NA
209s > print(x)
209s            [,1]      [,2]       [,3]        [,4]
209s [1,] -0.6264538        NA  1.5117812 -0.04493361
209s [2,]  0.1836433        NA         NA -0.01619026
209s [3,] -0.8356286 0.7383247 -0.6212406  0.94383621
209s [4,]  1.5952808        NA -2.2146999  0.82122120
209s [5,]  0.3295078        NA         NA  0.59390132
209s > 
209s > # Non-weighted row averages with missing values
209s > x_est0 <- rowMeans(x, na.rm = TRUE)
209s > x_est1 <- rowWeightedMeans(x, na.rm = TRUE)
209s > print(x_est1)
209s [1] 0.28013125 0.08372653 0.05632293 0.06726737 0.46170455
209s > stopifnot(all.equal(x_est1, x_est0))
209s > x_est2 <- colWeightedMeans(t(x), na.rm = TRUE)
209s > stopifnot(all.equal(x_est2, x_est0))
209s > # Check names attribute
209s > dimnames(x) <- dimnames
209s > x_est1 <- rowWeightedMeans(x, na.rm = TRUE, useNames = FALSE)
209s > x_est2 <- colWeightedMeans(t(x), na.rm = TRUE, useNames = FALSE)
209s > stopifnot(all.equal(x_est1, x_est0))
209s > stopifnot(all.equal(x_est2, x_est0))
209s > x_est0 <- rowMeans(x, na.rm = TRUE)
209s > x_est1 <- rowWeightedMeans(x, na.rm = TRUE, useNames = TRUE)
209s > x_est2 <- colWeightedMeans(t(x), na.rm = TRUE, useNames = TRUE)
209s > stopifnot(all.equal(x_est1, x_est0))
209s > stopifnot(all.equal(x_est2, x_est0))
209s > dimnames(x) <- NULL
209s > 
209s > 
209s > # Weighted row averages with missing values
209s > x_est0 <- apply(x, MARGIN = 1L, FUN = weighted.mean, w = w, na.rm = TRUE)
209s > print(x_est0)
209s [1]  0.46614441  0.02377645  0.25526439 -0.22049176  0.54102261
209s > x_est1 <- rowWeightedMeans(x, w = w, na.rm = TRUE)
209s > print(x_est1)
209s [1]  0.46614441  0.02377645  0.25526439 -0.22049176  0.54102261
209s > stopifnot(all.equal(x_est1, x_est0))
209s > x_est2 <- colWeightedMeans(t(x), w = w, na.rm = TRUE)
209s > stopifnot(all.equal(x_est2, x_est0))
209s > # Test with and without dimnames on x
209s > for (setDimnames in c(TRUE, FALSE)) {
209s +   if (setDimnames) dimnames(x) <- dimnames
209s +   else dimnames(x) <- NULL    
209s +   # Check names attribute
209s +   for (useNames in c(TRUE, FALSE)) {
209s +     x_est0 <- rowWeightedMeans_R(x, w = w, na.rm = TRUE, useNames = useNames)
209s +     x_est1 <- rowWeightedMeans(x, w = w, na.rm = TRUE, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +     x_est0 <- colWeightedMeans_R(t(x), w = w, na.rm = TRUE, useNames = useNames)
209s +     x_est1 <- colWeightedMeans(t(x), w = w, na.rm = TRUE, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +   }
209s + }
209s > 
209s > 
209s > # Weighted averages by rows and columns
209s > w <- 1:4
209s > x_est1 <- rowWeightedMeans(x, w = w, na.rm = TRUE)
209s > x_est2 <- colWeightedMeans(t(x), w = w, na.rm = TRUE)
209s > stopifnot(all.equal(x_est2, x_est1))
209s > # Test with and without dimnames on x
209s > for (setDimnames in c(TRUE, FALSE)) {
209s +   if (setDimnames) dimnames(x) <- dimnames
209s +   else dimnames(x) <- NULL    
209s +   # Check names attribute
209s +   for (useNames in c(TRUE, FALSE)) {
209s +     x_est0 <- rowWeightedMeans_R(x, w = w, na.rm = TRUE, useNames = useNames)
209s +     x_est1 <- rowWeightedMeans(x, w = w, na.rm = TRUE, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +     x_est0 <- colWeightedMeans_R(t(x), w = w, na.rm = TRUE, useNames = useNames)
209s +     x_est1 <- colWeightedMeans(t(x), w = w, na.rm = TRUE, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +   }
209s + }
209s > 
209s > 
209s > # w contains missing value
209s > w[1] <- NA_integer_
209s > x_est1 <- rowWeightedMeans(x, w = w, na.rm = TRUE)
209s > x_est2 <- colWeightedMeans(t(x), w = w, na.rm = TRUE)
209s > stopifnot(all.equal(x_est2, x_est1))
209s > # Test with and without dimnames on x
209s > for (setDimnames in c(TRUE, FALSE)) {
209s +   if (setDimnames) dimnames(x) <- dimnames
209s +   else dimnames(x) <- NULL    
209s +   # Check names attribute
209s +   for (useNames in c(TRUE, FALSE)) {
209s +     x_est0 <- rowWeightedMeans_R(x, w = w, na.rm = TRUE, useNames = useNames)
209s +     x_est1 <- rowWeightedMeans(x, w = w, na.rm = TRUE, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +     x_est0 <- colWeightedMeans_R(t(x), w = w, na.rm = TRUE, useNames = useNames)
209s +     x_est1 <- colWeightedMeans(t(x), w = w, na.rm = TRUE, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +   }
209s + }
209s > 
209s > x_est1 <- rowWeightedMeans(x, w = w, na.rm = FALSE)
209s > x_est2 <- colWeightedMeans(t(x), w = w, na.rm = FALSE)
209s > stopifnot(all.equal(x_est2, x_est1))
209s > # Test with and without dimnames on x
209s > for (setDimnames in c(TRUE, FALSE)) {
209s +   if (setDimnames) dimnames(x) <- dimnames
209s +   else dimnames(x) <- NULL    
209s +   # Check names attribute
209s +   for (useNames in c(TRUE, FALSE)) {
209s +     x_est0 <- rowWeightedMeans_R(x, w = w, na.rm = FALSE, useNames = useNames)
209s +     x_est1 <- rowWeightedMeans(x, w = w, na.rm = FALSE, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +     x_est0 <- colWeightedMeans_R(t(x), w = w, na.rm = FALSE, useNames = useNames)
209s +     x_est1 <- colWeightedMeans(t(x), w = w, na.rm = FALSE, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +   }
209s + }
209s > 
209s 
209s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
209s Copyright (C) 2025 The R Foundation for Statistical Computing
209s Platform: x86_64-pc-linux-gnu
209s 
209s R is free software and comes with ABSOLUTELY NO WARRANTY.
209s You are welcome to redistribute it under certain conditions.
209s Type 'license()' or 'licence()' for distribution details.
209s 
209s R is a collaborative project with many contributors.
209s Type 'contributors()' for more information and
209s 'citation()' on how to cite R or R packages in publications.
209s 
209s Type 'demo()' for some demos, 'help()' for on-line help, or
209s 'help.start()' for an HTML browser interface to help.
209s Type 'q()' to quit R.
209s 
209s > library("matrixStats")
209s > 
209s > ## Create isFALSE() if running on an old version of R
209s > if (!exists("isFALSE", mode="function")) {
209s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
209s + }
209s > 
209s > rowWeightedMeans_R <- function(x, w, na.rm = FALSE, ..., useNames = TRUE) {
209s +   res <- apply(x, MARGIN = 1L, FUN = weighted.mean, w = w, na.rm = na.rm, ...)
209s +   
209s +   # Keep naming support consistency same as rowWeightedMeans()
209s +   idxs <- which(is.na(w) | w != 0)
209s +   nw <- length(idxs)
209s +   if (na.rm) na.rm <- anyMissing(x)
209s +   if ((!is.null(w) && nw == 0L) || isFALSE(na.rm)) {
209s +     if (!useNames) names(res) <- NULL
209s +   }
209s +   else if (isFALSE(useNames)) names(res) <- NULL
209s +   
209s +   res
209s + }
209s > 
209s > colWeightedMeans_R <- function(x, w, na.rm = FALSE, ..., useNames = TRUE) {
209s +   res <- apply(x, MARGIN = 1L, FUN = weighted.mean, w = w, na.rm = na.rm, ...)
209s +   
209s +   # Keep naming support consistency same as colWeightedMeans()
209s +   idxs <- which(is.na(w) | w != 0)
209s +   nw <- length(idxs)
209s +   if (!is.null(w) && nw == 0L) {
209s +     if (!useNames) names(res) <- NULL
209s +   }
209s +   else if (isFALSE(useNames)) names(res) <- NULL
209s +   
209s +   res
209s + }
209s > 
209s > 
209s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
209s > # Subsetted tests
209s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
209s > source("utils/validateIndicesFramework.R")
209s > # To check names attribute
209s > dimnames <- list(letters[1:6], LETTERS[1:6])
209s > for (mode in c("numeric", "integer", "logical")) {
209s +   x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
209s +   w <- runif(6, min = 0, max = 6)
209s +   storage.mode(x) <- mode
209s +   storage.mode(w) <- if (mode == "logical") "integer" else mode
209s +   if (mode == "numeric") w[1] <- Inf
209s + 
209s +   # Test with and without dimnames on x
209s +   for (setDimnames in c(TRUE, FALSE)) {
209s +     if (setDimnames) dimnames(x) <- dimnames
209s +     else dimnames(x) <- NULL
209s + 
209s +     count <- 0L
209s +     for (rows in index_cases) {
209s +       for (cols in index_cases) {
209s +         count <- count + 1L
209s +         na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
209s +         useNames <- c(TRUE, FALSE)
209s +         useNames <- useNames[count %% length(useNames) + 1]
209s + 
209s +         validateIndicesTestMatrix_w(x, w, rows, cols, 
209s +                                     ftest = rowWeightedMeans, fsure = rowWeightedMeans_R,
209s +                                     na.rm = na.rm, useNames = useNames)
209s +         validateIndicesTestMatrix_w(x, w, rows, cols,
209s +                                     fcoltest = colWeightedMeans, fsure = colWeightedMeans_R,
209s +                                     na.rm = na.rm, useNames = useNames)
209s +       }
209s +     }
209s +   }
209s + }
209s > 
209s 
209s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
209s Copyright (C) 2025 The R Foundation for Statistical Computing
209s Platform: x86_64-pc-linux-gnu
209s 
209s R is free software and comes with ABSOLUTELY NO WARRANTY.
209s You are welcome to redistribute it under certain conditions.
209s Type 'license()' or 'licence()' for distribution details.
209s 
209s R is a collaborative project with many contributors.
209s Type 'contributors()' for more information and
209s 'citation()' on how to cite R or R packages in publications.
209s 
209s Type 'demo()' for some demos, 'help()' for on-line help, or
209s 'help.start()' for an HTML browser interface to help.
209s Type 'q()' to quit R.
209s 
209s > library("matrixStats")
209s > 
209s > ## Create isFALSE() if running on an old version of R
209s > if (!exists("isFALSE", mode="function")) {
209s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
209s + }
209s > 
209s > rowWeightedMedians_R <- function(x, w, na.rm = FALSE, ..., useNames = TRUE) {
209s +   res <- apply(x, MARGIN = 1L, FUN = weightedMedian, w = w, na.rm = na.rm, ...)
209s +   
209s +   # Keep naming support consistency same as rowWeightedMedians()
209s +   if (!is.null(w)) {
209s +     if (isFALSE(useNames)) names(res) <- NULL
209s +   }
209s +   else if (!useNames) names(res) <- NULL
209s +   
209s +   res
209s + }
209s > 
209s > colWeightedMedians_R <- function(x, w, na.rm = FALSE, ..., useNames = TRUE) {
209s +   res <- apply(x, MARGIN = 2L, FUN = weightedMedian, w = w, na.rm = na.rm, ...)
209s +   
209s +   # Keep naming support consistency same as colWeightedMedians()
209s +   if (!is.null(w)) {
209s +     if (isFALSE(useNames)) names(res) <- NULL
209s +   }
209s +   else if (!useNames) names(res) <- NULL
209s +   
209s +   res
209s + }
209s > 
209s > set.seed(1)
209s > 
209s > x <- matrix(rnorm(20), nrow = 5, ncol = 4)
209s > print(x)
209s            [,1]       [,2]       [,3]        [,4]
209s [1,] -0.6264538 -0.8204684  1.5117812 -0.04493361
209s [2,]  0.1836433  0.4874291  0.3898432 -0.01619026
209s [3,] -0.8356286  0.7383247 -0.6212406  0.94383621
209s [4,]  1.5952808  0.5757814 -2.2146999  0.82122120
209s [5,]  0.3295078 -0.3053884  1.1249309  0.59390132
209s > 
209s > # To check names attribute
209s > dimnames <- list(letters[1:5], LETTERS[1:4])
209s > 
209s > # Non-weighted row medians
209s > x_est0 <- rowMedians(x)
209s > x_est1 <- rowWeightedMedians(x)
209s > stopifnot(all.equal(x_est1, x_est0))
209s > x_est2 <- colWeightedMedians(t(x))
209s > stopifnot(all.equal(x_est2, x_est0))
209s > # Test with and without dimnames on x
209s > for (setDimnames in c(TRUE, FALSE)) {
209s +   if (setDimnames) dimnames(x) <- dimnames
209s +   else dimnames(x) <- NULL
209s +   # Check names attribute
209s +   for (useNames in c(TRUE, FALSE)) {
209s +     x_est0 <- rowMedians(x, useNames = useNames)
209s +     x_est1 <- rowWeightedMedians(x, useNames = useNames)
209s +     x_est2 <- colWeightedMedians(t(x), useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +     stopifnot(all.equal(x_est2, x_est0))
209s +   }
209s + }
209s > 
209s > 
209s > # Weighted row medians (uniform weights)
209s > w <- rep(2.5, times = ncol(x))
209s > x_est0 <- rowMedians(x)
209s > x_est1 <- rowWeightedMedians(x, w = w)
209s > stopifnot(all.equal(x_est1, x_est0))
209s > x_est2 <- colWeightedMedians(t(x), w = w)
209s > stopifnot(all.equal(x_est2, x_est0))
209s > # Test with and without dimnames on x
209s > for (setDimnames in c(TRUE, FALSE)) {
209s +   if (setDimnames) dimnames(x) <- dimnames
209s +   else dimnames(x) <- NULL    
209s +   # Check names attribute
209s +   for (useNames in c(TRUE, FALSE)) {
209s +     x_est0 <- rowWeightedMedians_R(x, w = w, useNames = useNames)
209s +     x_est1 <- rowWeightedMedians(x, w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +     x_est0 <- colWeightedMedians_R(t(x), w = w, useNames = useNames)
209s +     x_est1 <- colWeightedMedians(t(x), w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +   }
209s + }
209s > 
209s > 
209s > # Weighted row medians (excluding some columns)
209s > w <- c(1, 1, 0, 1)
209s > x_est0 <- rowMedians(x[, (w == 1), drop = FALSE])
209s > x_est1 <- rowWeightedMedians(x, w = w)
209s > stopifnot(all.equal(x_est1, x_est0))
209s > x_est2 <- colWeightedMedians(t(x), w = w)
209s > stopifnot(all.equal(x_est2, x_est0))
209s > # Test with and without dimnames on x
209s > for (setDimnames in c(TRUE, FALSE)) {
209s +   if (setDimnames) dimnames(x) <- dimnames
209s +   else dimnames(x) <- NULL    
209s +   # Check names attribute
209s +   for (useNames in c(TRUE, FALSE)) {
209s +     x_est0 <- rowWeightedMedians_R(x, w = w, useNames = useNames)
209s +     x_est1 <- rowWeightedMedians(x, w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +     x_est0 <- colWeightedMedians_R(t(x), w = w, useNames = useNames)
209s +     x_est1 <- colWeightedMedians(t(x), w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +   }
209s + }
209s > 
209s > # Weighted row medians (excluding some columns)
209s > w <- c(0, 1, 0, 0)
209s > x_est0 <- rowMedians(x[, (w == 1), drop = FALSE])
209s > x_est1 <- rowWeightedMedians(x, w = w)
209s > stopifnot(all.equal(x_est1, x_est0))
209s > x_est2 <- colWeightedMedians(t(x), w = w)
209s > stopifnot(all.equal(x_est2, x_est0))
209s > # Test with and without dimnames on x
209s > for (setDimnames in c(TRUE, FALSE)) {
209s +   if (setDimnames) dimnames(x) <- dimnames
209s +   else dimnames(x) <- NULL    
209s +   # Check names attribute
209s +   for (useNames in c(TRUE, FALSE)) {
209s +     x_est0 <- rowWeightedMedians_R(x, w = w, useNames = useNames)
209s +     x_est1 <- rowWeightedMedians(x, w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +     x_est0 <- colWeightedMedians_R(t(x), w = w, useNames = useNames)
209s +     x_est1 <- colWeightedMedians(t(x), w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +   }
209s + }
209s > 
209s > # Weighted row medians (all zero weights)
209s > w <- c(0, 0, 0, 0)
209s > x_est0 <- rowMedians(x[, (w == 1), drop = FALSE])
209s > x_est1 <- rowWeightedMedians(x, w = w)
209s > stopifnot(all.equal(x_est1, x_est0))
209s > x_est2 <- colWeightedMedians(t(x), w = w)
209s > stopifnot(all.equal(x_est2, x_est0))
209s > # Test with and without dimnames on x
209s > for (setDimnames in c(TRUE, FALSE)) {
209s +   if (setDimnames) dimnames(x) <- dimnames
209s +   else dimnames(x) <- NULL    
209s +   # Check names attribute
209s +   for (useNames in c(TRUE, FALSE)) {
209s +     x_est0 <- rowWeightedMedians_R(x, w = w, useNames = useNames)
209s +     x_est1 <- rowWeightedMedians(x, w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +     x_est0 <- colWeightedMedians_R(t(x), w = w, useNames = useNames)
209s +     x_est1 <- colWeightedMedians(t(x), w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +   }
209s + }
209s > 
209s > # Weighted medians by rows and columns
209s > w <- 1:4
209s > x_est1 <- rowWeightedMedians(x, w = w)
209s > x_est2 <- colWeightedMedians(t(x), w = w)
209s > stopifnot(all.equal(x_est2, x_est1))
209s > # Test with and without dimnames on x
209s > for (setDimnames in c(TRUE, FALSE)) {
209s +   if (setDimnames) dimnames(x) <- dimnames
209s +   else dimnames(x) <- NULL    
209s +   # Check names attribute
209s +   for (useNames in c(TRUE, FALSE)) {
209s +     x_est0 <- rowWeightedMedians_R(x, w = w, useNames = useNames)
209s +     x_est1 <- rowWeightedMedians(x, w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +     x_est0 <- colWeightedMedians_R(t(x), w = w, useNames = useNames)
209s +     x_est1 <- colWeightedMedians(t(x), w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +   }
209s + }
209s > 
209s > 
209s > # Weighted row medians with missing values
209s > x_est0 <- apply(x, MARGIN = 1L, FUN = weightedMedian, w = w, na.rm = TRUE)
209s > print(x_est0)
209s [1] -0.04493361  0.23519330  0.73832471  0.65759463  0.59390132
209s > x_est1 <- rowWeightedMedians(x, w = w, na.rm = TRUE)
209s > print(x_est1)
209s [1] -0.04493361  0.23519330  0.73832471  0.65759463  0.59390132
209s > stopifnot(all.equal(x_est1, x_est0))
209s > x_est2 <- colWeightedMedians(t(x), w = w)
209s > stopifnot(all.equal(x_est2, x_est0))
209s > # Test with and without dimnames on x
209s > for (setDimnames in c(TRUE, FALSE)) {
209s +   if (setDimnames) dimnames(x) <- dimnames
209s +   else dimnames(x) <- NULL    
209s +   # Check names attribute
209s +   for (useNames in c(TRUE, FALSE)) {
209s +     x_est0 <- rowWeightedMedians_R(x, w = w, na.rm = TRUE, useNames = useNames)
209s +     x_est1 <- rowWeightedMedians(x, w = w, na.rm = TRUE, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +     x_est0 <- colWeightedMedians_R(t(x), w = w, na.rm = TRUE, useNames = useNames)
209s +     x_est1 <- colWeightedMedians(t(x), w = w, na.rm = TRUE, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +   }
209s + }
209s > 
209s > # Weighted medians by rows and columns
209s > w <- 1:4
209s > x_est1 <- rowWeightedMedians(x, w = w, na.rm = TRUE)
209s > x_est2 <- colWeightedMedians(t(x), w = w, na.rm = TRUE)
209s > stopifnot(all.equal(x_est2, x_est1))
209s > # Test with and without dimnames on x
209s > for (setDimnames in c(TRUE, FALSE)) {
209s +   if (setDimnames) dimnames(x) <- dimnames
209s +   else dimnames(x) <- NULL    
209s +   # Check names attribute
209s +   for (useNames in c(TRUE, FALSE)) {
209s +     x_est0 <- rowWeightedMedians_R(x, w = w, na.rm = TRUE, useNames = useNames)
209s +     x_est1 <- rowWeightedMedians(x, w = w, na.rm = TRUE, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +     x_est0 <- colWeightedMedians_R(t(x), w = w, na.rm = TRUE, useNames = useNames)
209s +     x_est1 <- colWeightedMedians(t(x), w = w, na.rm = TRUE, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +   }
209s + }
209s > 
209s > 
209s > # Inf weight
209s > x <- matrix(1:2, nrow = 1, ncol = 2)
209s > w <- c(7, Inf)
209s > x_est1 <- rowWeightedMedians(x, w = w)
209s > x_est2 <- colWeightedMedians(t(x), w = w)
209s > stopifnot(identical(2, x_est1))
209s > stopifnot(identical(2, x_est2))
209s > # Test with and without dimnames on x
209s > dimnames <- list("a", LETTERS[1:2])
209s > for (setDimnames in c(TRUE, FALSE)) {
209s +   if (setDimnames) dimnames(x) <- dimnames
209s +   else dimnames(x) <- NULL    
209s +   # Check names attribute
209s +   for (useNames in c(TRUE, FALSE)) {
209s +     x_est0 <- rowWeightedMedians_R(x, w = w, useNames = useNames)
209s +     x_est1 <- rowWeightedMedians(x, w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +     x_est0 <- colWeightedMedians_R(t(x), w = w, useNames = useNames)
209s +     x_est1 <- colWeightedMedians(t(x), w = w, useNames = useNames)
209s +     stopifnot(all.equal(x_est1, x_est0))
209s +   }
209s + }
209s > 
209s 
209s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
209s Copyright (C) 2025 The R Foundation for Statistical Computing
209s Platform: x86_64-pc-linux-gnu
209s 
209s R is free software and comes with ABSOLUTELY NO WARRANTY.
209s You are welcome to redistribute it under certain conditions.
209s Type 'license()' or 'licence()' for distribution details.
209s 
209s R is a collaborative project with many contributors.
209s Type 'contributors()' for more information and
209s 'citation()' on how to cite R or R packages in publications.
209s 
209s Type 'demo()' for some demos, 'help()' for on-line help, or
209s 'help.start()' for an HTML browser interface to help.
209s Type 'q()' to quit R.
209s 
210s > library("matrixStats")
210s > 
210s > ## Create isFALSE() if running on an old version of R
210s > if (!exists("isFALSE", mode="function")) {
210s +   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
210s + }
210s > 
210s > rowWeightedMedians_R <- function(x, w, na.rm = FALSE, ..., useNames = TRUE) {
210s +   res <- apply(x, MARGIN = 1L, FUN = weightedMedian, w = w, na.rm = na.rm, ...)
210s +   
210s +   # Keep naming support consistency same as rowWeightedMedians()
210s +   if (!is.null(w)) {
210s +     if (isFALSE(useNames)) names(res) <- NULL
210s +   }
210s +   else if (!useNames) names(res) <- NULL
210s +   
210s +   res
210s + }
210s > 
210s > 
210s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
210s > # Subsetted tests
210s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
210s > source("utils/validateIndicesFramework.R")
210s > # To check names attribute
210s > dimnames <- list(letters[1:6], LETTERS[1:6])
210s > for (mode in c("numeric", "integer", "logical")) {
210s +   x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
210s +   w <- runif(6, min = 0, max = 6)
210s +   storage.mode(x) <- mode
210s +   storage.mode(w) <- if (mode == "logical") "integer" else mode
210s +   if (mode == "numeric") w[1] <- Inf
210s + 
210s +   # Test with and without dimnames on x
210s +   for (setDimnames in c(TRUE, FALSE)) {
210s +     if (setDimnames) dimnames(x) <- dimnames
210s +     else dimnames(x) <- NULL
210s + 
210s +     count <- 0L
210s +     for (rows in index_cases) {
210s +       for (cols in index_cases) {
210s +         count <- count + 1L
210s +         na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
210s +         useNames <- c(TRUE, FALSE)
210s +         useNames <- useNames[count %% length(useNames) + 1]
210s + 
210s +         validateIndicesTestMatrix_w(x, w, rows, cols,
210s +                                     ftest = rowWeightedMedians,
210s +                                     fsure = rowWeightedMedians_R,
210s +                                     na.rm = na.rm, useNames = useNames)
210s +         validateIndicesTestMatrix_w(x, w, rows, cols,
210s +                                     fcoltest = colWeightedMedians,
210s +                                     fsure = rowWeightedMedians_R,
210s +                                     na.rm = na.rm, useNames = useNames)
210s +       }
210s +     }
210s +   }
210s + }
210s > 
210s 
210s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
210s Copyright (C) 2025 The R Foundation for Statistical Computing
210s Platform: x86_64-pc-linux-gnu
210s 
210s R is free software and comes with ABSOLUTELY NO WARRANTY.
210s You are welcome to redistribute it under certain conditions.
210s Type 'license()' or 'licence()' for distribution details.
210s 
210s R is a collaborative project with many contributors.
210s Type 'contributors()' for more information and
210s 'citation()' on how to cite R or R packages in publications.
210s 
210s Type 'demo()' for some demos, 'help()' for on-line help, or
210s 'help.start()' for an HTML browser interface to help.
210s Type 'q()' to quit R.
210s 
210s > library("matrixStats")
210s > 
210s > set.seed(1)
210s > 
210s > x <- matrix(rnorm(20), nrow = 5L, ncol = 4L)
210s > print(x)
210s            [,1]       [,2]       [,3]        [,4]
210s [1,] -0.6264538 -0.8204684  1.5117812 -0.04493361
210s [2,]  0.1836433  0.4874291  0.3898432 -0.01619026
210s [3,] -0.8356286  0.7383247 -0.6212406  0.94383621
210s [4,]  1.5952808  0.5757814 -2.2146999  0.82122120
210s [5,]  0.3295078 -0.3053884  1.1249309  0.59390132
210s > 
210s > # To check names attribute
210s > dimnames <- list(letters[1:5], LETTERS[1:4])
210s > 
210s > # Weighted row variances (uniform weights - all w = 1)
210s > # Non-weighted row variances
210s > x_est0 <- rowVars(x)
210s > w <- rep(1, times = ncol(x))
210s > x_est1 <- rowWeightedVars(x, w = w)
210s > print(x_est1)
210s [1] 1.11767161 0.05022969 0.83582537 2.76819528 0.35351857
210s > stopifnot(all.equal(x_est1, x_est0))
210s > x_est2 <- colWeightedVars(t(x), w = w)
210s > stopifnot(all.equal(x_est2, x_est0))
210s > # Check names attribute
210s > dimnames(x) <- dimnames
210s > x_est1 <- rowWeightedVars(x, w = w, useNames = FALSE)
210s > x_est2 <- colWeightedVars(t(x), w = w, useNames = FALSE)
210s > stopifnot(all.equal(x_est1, x_est0))
210s > stopifnot(all.equal(x_est2, x_est0))
210s > x_est0 <- rowVars(x, useNames = TRUE)
210s > x_est1 <- rowWeightedVars(x, w = w, useNames = TRUE)
210s > x_est2 <- colWeightedVars(t(x), w = w, useNames = TRUE)
210s > stopifnot(all.equal(x_est1, x_est0))
210s > stopifnot(all.equal(x_est2, x_est0))
210s > dimnames(x) <- NULL
210s > 
210s > 
210s > # Weighted row variances (uniform weights - all w = 3)
210s > x3 <- cbind(x, x, x)
210s > x_est0 <- rowVars(x3)
210s > w <- rep(3, times = ncol(x))
210s > x_est1 <- rowWeightedVars(x, w = w)
210s > print(x_est1)
210s [1] 0.91445859 0.04109702 0.68385712 2.26488705 0.28924246
210s > stopifnot(all.equal(x_est1, x_est0))
210s > x_est2 <- colWeightedVars(t(x), w = w)
210s > stopifnot(all.equal(x_est2, x_est0))
210s > # Check names attribute
210s > dimnames(x) <- dimnames
210s > x_est1 <- rowWeightedVars(x, w = w, useNames = FALSE)
210s > x_est2 <- colWeightedVars(t(x), w = w, useNames = FALSE)
210s > stopifnot(all.equal(x_est1, x_est0))
210s > stopifnot(all.equal(x_est2, x_est0))
210s > x3 <- cbind(x, x, x)
210s > x_est0 <- rowVars(x3, useNames = TRUE)
210s > x_est1 <- rowWeightedVars(x, w = w, useNames = TRUE)
210s > x_est2 <- colWeightedVars(t(x), w = w, useNames = TRUE)
210s > stopifnot(all.equal(x_est1, x_est0))
210s > stopifnot(all.equal(x_est2, x_est0))
210s > dimnames(x) <- NULL
210s > 
210s > 
210s > # Weighted row variances (excluding some columns)
210s > w <- c(1, 1, 0, 1)
210s > x_est0 <- rowVars(x[, (w == 1), drop = FALSE])
210s > x_est1 <- rowWeightedVars(x, w = w)
210s > print(x_est1)
210s [1] 0.16287693 0.06430861 0.94767651 0.28313135 0.21361984
210s > stopifnot(all.equal(x_est1, x_est0))
210s > x_est2 <- colWeightedVars(t(x), w = w)
210s > stopifnot(all.equal(x_est2, x_est0))
210s > # Check names attribute
210s > dimnames(x) <- dimnames
210s > x_est1 <- rowWeightedVars(x, w = w, useNames = FALSE)
210s > x_est2 <- colWeightedVars(t(x), w = w, useNames = FALSE)
210s > stopifnot(all.equal(x_est1, x_est0))
210s > stopifnot(all.equal(x_est2, x_est0))
210s > x_est0 <- rowVars(x[, (w == 1), drop = FALSE], useNames = TRUE)
210s > x_est1 <- rowWeightedVars(x, w = w, useNames = TRUE)
210s > x_est2 <- colWeightedVars(t(x), w = w, useNames = TRUE)
210s > stopifnot(all.equal(x_est1, x_est0))
210s > stopifnot(all.equal(x_est2, x_est0))
210s > dimnames(x) <- NULL
210s > 
210s > 
210s > # Weighted row variances (excluding some columns)
210s > w <- c(0, 1, 0, 0)
210s > x_est0 <- rowVars(x[, (w == 1), drop = FALSE])
210s > x_est1 <- rowWeightedVars(x, w = w)
210s > #stopifnot(all.equal(x_est1, x_est0))
210s > x_est2 <- colWeightedVars(t(x), w = w)
210s > stopifnot(all.equal(x_est2, x_est1))
210s > # Check names attribute
210s > dimnames(x) <- dimnames
210s > x_est1 <- rowWeightedVars(x, w = w, useNames = FALSE)
210s > x_est2 <- colWeightedVars(t(x), w = w, useNames = FALSE)
210s > stopifnot(all.equal(x_est1, x_est0))
210s > stopifnot(all.equal(x_est2, x_est0))
210s > x_est0 <- rowVars(x[, (w == 1), drop = FALSE], useNames = TRUE)
210s > x_est1 <- rowWeightedVars(x, w = w, useNames = TRUE)
210s > x_est2 <- colWeightedVars(t(x), w = w, useNames = TRUE)
210s > stopifnot(all.equal(x_est1, x_est0))
210s > stopifnot(all.equal(x_est2, x_est0))
210s > dimnames(x) <- NULL
210s > 
210s > 
210s > # Weighted row variances (all zero weights)
210s > w <- c(0, 0, 0, 0)
210s > x_est0 <- rowVars(x[, (w == 1), drop = FALSE])
210s > x_est1 <- rowWeightedVars(x, w = w)
210s > stopifnot(all.equal(x_est1, x_est0))
210s > x_est2 <- colWeightedVars(t(x), w = w)
210s > stopifnot(all.equal(x_est2, x_est0))
210s > # Check names attribute
210s > dimnames(x) <- dimnames
210s > x_est1 <- rowWeightedVars(x, w = w, useNames = FALSE)
210s > x_est2 <- colWeightedVars(t(x), w = w, useNames = FALSE)
210s > stopifnot(all.equal(x_est1, x_est0))
210s > stopifnot(all.equal(x_est2, x_est0))
210s > x_est0 <- rowVars(x[, (w == 1), drop = FALSE], useNames = TRUE)
210s > x_est1 <- rowWeightedVars(x, w = w, useNames = TRUE)
210s > x_est2 <- colWeightedVars(t(x), w = w, useNames = TRUE)
210s > stopifnot(all.equal(x_est1, x_est0))
210s > stopifnot(all.equal(x_est2, x_est0))
210s > dimnames(x) <- NULL
210s > 
210s > # Weighted variances by rows and columns
210s > w <- 1:4
210s > # Test with and without dimnames on x
210s > for (setDimnames in c(TRUE, FALSE)) {
210s +   if (setDimnames) dimnames(x) <- dimnames
210s +   else dimnames(x) <- NULL    
210s +   # Check names attribute
210s +   for (useNames in c(TRUE, FALSE)) {
210s +     x_est1 <- rowWeightedVars(x, w = w, useNames = useNames)
210s +     print(x_est1)
210s +     x_est2 <- colWeightedVars(t(x), w = w, useNames = useNames)
210s +     stopifnot(all.equal(x_est2, x_est1))
210s +   }
210s + }
210s          a          b          c          d          e 
210s 0.90747094 0.05040463 0.65089440 2.28697479 0.27902734 
210s [1] 0.90747094 0.05040463 0.65089440 2.28697479 0.27902734
210s [1] 0.90747094 0.05040463 0.65089440 2.28697479 0.27902734
210s [1] 0.90747094 0.05040463 0.65089440 2.28697479 0.27902734
210s > 
210s > 
210s > x[sample(length(x), size = 0.3 * length(x))] <- NA
210s > print(x)
210s            [,1]      [,2]       [,3]        [,4]
210s [1,] -0.6264538        NA  1.5117812 -0.04493361
210s [2,]  0.1836433        NA         NA -0.01619026
210s [3,] -0.8356286 0.7383247 -0.6212406  0.94383621
210s [4,]  1.5952808        NA -2.2146999  0.82122120
210s [5,]  0.3295078        NA         NA  0.59390132
210s > 
210s > # Non-weighted row variances with missing values
210s > x_est0 <- rowVars(x, na.rm = TRUE)
210s > x_est1 <- rowWeightedVars(x, w = rep(1, times = ncol(x)), na.rm = TRUE)
210s > print(x_est1)
210s [1] 1.22226258 0.01996673 0.83582537 4.05532299 0.03495197
210s > stopifnot(all.equal(x_est1, x_est0))
210s > x_est2 <- colWeightedVars(t(x), w = rep(1, times = ncol(x)), na.rm = TRUE)
210s > stopifnot(all.equal(x_est2, x_est0))
210s > # Check names attribute
210s > dimnames(x) <- dimnames
210s > x_est1 <- rowWeightedVars(x, w = rep(1, times = ncol(x)), na.rm = TRUE, useNames = FALSE)
210s > x_est2 <- colWeightedVars(t(x), w = rep(1, times = ncol(x)), na.rm = TRUE, useNames = FALSE)
210s > stopifnot(all.equal(x_est1, x_est0))
210s > stopifnot(all.equal(x_est2, x_est0))
210s > x_est0 <- rowVars(x, na.rm = TRUE, useNames = TRUE)
210s > x_est1 <- rowWeightedVars(x, w = rep(1, times = ncol(x)), na.rm = TRUE, useNames = TRUE)
210s > x_est2 <- colWeightedVars(t(x), w = rep(1, times = ncol(x)), na.rm = TRUE, useNames = TRUE)
210s > stopifnot(all.equal(x_est1, x_est0))
210s > stopifnot(all.equal(x_est2, x_est0))
210s > dimnames(x) <- NULL
210s > 
210s > 
210s > # Weighted row variances with missing values
210s > # Test with and without dimnames on x
210s > for (setDimnames in c(TRUE, FALSE)) {
210s +   if (setDimnames) dimnames(x) <- dimnames
210s +   else dimnames(x) <- NULL    
210s +   # Check names attribute
210s +   for (useNames in c(TRUE, FALSE)) {
210s +     x_est1 <- rowWeightedVars(x, w = w, na.rm = TRUE, useNames = useNames)
210s +     print(x_est1)
210s +     x_est2 <- colWeightedVars(t(x), w = w, na.rm = TRUE, useNames = useNames)
210s +     stopifnot(all.equal(x_est2, x_est1))
210s +   }
210s + }
210s           a           b           c           d           e 
210s 0.788377504 0.007986693 0.650894398 2.795470241 0.013980790 
210s [1] 0.788377504 0.007986693 0.650894398 2.795470241 0.013980790
210s [1] 0.788377504 0.007986693 0.650894398 2.795470241 0.013980790
210s [1] 0.788377504 0.007986693 0.650894398 2.795470241 0.013980790
210s > 
210s > 
210s > # Weighted variances by rows and columns
210s > w <- 1:4
210s > # Test with and without dimnames on x
210s > for (setDimnames in c(TRUE, FALSE)) {
210s +   if (setDimnames) dimnames(x) <- dimnames
210s +   else dimnames(x) <- NULL    
210s +   # Check names attribute
210s +   for (useNames in c(TRUE, FALSE)) {
210s +     x_est1 <- rowWeightedVars(x, w = w, na.rm = TRUE, useNames = useNames)
210s +     print(x_est1)
210s +     x_est2 <- colWeightedVars(t(x), w = w, na.rm = TRUE, useNames = useNames)
210s +     stopifnot(all.equal(x_est2, x_est1))
210s +   }
210s + }
210s           a           b           c           d           e 
210s 0.788377504 0.007986693 0.650894398 2.795470241 0.013980790 
210s [1] 0.788377504 0.007986693 0.650894398 2.795470241 0.013980790
210s [1] 0.788377504 0.007986693 0.650894398 2.795470241 0.013980790
210s [1] 0.788377504 0.007986693 0.650894398 2.795470241 0.013980790
210s > 
210s > 
210s > # Weighted row standard deviation (excluding some columns)
210s > w <- c(1, 1, 0, 1)
210s > ## FIXME: rowVars()/rowSds() needs na.rm = FALSE (wrong default)
210s > x_est0 <- rowSds(x[, (w == 1), drop = FALSE], na.rm = FALSE)
210s > x_est1 <- rowWeightedSds(x, w = w)
210s > print(x_est1)
210s [1]        NA        NA 0.9734868        NA        NA
210s > stopifnot(all.equal(x_est1, x_est0))
210s > x_est2 <- colWeightedSds(t(x), w = w, na.rm = FALSE)
210s > stopifnot(all.equal(x_est2, x_est0))
210s > # Check names attribute
210s > dimnames(x) <- dimnames
210s > x_est1 <- rowWeightedSds(x, w = w, na.rm = FALSE, useNames = FALSE)
210s > x_est2 <- colWeightedSds(t(x), w = w, na.rm = FALSE, useNames = FALSE)
210s > stopifnot(all.equal(x_est1, x_est0))
210s > stopifnot(all.equal(x_est2, x_est0))
210s > x_est0 <- rowSds(x[, (w == 1), drop = FALSE], na.rm = FALSE, useNames = TRUE)
210s > x_est1 <- rowWeightedSds(x, w = w, na.rm = FALSE, useNames = TRUE)
210s > x_est2 <- colWeightedSds(t(x), w = w, na.rm = FALSE, useNames = TRUE)
210s > stopifnot(all.equal(x_est1, x_est0))
210s > stopifnot(all.equal(x_est2, x_est0))
210s > dimnames(x) <- NULL
210s > 
210s > 
210s > # Weighted row MADs (excluding some columns)
210s > w <- c(1, 1, 0, 1)
210s > x_est0 <- rowMads(x[, (w == 1), drop = FALSE])
210s > x_est1 <- rowWeightedMads(x, w = w)
210s > print(x_est1)
210s [1]        NA        NA 0.3046914        NA        NA
210s > stopifnot(all.equal(x_est1, x_est0))
210s > x_est2 <- colWeightedMads(t(x), w = w)
210s > stopifnot(all.equal(x_est2, x_est0))
210s > # Check names attribute
210s > dimnames(x) <- dimnames
210s > x_est1 <- rowWeightedMads(x, w = w, useNames = FALSE)
210s > x_est2 <- colWeightedMads(t(x), w = w, useNames = FALSE)
210s > stopifnot(all.equal(x_est1, x_est0))
210s > stopifnot(all.equal(x_est2, x_est0))
210s > x_est0 <- rowMads(x[, (w == 1), drop = FALSE], useNames = TRUE)
210s > x_est1 <- rowWeightedMads(x, w = w, useNames = TRUE)
210s > x_est2 <- colWeightedMads(t(x), w = w, useNames = TRUE)
210s > stopifnot(all.equal(x_est1, x_est0))
210s > stopifnot(all.equal(x_est2, x_est0))
210s > dimnames(x) <- NULL
210s > 
210s 
210s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
210s Copyright (C) 2025 The R Foundation for Statistical Computing
210s Platform: x86_64-pc-linux-gnu
210s 
210s R is free software and comes with ABSOLUTELY NO WARRANTY.
210s You are welcome to redistribute it under certain conditions.
210s Type 'license()' or 'licence()' for distribution details.
210s 
210s R is a collaborative project with many contributors.
210s Type 'contributors()' for more information and
210s 'citation()' on how to cite R or R packages in publications.
210s 
210s Type 'demo()' for some demos, 'help()' for on-line help, or
210s 'help.start()' for an HTML browser interface to help.
210s Type 'q()' to quit R.
210s 
210s > library("matrixStats")
210s > 
210s > fcns <- list(
210s +   weightedVar = c(rowWeightedVars, colWeightedVars),
210s +   weightedSd = c(rowWeightedSds, colWeightedSds),
210s +   weightedMad = c(rowWeightedMads, colWeightedMads)
210s + )
210s > 
210s > 
210s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
210s > # Subsetted tests
210s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
210s > source("utils/validateIndicesFramework.R")
210s > # To check names attribute
210s > dimnames <- list(letters[1:6], LETTERS[1:6])
210s > for (fcn in names(fcns)) {
210s +   cat(sprintf("subsetted tests on matrix %s()...\n", fcn))
210s +   row_fcn <- fcns[[fcn]][[1]]
210s +   col_fcn <- fcns[[fcn]][[2]]
210s + 
210s +   for (mode in c("numeric", "integer")) {
210s +     x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
210s +     w <- runif(6, min = 0, max = 6)
210s +     storage.mode(x) <- mode
210s +     storage.mode(w) <- mode
210s +     if (mode == "numeric") w[1] <- Inf
210s + 
210s +     # Test with and without dimnames on x
210s +     for (setDimnames in c(TRUE, FALSE)) {
210s +       if (setDimnames) dimnames(x) <- dimnames
210s +       else dimnames(x) <- NULL
210s + 
210s +       count <- 0L
210s +       for (rows in index_cases) {
210s +         for (cols in index_cases) {
210s +           count <- count + 1L
210s +           na.rm <- c(TRUE, FALSE)[count %% 2 + 1]
210s +           useNames <- c(TRUE, FALSE)
210s +           useNames <- useNames[count %% length(useNames) + 1]
210s + 
210s +           validateIndicesTestMatrix_w(x, w, rows, cols,
210s +                                       ftest = row_fcn, fsure = row_fcn,
210s +                                       na.rm = na.rm, useNames = useNames)
210s +           validateIndicesTestMatrix_w(x, w, rows, cols,
210s +                                       fcoltest = col_fcn, fsure = row_fcn,
210s +                                       na.rm = na.rm, useNames = useNames)
210s +         }
210s +       }
210s +     }
210s +   }
210s +   cat(sprintf("%s()...DONE\n", fcn))
210s + }
210s subsetted tests on matrix weightedVar()...
211s weightedVar()...DONE
211s subsetted tests on matrix weightedSd()...
211s weightedSd()...DONE
211s subsetted tests on matrix weightedMad()...
211s weightedMad()...DONE
211s > 
211s 
211s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
211s Copyright (C) 2025 The R Foundation for Statistical Computing
211s Platform: x86_64-pc-linux-gnu
211s 
211s R is free software and comes with ABSOLUTELY NO WARRANTY.
211s You are welcome to redistribute it under certain conditions.
211s Type 'license()' or 'licence()' for distribution details.
211s 
211s R is a collaborative project with many contributors.
211s Type 'contributors()' for more information and
211s 'citation()' on how to cite R or R packages in publications.
211s 
211s Type 'demo()' for some demos, 'help()' for on-line help, or
211s 'help.start()' for an HTML browser interface to help.
211s Type 'q()' to quit R.
211s 
211s > library("matrixStats")
211s > 
211s > signTabulate0 <- function(x, ...) {
211s +   nneg <- sum(x < 0, na.rm = TRUE)
211s +   nzero <- sum(x == 0, na.rm = TRUE)
211s +   npos <- sum(x > 0, na.rm = TRUE)
211s +   nna <- sum(is.na(x))
211s +   nneginf <- sum(is.infinite(x) & x < 0, na.rm = TRUE)
211s +   nposinf <- sum(is.infinite(x) & x > 0, na.rm = TRUE)
211s +   res <- c(nneg, nzero, npos, nna, nneginf, nposinf)
211s +   res <- as.double(res)
211s +   names(res) <- c("-1", "0", "+1", "NA", "-Inf", "+Inf")
211s +   if (is.integer(x)) res <- res[1:4]
211s +   res
211s + } # signTabulate0()
211s > 
211s > 
211s > # Simulate data
211s > set.seed(0xBEEF)
211s > n <- 100L
211s > x <- runif(n)
211s > x[sample(n, size = 0.1 * n)] <- 0
211s > x[sample(n, size = 0.1 * n)] <- NA_real_
211s > x[sample(n, size = 0.1 * n)] <- -Inf
211s > x[sample(n, size = 0.1 * n)] <- +Inf
211s > 
211s > # Doubles
211s > message("Doubles:")
211s > counts0 <- signTabulate0(x)
211s Doubles:
211s Integers:
211s > print(counts0)
211s   -1    0   +1   NA -Inf +Inf 
211s    9    7   77    7    9   10 
211s > counts1 <- signTabulate(x)
211s > print(counts1)
211s   -1    0   +1   NA -Inf +Inf 
211s    9    7   77    7    9   10 
211s > stopifnot(identical(counts1, counts0))
211s > 
211s > # Integers
211s > message("Integers:")
211s > x <- suppressWarnings(as.integer(x))
211s > counts0 <- signTabulate0(x)
211s > print(counts0)
211s -1  0 +1 NA 
211s  0 74  0 26 
211s > counts1 <- signTabulate(x)
211s > print(counts1)
211s -1  0 +1 NA 
211s  0 74  0 26 
211s > stopifnot(identical(counts1, counts0))
211s > 
211s 
211s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
211s Copyright (C) 2025 The R Foundation for Statistical Computing
211s Platform: x86_64-pc-linux-gnu
211s 
211s R is free software and comes with ABSOLUTELY NO WARRANTY.
211s You are welcome to redistribute it under certain conditions.
211s Type 'license()' or 'licence()' for distribution details.
211s 
211s R is a collaborative project with many contributors.
211s Type 'contributors()' for more information and
211s 'citation()' on how to cite R or R packages in publications.
211s 
211s Type 'demo()' for some demos, 'help()' for on-line help, or
211s 'help.start()' for an HTML browser interface to help.
211s Type 'q()' to quit R.
211s 
212s > library("matrixStats")
212s > 
212s > signTabulate0 <- function(x, ...) {
212s +   nneg <- sum(x < 0, na.rm = TRUE)
212s +   nzero <- sum(x == 0, na.rm = TRUE)
212s +   npos <- sum(x > 0, na.rm = TRUE)
212s +   nna <- sum(is.na(x))
212s +   nneginf <- sum(is.infinite(x) & x < 0, na.rm = TRUE)
212s +   nposinf <- sum(is.infinite(x) & x > 0, na.rm = TRUE)
212s +   res <- c(nneg, nzero, npos, nna, nneginf, nposinf)
212s +   res <- as.double(res)
212s +   names(res) <- c("-1", "0", "+1", "NA", "-Inf", "+Inf")
212s +   if (is.integer(x)) res <- res[1:4]
212s +   res
212s + } # signTabulate0()
212s > 
212s > 
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > # Subsetted tests
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > source("utils/validateIndicesFramework.R")
212s > x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6, ncol = 6)
212s > x[2:3, 4:5] <- +Inf
212s > x[4:5, 1:2] <- -Inf
212s > for (idxs in index_cases) {
212s +   validateIndicesTestVector(x, idxs,
212s +                             ftest = signTabulate, fsure = signTabulate0)
212s + }
212s > 
212s 
212s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
212s Copyright (C) 2025 The R Foundation for Statistical Computing
212s Platform: x86_64-pc-linux-gnu
212s 
212s R is free software and comes with ABSOLUTELY NO WARRANTY.
212s You are welcome to redistribute it under certain conditions.
212s Type 'license()' or 'licence()' for distribution details.
212s 
212s R is a collaborative project with many contributors.
212s Type 'contributors()' for more information and
212s 'citation()' on how to cite R or R packages in publications.
212s 
212s Type 'demo()' for some demos, 'help()' for on-line help, or
212s 'help.start()' for an HTML browser interface to help.
212s Type 'q()' to quit R.
212s 
212s > library("matrixStats")
212s > options(warn = 1)
212s > 
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > # Consistency checks
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > set.seed(1)
212s > 
212s > sum2_R <- function(x, na.rm = FALSE, idxs = NULL) {
212s +   if (is.null(idxs)) {
212s +     sum(x, na.rm = na.rm)
212s +   } else {
212s +     sum(x[idxs], na.rm = na.rm)
212s +   }
212s + } # sum2_R()
212s > 
212s > 
212s > cat("Consistency checks:\n")
212s Consistency checks:
212s > for (kk in 1:20) {
212s +   cat("Random test #", kk, "\n", sep = "")
212s + 
212s +   # Simulate data in a matrix of any shape
212s +   n <- sample(1e3, size = 1L)
212s +   x <- rnorm(n, sd = 100)
212s + 
212s +   # Add NAs?
212s +   if ((kk %% 4) %in% c(3, 0)) {
212s +     cat("Adding NAs\n")
212s +     nna <- sample(n, size = 1L)
212s +     na_values <- c(NA_real_, NaN)
212s +     t <- sample(na_values, size = nna, replace = TRUE)
212s +     x[sample(length(x), size = nna)] <- t
212s +   }
212s + 
212s +   # Integer or double?
212s +   if ((kk %% 4) %in% c(2, 0)) {
212s +     cat("Coercing to integers\n")
212s +     storage.mode(x) <- "integer"
212s +   }
212s + 
212s +   na.rm <- sample(c(TRUE, FALSE), size = 1L)
212s + 
212s +   # Sum over all
212s +   y0 <- sum2_R(x, na.rm = na.rm)
212s +   y1 <- sum2(x, na.rm = na.rm)
212s +   stopifnot(all.equal(y1, y0))
212s + 
212s +   # Sum over subset
212s +   nidxs <- sample(n, size = 1L)
212s +   idxs <- sample(n, size = nidxs)
212s +   y0 <- sum2_R(x, na.rm = na.rm, idxs = idxs)
212s +   y1 <- sum2(x, na.rm = na.rm, idxs = idxs)
212s +   stopifnot(all.equal(y1, y0))
212s + 
212s +   if (storage.mode(x) == "integer") {
212s +     storage.mode(x) <- "logical"
212s +     
212s +     y0 <- sum2_R(x, na.rm = na.rm)
212s +     y1 <- sum2(x, na.rm = na.rm)
212s +     stopifnot(all.equal(y1, y0))
212s +     
212s +     y0 <- sum2_R(x, na.rm = na.rm, idxs = idxs)
212s +     y1 <- sum2(x, na.rm = na.rm, idxs = idxs)
212s +     stopifnot(all.equal(y1, y0))
212s +   }
212s + } # for (kk ...)
212s Random test #1
212s Random test #2
212s Coercing to integers
212s Random test #3
212s Adding NAs
212s Random test #4
212s Adding NAs
212s Coercing to integers
212s Random test #5
212s Random test #6
212s Coercing to integers
212s Random test #7
212s Adding NAs
212s Random test #8
212s Adding NAs
212s Coercing to integers
212s Random test #9
212s Random test #10
212s Coercing to integers
212s Random test #11
212s Adding NAs
212s Random test #12
212s Adding NAs
212s Coercing to integers
212s Random test #13
212s Random test #14
212s Coercing to integers
212s Random test #15
212s Adding NAs
212s Random test #16
212s Adding NAs
212s Coercing to integers
212s Random test #17
212s Random test #18
212s Coercing to integers
212s Random test #19
212s Adding NAs
212s Random test #20
212s Adding NAs
212s Coercing to integers
212s > 
212s > 
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > # All missing values
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > for (n in 0:2) {
212s +   for (na.rm in c(FALSE, TRUE)) {
212s +     x <- rep(NA_real_, times = n)
212s +     y0 <- sum(x, na.rm = na.rm)
212s +     y <- sum2(x, na.rm = na.rm)
212s +     stopifnot(all.equal(y, y0))
212s + 
212s +     x <- rep(NA_integer_, times = n)
212s +     y0 <- sum(x, na.rm = na.rm)
212s +     y <- sum2(x, na.rm = na.rm)
212s +     stopifnot(all.equal(y, y0))
212s +     
212s +     x <- rep(NA, times = n)
212s +     y0 <- sum(x, na.rm = na.rm)
212s +     y <- sum2(x, na.rm = na.rm)
212s +     stopifnot(all.equal(y, y0))
212s +   }
212s + }
212s > 
212s > 
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > # Special cases
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > for (na.rm in c(FALSE, TRUE)) {
212s +   # Summing over zero elements (integers)
212s +   x <- integer(0)
212s +   s1 <- sum(x, na.rm = na.rm)
212s +   s2 <- sum2(x, na.rm = na.rm)
212s +   stopifnot(identical(s1, s2))
212s + 
212s +   x <- 1:10
212s +   idxs <- integer(0)
212s +   s1 <- sum(x[idxs], na.rm = na.rm)
212s +   s2 <- sum2(x, idxs = idxs, na.rm = na.rm)
212s +   stopifnot(identical(s1, s2))
212s + 
212s +   # Summing over NA_integer_:s
212s +   x <- rep(NA_integer_, times = 10L)
212s +   s1 <- sum(x, na.rm = na.rm)
212s +   s2 <- sum2(x, na.rm = na.rm)
212s +   stopifnot(identical(s1, s2))
212s + 
212s +   x <- rep(NA_integer_, times = 10L)
212s +   idxs <- 1:5
212s +   s1 <- sum(x[idxs], na.rm = na.rm)
212s +   s2 <- sum2(x, idxs = idxs, na.rm = na.rm)
212s +   stopifnot(identical(s1, s2))
212s + 
212s + 
212s +   # Summing over zero elements (doubles)
212s +   x <- double(0)
212s +   s1 <- sum(x)
212s +   s2 <- sum2(x)
212s +   stopifnot(
212s +     identical(s1, 0),
212s +     identical(s1, s2)
212s +   )
212s + 
212s +   x <- as.double(1:10)
212s +   idxs <- integer(0)
212s +   s1 <- sum(x[idxs])
212s +   s2 <- sum2(x, idxs = idxs)
212s +   stopifnot(
212s +     identical(s1, 0),
212s +     identical(s1, s2)
212s +   )
212s + 
212s +   # Summing over NA_real_:s
212s +   x <- rep(NA_real_, times = 10L)
212s +   s1 <- sum(x, na.rm = na.rm)
212s +   s2 <- sum2(x, na.rm = na.rm)
212s +   stopifnot(
212s +     !na.rm || s1 == 0,
212s +     identical(s1, s2)
212s +   )
212s + 
212s +   x <- rep(NA_real_, times = 10L)
212s +   idxs <- 1:5
212s +   s1 <- sum(x[idxs], na.rm = na.rm)
212s +   s2 <- sum2(x, idxs = idxs, na.rm = na.rm)
212s +   stopifnot(
212s +     !na.rm || s1 == 0,
212s +     identical(s1, s2)
212s +   )
212s + 
212s +   # Summing over -Inf:s
212s +   x <- rep(-Inf, times = 3L)
212s +   s1 <- sum(x, na.rm = na.rm)
212s +   s2 <- sum2(x, na.rm = na.rm)
212s +   stopifnot(
212s +     is.infinite(s1) && s1 < 0,
212s +     identical(s1, s2)
212s +   )
212s + 
212s +   # Summing over +Inf:s
212s +   x <- rep(+Inf, times = 3L)
212s +   s1 <- sum(x, na.rm = na.rm)
212s +   s2 <- sum2(x, na.rm = na.rm)
212s +   stopifnot(identical(s1, s2))
212s +   stopifnot(
212s +     is.infinite(s1) && s1 > 0,
212s +     identical(s1, s2)
212s +   )
212s + 
212s +   # Summing over mix of -Inf:s and +Inf:s
212s +   x <- rep(c(-Inf, +Inf), times = 3L)
212s +   s1 <- sum(x, na.rm = na.rm)
212s +   s2 <- sum2(x, na.rm = na.rm)
212s +   stopifnot(
212s +     is.nan(s1),
212s +     identical(s1, s2)
212s +   )
212s + 
212s +   # Summing over mix of -Inf:s and +Inf:s and numerics
212s +   x <- rep(c(-Inf, +Inf, 3.14), times = 2L)
212s +   s1 <- sum(x, na.rm = na.rm)
212s +   s2 <- sum2(x, na.rm = na.rm)
212s +   stopifnot(
212s +     is.nan(s1),
212s +     identical(s1, s2)
212s +   )
212s + 
212s +   # Summing over mix of NaN, NA, +Inf, and numerics
212s +   x <- c(NaN, NA, +Inf, 3.14)
212s +   s1 <- sum(x, na.rm = na.rm)
212s +   s2 <- sum2(x, na.rm = na.rm)
212s +   if (na.rm) {
212s +     stopifnot(
212s +       is.infinite(s1) && s1 > 0,
212s +       identical(s2, s1)
212s +     )
212s +   } else {
212s +     stopifnot(is.na(s1), is.na(s2))
212s +     ## NOTE, due to compiler optimization, it is not guaranteed that NA is
212s +     ## returned here (as one would expect). NaN might very well be returned,
212s +     ## when both NA and NaN are involved.  This is an accepted feature in R,
212s +     ## which is documented in help("is.nan").  See also
212s +     ## https://stat.ethz.ch/pipermail/r-devel/2017-April/074009.html.
212s +     ## Thus, we cannot guarantee that s1 is identical to s0.
212s +   }
212s + 
212s +   # Summing over mix of NaN, NA, +Inf, and numerics
212s +   x <- c(NA, NaN, +Inf, 3.14)
212s +   s1 <- sum(x, na.rm = na.rm)
212s +   s2 <- sum2(x, na.rm = na.rm)
212s +   if (na.rm) {
212s +     stopifnot(
212s +       is.infinite(s1) && s1 > 0,
212s +       identical(s2, s1)
212s +     )
212s +   } else {
212s +     stopifnot(is.na(s1), is.na(s2))
212s +     ## NOTE, due to compiler optimization, it is not guaranteed that NA is
212s +     ## returned here (as one would expect). NaN might very well be returned,
212s +     ## when both NA and NaN are involved.  This is an accepted feature in R,
212s +     ## which is documented in help("is.nan").  See also
212s +     ## https://stat.ethz.ch/pipermail/r-devel/2017-April/074009.html.
212s +     ## Thus, we cannot guarantee that s1 is identical to s0.
212s +   }
212s + }
212s Warning in sum2(x[1:2]) :
212s   Integer overflow. Use sum2(..., mode = "double") to avoid this.
212s Warning in sum2(x, mode = "integer") :
212s   sum2(x, mode = "integer") called with typeof(x) == "double"; did you mean to use as.integer(sum2(x))?
212s > 
212s > 
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > # Summing of large integers
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > x <- c(.Machine$integer.max, 1L, -.Machine$integer.max)
212s > 
212s > # Total gives integer overflow
212s > s1 <- sum(x[1:2])                        # NA_integer_ w/ warning
212s > s2 <- sum2(x[1:2])                       # NA_integer_ w/ warning
212s > stopifnot(
212s +   identical(s2, NA_integer_)
212s + )
212s > 
212s > ## Assert above warning
212s > res <- tryCatch({
212s +   s2 <- sum2(x[1:2])
212s + }, warning = identity)
212s > stopifnot(inherits(res, "warning"))
212s > 
212s > 
212s > # Total gives integer overflow (coerce to numeric)
212s > s1 <- sum(as.numeric(x[1:2]))            # 2147483648
212s > s2 <- sum2(as.numeric(x[1:2]))           # 2147483648
212s > s3 <- sum2(x[1:2], mode = "double")      # 2147483648
212s > stopifnot(
212s +   identical(s1, 2147483648),
212s +   identical(s1, s2),
212s +   identical(s1, s3)
212s + )
212s > 
212s > # Cumulative sum would give integer overflow but not the total
212s > s1 <- sum(x)                              # 1L
212s > s2 <- sum2(x)                             # 1L
212s > stopifnot(
212s +   identical(s1, 1L),
212s +   identical(s1, s2)
212s + )
212s > 
212s > # Input is double but coercing result to integer
212s > x <- c(1, 2, 3.1)
212s > s1 <- sum2(x)
212s > s2 <- sum2(x, mode = "integer")
212s > stopifnot(
212s +   identical(as.integer(s1), s2)
212s + )
212s > 
212s > ## Assert above warning
212s > res <- tryCatch({
212s +   s2 <- sum2(x, mode = "integer")
212s + }, warning = identity)
212s > stopifnot(inherits(res, "warning"))
212s > 
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > # Summing of large doubles
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > ## Double overflow
212s > x <- rep(.Machine$double.xmax, times = 2L)
212s > y0 <- sum(x)
212s > print(y0)
212s [1] Inf
212s > y <- sum2(x)
212s > print(y)
212s [1] Inf
212s > stopifnot(
212s +   is.infinite(y) && y > 0,
212s +   identical(y, y0)
212s + )
212s > 
212s > x <- rep(-.Machine$double.xmax, times = 2L)
212s > y0 <- sum(x)
212s > print(y0)
212s [1] -Inf
212s > y <- sum2(x)
212s > print(y)
212s [1] -Inf
212s > stopifnot(
212s +   is.infinite(y) && y < 0,
212s +   identical(y, y0)
212s + )
212s > 
212s > 
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > # Argument 'idxs'
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > x <- 1:10
212s > idxs_list <- list(
212s +   integer = 1:5,
212s +   double = as.double(1:5),
212s +   logical = (x <= 5)
212s + )
212s > 
212s > for (idxs in idxs_list) {
212s +   cat("idxs:\n")
212s +   str(idxs)
212s +   s1 <- sum(x[idxs], na.rm = TRUE)
212s +   s2 <- sum2(x, idxs = idxs, na.rm = TRUE)
212s +   stopifnot(identical(s1, s2))
212s + }
212s idxs:
212s  int [1:5] 1 2 3 4 5
212s idxs:
212s  num [1:5] 1 2 3 4 5
212s idxs:
212s  logi [1:10] TRUE TRUE TRUE TRUE TRUE FALSE ...
212s > 
212s 
212s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
212s Copyright (C) 2025 The R Foundation for Statistical Computing
212s Platform: x86_64-pc-linux-gnu
212s 
212s R is free software and comes with ABSOLUTELY NO WARRANTY.
212s You are welcome to redistribute it under certain conditions.
212s Type 'license()' or 'licence()' for distribution details.
212s 
212s R is a collaborative project with many contributors.
212s Type 'contributors()' for more information and
212s 'citation()' on how to cite R or R packages in publications.
212s 
212s Type 'demo()' for some demos, 'help()' for on-line help, or
212s 'help.start()' for an HTML browser interface to help.
212s Type 'q()' to quit R.
212s 
212s > library("matrixStats")
212s > 
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > # Subsetted tests
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > source("utils/validateIndicesFramework.R")
212s > x <- runif(6, min = -6, max = 6)
212s > storage.mode(x) <- "integer"
212s > for (idxs in index_cases) {
212s +   validateIndicesTestVector(x, idxs,
212s +                             ftest = sum2, fsure = sum,
212s +                             na.rm = FALSE)
212s +   validateIndicesTestVector(x, idxs,
212s +                             ftest = sum2, fsure = sum,
212s +                             na.rm = TRUE)
212s + }
212s > 
212s 
212s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
212s Copyright (C) 2025 The R Foundation for Statistical Computing
212s Platform: x86_64-pc-linux-gnu
212s 
212s R is free software and comes with ABSOLUTELY NO WARRANTY.
212s You are welcome to redistribute it under certain conditions.
212s Type 'license()' or 'licence()' for distribution details.
212s 
212s R is a collaborative project with many contributors.
212s Type 'contributors()' for more information and
212s 'citation()' on how to cite R or R packages in publications.
212s 
212s Type 'demo()' for some demos, 'help()' for on-line help, or
212s 'help.start()' for an HTML browser interface to help.
212s Type 'q()' to quit R.
212s 
212s > library("matrixStats")
212s > 
212s > set.seed(1)
212s > x <- rnorm(1e4)
212s > 
212s > 
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > # Variance estimators
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > sigma2_a <- var(x)
212s > cat(sprintf("var(x) = %g\n", sigma2_a))
212s var(x) = 1.02487
212s > 
212s > sigma2_b <- varDiff(x)
212s > cat(sprintf("varDiff(x) = %g\n", sigma2_b))
212s varDiff(x) = 1.01224
212s > 
212s > d <- abs(sigma2_b - sigma2_a)
212s > cat(sprintf("Absolute difference = %g\n", d))
212s Absolute difference = 0.0126268
212s > stopifnot(d < 0.02)
212s > 
212s > 
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > # Standard deviation estimators
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > sigma_a <- sd(x)
212s > cat(sprintf("sd(x) = %g\n", sigma_a))
212s sd(x) = 1.01236
212s > 
212s > sigma_b <- sdDiff(x)
212s > cat(sprintf("sdDiff(x) = %g\n", sigma_b))
212s sdDiff(x) = 1.0061
212s > 
212s > d <- abs(sigma_b - sigma_a)
212s > cat(sprintf("Absolute difference = %g\n", d))
212s Absolute difference = 0.00625567
212s > stopifnot(d < 0.01)
212s > 
212s > # Sanity checks
212s > stopifnot(abs(sigma2_a - sigma_a ^ 2) < 1e-9)
212s > stopifnot(abs(sigma2_b - sigma_b ^ 2) < 1e-9)
212s > 
212s > 
212s > sigma_a2 <- mad(x)
212s > cat(sprintf("mad(x) = %g\n", sigma_a2))
212s mad(x) = 0.998376
212s > 
212s > sigma_b2 <- madDiff(x)
212s > cat(sprintf("madDiff(x) = %g\n", sigma_b2))
212s madDiff(x) = 1.02513
212s > 
212s > d <- abs(sigma_b2 - sigma_a2)
212s > cat(sprintf("Absolute difference = %g\n", d))
212s Absolute difference = 0.0267497
212s > stopifnot(d < 0.05)
212s > 
212s > 
212s > sigma_a3 <- IQR(x)
212s > cat(sprintf("IQR(x) = %g\n", sigma_a3))
212s IQR(x) = 1.35105
212s > 
212s > sigma_b3 <- iqrDiff(x)
212s > cat(sprintf("iqrDiff(x) = %g\n", sigma_b3))
212s iqrDiff(x) = 1.37797
212s > 
212s > d <- abs(sigma_b3 - sigma_a3)
212s > cat(sprintf("Absolute difference = %g\n", d))
212s Absolute difference = 0.0269152
212s > stopifnot(d < 0.05)
212s > 
212s > 
212s > 
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > # Trimmed estimators
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > y <- x
212s > outliers <- sample(length(x), size = 0.1 * length(x))
212s > y[outliers] <- 100 * y[outliers]
212s > 
212s > sigma_ao <- sd(y[-outliers])
212s > cat(sprintf("sd(y) = %g\n", sigma_ao))
212s sd(y) = 1.01166
212s > 
212s > sigma_bo <- sdDiff(y[-outliers])
212s > cat(sprintf("sdDiff(y) = %g\n", sigma_bo))
212s sdDiff(y) = 1.00743
212s > 
212s > d <- abs(sigma_b - sigma_a)
212s > cat(sprintf("Absolute difference = %g\n", d))
212s Absolute difference = 0.00625567
212s > stopifnot(d < 0.01)
212s > 
212s > sigma_bot <- sdDiff(y, trim = 0.05)
212s > cat(sprintf("sdDiff(y, trim = 0.05) = %g\n", sigma_bot))
212s sdDiff(y, trim = 0.05) = 7.74327
212s > 
212s > d <- abs(sigma_bot - sigma_a)
212s > cat(sprintf("Absolute difference = %g\n", d))
212s Absolute difference = 6.73091
212s > #stopifnot(d < 1e-3)
212s > 
212s > sigma_cot <- madDiff(y, trim = 0.05)
212s > cat(sprintf("madDiff(y, trim = 0.05) = %g\n", sigma_cot))
212s madDiff(y, trim = 0.05) = 1.15278
212s > 
212s > sigma_dot <- iqrDiff(y, trim = 0.05)
212s > cat(sprintf("iqrDiff(y, trim = 0.05) = %g\n", sigma_dot))
212s iqrDiff(y, trim = 0.05) = 1.55762
212s > 
212s > 
212s > fcns <- list(
212s +   varDiff = varDiff,
212s +   sdDiff  = sdDiff,
212s +   madDiff = madDiff,
212s +   iqrDiff = iqrDiff
212s + )
212s > 
212s > for (name in names(fcns)) {
212s +   cat(sprintf("%s()...\n", name))
212s +   fcn <- fcns[[name]]
212s + 
212s +   for (mode in c("integer", "double")) {
212s +     cat("mode: ", mode, "", sep = "")
212s +     for (n in 0:3) {
212s +       x <- runif(n, min = -5, max = 5)
212s +       storage.mode(x) <- mode
212s +       str(x)
212s + 
212s +       y <- fcn(x)
212s +       yt <- fcn(x, trim = 0.1)
212s +       str(list("non-trimmed" = y, trimmed = yt))
212s +     } # for (mode ...)
212s +   }
212s + 
212s +   cat(sprintf("%s()...DONE\n", name))
212s + } # for (name ...)
212s varDiff()...
212s mode: integer int(0) 
212s List of 2
212s  $ non-trimmed: num NA
212s  $ trimmed    : num NA
212s  int -4
212s List of 2
212s  $ non-trimmed: num NA
212s  $ trimmed    : num NA
212s  int [1:2] 3 2
212s List of 2
212s  $ non-trimmed: num NA
212s  $ trimmed    : num NA
212s  int [1:3] 1 4 -1
212s List of 2
212s  $ non-trimmed: num 16
212s  $ trimmed    : num 16
212s mode: double num(0) 
212s List of 2
212s  $ non-trimmed: num NA
212s  $ trimmed    : num NA
212s  num -0.794
212s List of 2
212s  $ non-trimmed: num NA
212s  $ trimmed    : num NA
212s  num [1:2] 0.897 -3.728
212s List of 2
212s  $ non-trimmed: num NA
212s  $ trimmed    : num NA
212s  num [1:3] 2.07 -1.13 1.94
212s List of 2
212s  $ non-trimmed: num 9.83
212s  $ trimmed    : num 9.83
212s varDiff()...DONE
212s sdDiff()...
212s mode: integer int(0) 
212s List of 2
212s  $ non-trimmed: num NA
212s  $ trimmed    : num NA
212s  int 2
212s List of 2
212s  $ non-trimmed: num NA
212s  $ trimmed    : num NA
212s  int [1:2] -4 1
212s List of 2
212s  $ non-trimmed: num NA
212s  $ trimmed    : num NA
212s  int [1:3] -2 1 -1
212s List of 2
212s  $ non-trimmed: num 2.5
212s  $ trimmed    : num 2.5
212s mode: double num(0) 
212s List of 2
212s  $ non-trimmed: num NA
212s  $ trimmed    : num NA
212s  num -3.78
212s List of 2
212s  $ non-trimmed: num NA
212s  $ trimmed    : num NA
212s  num [1:2] -2.04 2.38
212s List of 2
212s  $ non-trimmed: num NA
212s  $ trimmed    : num NA
212s  num [1:3] 1.42 -2.14 1.14
212s List of 2
212s  $ non-trimmed: num 3.42
212s  $ trimmed    : num 3.42
212s sdDiff()...DONE
212s madDiff()...
212s mode: integer int(0) 
212s List of 2
212s  $ non-trimmed: num NA
212s  $ trimmed    : num NA
212s  int -1
212s List of 2
212s  $ non-trimmed: num NA
212s  $ trimmed    : num NA
212s  int [1:2] -1 4
212s List of 2
212s  $ non-trimmed: num NA
212s  $ trimmed    : num NA
212s  int [1:3] -1 0 -3
212s List of 2
212s  $ non-trimmed: num 2.1
212s  $ trimmed    : num 2.1
212s mode: double num(0) 
212s List of 2
212s  $ non-trimmed: num NA
212s  $ trimmed    : num NA
212s  num -1.13
212s List of 2
212s  $ non-trimmed: num NA
212s  $ trimmed    : num NA
212s  num [1:2] -1.7 -1.21
212s List of 2
212s  $ non-trimmed: num NA
212s  $ trimmed    : num NA
212s  num [1:3] -2.39 -0.464 3.086
212s List of 2
212s  $ non-trimmed: num 0.851
212s  $ trimmed    : num 0.851
212s madDiff()...DONE
212s iqrDiff()...
212s mode: integer int(0) 
212s List of 2
212s  $ non-trimmed: num NA
212s  $ trimmed    : num NA
212s  int 3
212s List of 2
212s  $ non-trimmed: num 0
212s  $ trimmed    : num 0
212s  int [1:2] -3 4
212s List of 2
212s  $ non-trimmed: num 0
212s  $ trimmed    : num 0
212s  int [1:3] 0 -2 -2
212s List of 2
212s  $ non-trimmed: num 0.707
212s  $ trimmed    : num 0.707
212s mode: double num(0) 
212s List of 2
212s  $ non-trimmed: num NA
212s  $ trimmed    : num NA
212s  num -4.46
212s List of 2
212s  $ non-trimmed: num 0
212s  $ trimmed    : num 0
212s  num [1:2] 3.67 1.02
212s List of 2
212s  $ non-trimmed: num 0
212s  $ trimmed    : num 0
212s  num [1:3] -0.537 -2.733 2.857
212s List of 2
212s  $ non-trimmed: num 2.75
212s  $ trimmed    : num 2.75
212s iqrDiff()...DONE
212s > 
212s 
212s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
212s Copyright (C) 2025 The R Foundation for Statistical Computing
212s Platform: x86_64-pc-linux-gnu
212s 
212s R is free software and comes with ABSOLUTELY NO WARRANTY.
212s You are welcome to redistribute it under certain conditions.
212s Type 'license()' or 'licence()' for distribution details.
212s 
212s R is a collaborative project with many contributors.
212s Type 'contributors()' for more information and
212s 'citation()' on how to cite R or R packages in publications.
212s 
212s Type 'demo()' for some demos, 'help()' for on-line help, or
212s 'help.start()' for an HTML browser interface to help.
212s Type 'q()' to quit R.
212s 
212s > library("matrixStats")
212s > 
212s > fcns <- list(
212s +   varDiff = varDiff,
212s +   sdDiff  = sdDiff,
212s +   madDiff = madDiff,
212s +   iqrDiff = iqrDiff
212s + )
212s > 
212s > 
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > # Subsetted tests
212s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
212s > source("utils/validateIndicesFramework.R")
212s > for (name in names(fcns)) {
212s +   cat(sprintf("subsetted tests on %s()...\n", name))
212s +   fcn <- fcns[[name]]
212s + 
212s +   for (mode in c("numeric", "integer")) {
212s +     x <- runif(6, min = -6, max = 6)
212s +     storage.mode(x) <- mode
212s +     trim <- runif(1, min = 0, max = 0.5)
212s +     if (mode == "numeric") x[1] <- Inf
212s + 
212s +     for (diff in 1:2) {
212s +       for (idxs in index_cases) {
212s +         validateIndicesTestVector(x, idxs,
212s +                                   ftest = fcn, fsure = fcn,
212s +                                   na.rm = TRUE, diff = diff, trim = trim)
212s +         validateIndicesTestVector(x, idxs,
212s +                                   ftest = fcn, fsure = fcn,
212s +                                   na.rm = FALSE, diff = diff, trim = trim)
212s +       }
212s +     }
212s +   }
212s +   cat(sprintf("%s()...DONE\n", name))
212s + }
212s subsetted tests on varDiff()...
212s varDiff()...DONE
212s subsetted tests on sdDiff()...
212s sdDiff()...DONE
212s subsetted tests on madDiff()...
212s madDiff()...DONE
212s subsetted tests on iqrDiff()...
212s iqrDiff()...DONE
212s > 
212s 
212s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
212s Copyright (C) 2025 The R Foundation for Statistical Computing
212s Platform: x86_64-pc-linux-gnu
212s 
212s R is free software and comes with ABSOLUTELY NO WARRANTY.
212s You are welcome to redistribute it under certain conditions.
212s Type 'license()' or 'licence()' for distribution details.
212s 
212s R is a collaborative project with many contributors.
212s Type 'contributors()' for more information and
212s 'citation()' on how to cite R or R packages in publications.
212s 
212s Type 'demo()' for some demos, 'help()' for on-line help, or
212s 'help.start()' for an HTML browser interface to help.
212s Type 'q()' to quit R.
212s 
212s > library("matrixStats")
212s > 
212s > for (mode in c("logical", "integer", "double")) {
212s +   cat("mode: ", mode, "", sep = "")
212s +   n <- 2L
212s +   x <- runif(n, min = -5, max = 5)
212s +   if (mode == "logical") {
212s +     x <- x > 0
212s +   }
212s +   storage.mode(x) <- mode
212s +   str(x)
212s + 
212s +   cat("All weights are 1\n")
212s +   w <- rep(1, times = n)
212s +   m0 <- weighted.mean(x, w)
212s +   m1 <- weightedMean(x, w)
212s +   str(list(m0 = m0, m1 = m1))
212s +   stopifnot(identical(m1, m0))
212s + 
212s +   cat("First weight is 5\n")
212s +   # Pull the mean towards zero
212s +   w[1] <- 5
212s +   str(w)
212s +   m0 <- weighted.mean(x, w)
212s +   m1 <- weightedMean(x, w)
212s +   str(list(m0 = m0, m1 = m1))
212s +   stopifnot(identical(m1, m0))
212s + 
212s +   cat("All weights are 0\n")
212s +   # All weights set to zero
212s +   w <- rep(0, times = n)
212s +   m0 <- weighted.mean(x, w)
212s +   m1 <- weightedMean(x, w)
212s +   str(list(m0 = m0, m1 = m1))
212s +   stopifnot(identical(m1, m0))
212s + 
212s +   cat("First weight is 8.5\n")
212s +   # Put even more weight on the zero
212s +   w[1] <- 8.5
212s +   m0 <- weighted.mean(x, w)
212s +   m1 <- weightedMean(x, w)
212s +   str(list(m0 = m0, m1 = m1))
212s +   stopifnot(identical(m1, m0))
212s + 
212s +   cat("First weight is Inf\n")
212s +   # All weight on the first value
212s +   w[1] <- Inf
212s +   m0 <- weighted.mean(x, w)
212s +   m1 <- weightedMean(x, w)
212s +   str(list(m0 = m0, m1 = m1))
212s +   stopifnot(identical(m1, m0))
212s + 
212s +   cat("Last weight is Inf\n")
212s +   # All weight on the last value
212s +   w[1] <- 1
212s +   w[n] <- Inf
212s +   m0 <- weighted.mean(x, w)
212s +   m1 <- weightedMean(x, w)
212s +   str(list(m0 = m0, m1 = m1))
212s +   stopifnot(identical(m1, m0))
212s + } # for (mode ...)
212s mode: logical logi [1:2] FALSE TRUE
212s All weights are 1
212s List of 2
212s  $ m0: num 0.5
212s  $ m1: num 0.5
212s First weight is 5
212s  num [1:2] 5 1
212s List of 2
212s  $ m0: num 0.167
212s  $ m1: num 0.167
212s All weights are 0
212s List of 2
212s  $ m0: num NaN
212s  $ m1: num NaN
212s First weight is 8.5
212s List of 2
212s  $ m0: num 0
212s  $ m1: num 0
212s First weight is Inf
212s List of 2
212s  $ m0: num NaN
212s  $ m1: num NaN
212s Last weight is Inf
212s List of 2
212s  $ m0: num NaN
212s  $ m1: num NaN
212s mode: integer int [1:2] 1 3
212s All weights are 1
212s List of 2
212s  $ m0: num 2
212s  $ m1: num 2
212s First weight is 5
212s  num [1:2] 5 1
212s List of 2
212s  $ m0: num 1.33
212s  $ m1: num 1.33
212s All weights are 0
212s List of 2
212s  $ m0: num NaN
212s  $ m1: num NaN
212s First weight is 8.5
212s List of 2
212s  $ m0: num 1
212s  $ m1: num 1
212s First weight is Inf
212s List of 2
212s  $ m0: num NaN
212s  $ m1: num NaN
212s Last weight is Inf
212s List of 2
212s  $ m0: num NaN
212s  $ m1: num NaN
212s mode: double num [1:2] 3.68 3.42
212s All weights are 1
212s List of 2
212s  $ m0: num 3.55
212s  $ m1: num 3.55
212s First weight is 5
212s  num [1:2] 5 1
212s List of 2
212s  $ m0: num 3.63
212s  $ m1: num 3.63
212s All weights are 0
212s List of 2
212s  $ m0: num NaN
212s  $ m1: num NaN
212s First weight is 8.5
212s List of 2
212s  $ m0: num 3.68
212s  $ m1: num 3.68
212s First weight is Inf
212s List of 2
212s  $ m0: num NaN
212s  $ m1: num NaN
212s Last weight is Inf
212s List of 2
212s  $ m0: num NaN
212s  $ m1: num NaN
212s > 
212s > 
212s > message("*** Testing for missing values")
212s > # NA tests
212s > xs <- list(A = c(1, 2, 3), B = c(NA, 2, 3), C = c(NA, 2, 3))
212s > ws <- list(A = c(1, 1, 1), B = c(NA, 1, 1), C = c(1, NA, 1))
212s > ## NOTE: The (B, B) case with na.rm = TRUE is interesting because
212s > ## even if NAs in 'w' are not dropped by na.rm = TRUE, this one
212s > ## is because 'x' is dropped and therefore that first element
212s > ## is skipped in the computation.  It basically does
212s > ##   keep <- !is.na(x); x <- x[keep]; w <- w[keep]
212s > ## without looking at 'w'.
212s > for (x in xs) {
212s +   for (mode in c("logical", "integer", "double")) {
212s +     storage.mode(x) <- mode
212s +     for (w in ws) {
212s +       for (na.rm in c(FALSE, TRUE)) {
212s +         cat(sprintf("mode: %s, na.rm = %s\n", mode, na.rm))
212s +         str(list(x = x, w = w))
212s +         m0 <- weighted.mean(x, w, na.rm = na.rm)
212s +         m1 <- weightedMean(x, w, na.rm = na.rm)
212s +         str(list(m0 = m0, m1 = m1))
212s +         stopifnot(all.equal(m1, m0))
212s +       }
212s +     }
212s +   }
212s + }
212s *** Testing for missing values
212s mode: logical, na.rm = FALSE
212s List of 2
212s  $ x: logi [1:3] TRUE TRUE TRUE
212s  $ w: num [1:3] 1 1 1
212s List of 2
212s  $ m0: num 1
212s  $ m1: num 1
212s mode: logical, na.rm = TRUE
212s List of 2
212s  $ x: logi [1:3] TRUE TRUE TRUE
212s  $ w: num [1:3] 1 1 1
212s List of 2
212s  $ m0: num 1
212s  $ m1: num 1
212s mode: logical, na.rm = FALSE
212s List of 2
212s  $ x: logi [1:3] TRUE TRUE TRUE
212s  $ w: num [1:3] NA 1 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: logical, na.rm = TRUE
212s List of 2
212s  $ x: logi [1:3] TRUE TRUE TRUE
212s  $ w: num [1:3] NA 1 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: logical, na.rm = FALSE
212s List of 2
212s  $ x: logi [1:3] TRUE TRUE TRUE
212s  $ w: num [1:3] 1 NA 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: logical, na.rm = TRUE
212s List of 2
212s  $ x: logi [1:3] TRUE TRUE TRUE
212s  $ w: num [1:3] 1 NA 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: integer, na.rm = FALSE
212s List of 2
212s  $ x: int [1:3] 1 1 1
212s  $ w: num [1:3] 1 1 1
212s List of 2
212s  $ m0: num 1
212s  $ m1: num 1
212s mode: integer, na.rm = TRUE
212s List of 2
212s  $ x: int [1:3] 1 1 1
212s  $ w: num [1:3] 1 1 1
212s List of 2
212s  $ m0: num 1
212s  $ m1: num 1
212s mode: integer, na.rm = FALSE
212s List of 2
212s  $ x: int [1:3] 1 1 1
212s  $ w: num [1:3] NA 1 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: integer, na.rm = TRUE
212s List of 2
212s  $ x: int [1:3] 1 1 1
212s  $ w: num [1:3] NA 1 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: integer, na.rm = FALSE
212s List of 2
212s  $ x: int [1:3] 1 1 1
212s  $ w: num [1:3] 1 NA 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: integer, na.rm = TRUE
212s List of 2
212s  $ x: int [1:3] 1 1 1
212s  $ w: num [1:3] 1 NA 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: double, na.rm = FALSE
212s List of 2
212s  $ x: num [1:3] 1 1 1
212s  $ w: num [1:3] 1 1 1
212s List of 2
212s  $ m0: num 1
212s  $ m1: num 1
212s mode: double, na.rm = TRUE
212s List of 2
212s  $ x: num [1:3] 1 1 1
212s  $ w: num [1:3] 1 1 1
212s List of 2
212s  $ m0: num 1
212s  $ m1: num 1
212s mode: double, na.rm = FALSE
212s List of 2
212s  $ x: num [1:3] 1 1 1
212s  $ w: num [1:3] NA 1 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: double, na.rm = TRUE
212s List of 2
212s  $ x: num [1:3] 1 1 1
212s  $ w: num [1:3] NA 1 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: double, na.rm = FALSE
212s List of 2
212s  $ x: num [1:3] 1 1 1
212s  $ w: num [1:3] 1 NA 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: double, na.rm = TRUE
212s List of 2
212s  $ x: num [1:3] 1 1 1
212s  $ w: num [1:3] 1 NA 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: logical, na.rm = FALSE
212s List of 2
212s  $ x: logi [1:3] NA TRUE TRUE
212s  $ w: num [1:3] 1 1 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: logical, na.rm = TRUE
212s List of 2
212s  $ x: logi [1:3] NA TRUE TRUE
212s  $ w: num [1:3] 1 1 1
212s List of 2
212s  $ m0: num 1
212s  $ m1: num 1
212s mode: logical, na.rm = FALSE
212s List of 2
212s  $ x: logi [1:3] NA TRUE TRUE
212s  $ w: num [1:3] NA 1 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: logical, na.rm = TRUE
212s List of 2
212s  $ x: logi [1:3] NA TRUE TRUE
212s  $ w: num [1:3] NA 1 1
212s List of 2
212s  $ m0: num 1
212s  $ m1: num 1
212s mode: logical, na.rm = FALSE
212s List of 2
212s  $ x: logi [1:3] NA TRUE TRUE
212s  $ w: num [1:3] 1 NA 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: logical, na.rm = TRUE
212s List of 2
212s  $ x: logi [1:3] NA TRUE TRUE
212s  $ w: num [1:3] 1 NA 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: integer, na.rm = FALSE
212s List of 2
212s  $ x: int [1:3] NA 1 1
212s  $ w: num [1:3] 1 1 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: integer, na.rm = TRUE
212s List of 2
212s  $ x: int [1:3] NA 1 1
212s  $ w: num [1:3] 1 1 1
212s List of 2
212s  $ m0: num 1
212s  $ m1: num 1
212s mode: integer, na.rm = FALSE
212s List of 2
212s  $ x: int [1:3] NA 1 1
212s  $ w: num [1:3] NA 1 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: integer, na.rm = TRUE
212s List of 2
212s  $ x: int [1:3] NA 1 1
212s  $ w: num [1:3] NA 1 1
212s List of 2
212s  $ m0: num 1
212s  $ m1: num 1
212s mode: integer, na.rm = FALSE
212s List of 2
212s  $ x: int [1:3] NA 1 1
212s  $ w: num [1:3] 1 NA 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: integer, na.rm = TRUE
212s List of 2
212s  $ x: int [1:3] NA 1 1
212s  $ w: num [1:3] 1 NA 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: double, na.rm = FALSE
212s List of 2
212s  $ x: num [1:3] NA 1 1
212s  $ w: num [1:3] 1 1 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: double, na.rm = TRUE
212s List of 2
212s  $ x: num [1:3] NA 1 1
212s  $ w: num [1:3] 1 1 1
212s List of 2
212s  $ m0: num 1
212s  $ m1: num 1
212s mode: double, na.rm = FALSE
212s List of 2
212s  $ x: num [1:3] NA 1 1
212s  $ w: num [1:3] NA 1 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: double, na.rm = TRUE
212s List of 2
212s  $ x: num [1:3] NA 1 1
212s  $ w: num [1:3] NA 1 1
212s List of 2
212s  $ m0: num 1
212s  $ m1: num 1
212s mode: double, na.rm = FALSE
212s List of 2
212s  $ x: num [1:3] NA 1 1
212s  $ w: num [1:3] 1 NA 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: double, na.rm = TRUE
212s List of 2
212s  $ x: num [1:3] NA 1 1
212s  $ w: num [1:3] 1 NA 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: logical, na.rm = FALSE
212s List of 2
212s  $ x: logi [1:3] NA TRUE TRUE
212s  $ w: num [1:3] 1 1 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: logical, na.rm = TRUE
212s List of 2
212s  $ x: logi [1:3] NA TRUE TRUE
212s  $ w: num [1:3] 1 1 1
212s List of 2
212s  $ m0: num 1
212s  $ m1: num 1
212s mode: logical, na.rm = FALSE
212s List of 2
212s  $ x: logi [1:3] NA TRUE TRUE
212s  $ w: num [1:3] NA 1 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: logical, na.rm = TRUE
212s List of 2
212s  $ x: logi [1:3] NA TRUE TRUE
212s  $ w: num [1:3] NA 1 1
212s List of 2
212s  $ m0: num 1
212s  $ m1: num 1
212s mode: logical, na.rm = FALSE
212s List of 2
212s  $ x: logi [1:3] NA TRUE TRUE
212s  $ w: num [1:3] 1 NA 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: logical, na.rm = TRUE
212s List of 2
212s  $ x: logi [1:3] NA TRUE TRUE
212s  $ w: num [1:3] 1 NA 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: integer, na.rm = FALSE
212s List of 2
212s  $ x: int [1:3] NA 1 1
212s  $ w: num [1:3] 1 1 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: integer, na.rm = TRUE
212s List of 2
212s  $ x: int [1:3] NA 1 1
212s  $ w: num [1:3] 1 1 1
212s List of 2
212s  $ m0: num 1
212s  $ m1: num 1
212s mode: integer, na.rm = FALSE
212s List of 2
212s  $ x: int [1:3] NA 1 1
212s  $ w: num [1:3] NA 1 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: integer, na.rm = TRUE
212s List of 2
212s  $ x: int [1:3] NA 1 1
212s  $ w: num [1:3] NA 1 1
212s List of 2
212s  $ m0: num 1
212s  $ m1: num 1
212s mode: integer, na.rm = FALSE
212s List of 2
212s  $ x: int [1:3] NA 1 1
212s  $ w: num [1:3] 1 NA 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: integer, na.rm = TRUE
212s List of 2
212s  $ x: int [1:3] NA 1 1
212s  $ w: num [1:3] 1 NA 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: double, na.rm = FALSE
212s List of 2
212s  $ x: num [1:3] NA 1 1
212s  $ w: num [1:3] 1 1 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: double, na.rm = TRUE
212s List of 2
212s  $ x: num [1:3] NA 1 1
212s  $ w: num [1:3] 1 1 1
212s List of 2
212s  $ m0: num 1
212s  $ m1: num 1
212s mode: double, na.rm = FALSE
212s List of 2
212s  $ x: num [1:3] NA 1 1
212s  $ w: num [1:3] NA 1 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: double, na.rm = TRUE
212s List of 2
212s  $ x: num [1:3] NA 1 1
212s  $ w: num [1:3] NA 1 1
212s List of 2
212s  $ m0: num 1
212s  $ m1: num 1
212s mode: double, na.rm = FALSE
212s List of 2
212s  $ x: num [1:3] NA 1 1
212s  $ w: num [1:3] 1 NA 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s mode: double, na.rm = TRUE
212s List of 2
212s  $ x: num [1:3] NA 1 1
212s  $ w: num [1:3] 1 NA 1
212s List of 2
212s  $ m0: num NA
212s  $ m1: num NA
212s > 
212s 
212s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
212s Copyright (C) 2025 The R Foundation for Statistical Computing
212s Platform: x86_64-pc-linux-gnu
212s 
212s R is free software and comes with ABSOLUTELY NO WARRANTY.
212s You are welcome to redistribute it under certain conditions.
212s Type 'license()' or 'licence()' for distribution details.
212s 
212s R is a collaborative project with many contributors.
212s Type 'contributors()' for more information and
212s 'citation()' on how to cite R or R packages in publications.
212s 
212s Type 'demo()' for some demos, 'help()' for on-line help, or
212s 'help.start()' for an HTML browser interface to help.
212s Type 'q()' to quit R.
212s 
213s > library("matrixStats")
213s > 
213s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
213s > # Subsetted tests
213s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
213s > source("utils/validateIndicesFramework.R")
213s > for (mode in c("numeric", "integer")) {
213s +   x <- runif(6, min = -6, max = 6)
213s +   w <- runif(6, min = 0, max = 6)
213s +   storage.mode(x) <- mode
213s +   storage.mode(w) <- mode
213s +   if (mode == "numeric") w[1] <- Inf
213s + 
213s +   for (idxs in index_cases) {
213s +     validateIndicesTestVector_w(x, w, idxs,
213s +                                 ftest = weightedMean, fsure = weighted.mean,
213s +                                 na.rm = TRUE, refine = TRUE)
213s +     validateIndicesTestVector_w(x, w, idxs,
213s +                                 ftest = weightedMean, fsure = weighted.mean,
213s +                                 na.rm = FALSE, refine = TRUE)
213s +   }
213s + }
213s > 
213s 
213s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
213s Copyright (C) 2025 The R Foundation for Statistical Computing
213s Platform: x86_64-pc-linux-gnu
213s 
213s R is free software and comes with ABSOLUTELY NO WARRANTY.
213s You are welcome to redistribute it under certain conditions.
213s Type 'license()' or 'licence()' for distribution details.
213s 
213s R is a collaborative project with many contributors.
213s Type 'contributors()' for more information and
213s 'citation()' on how to cite R or R packages in publications.
213s 
213s Type 'demo()' for some demos, 'help()' for on-line help, or
213s 'help.start()' for an HTML browser interface to help.
213s Type 'q()' to quit R.
213s 
213s > library("matrixStats")
213s > 
213s > x <- 1:5
213s > y <- weightedMedian(x)
213s > y <- weightedMedian(x, w = c(NA, Inf, NA, Inf, NA), na.rm = TRUE)
213s > print(y)
213s [1] 3
213s > 
213s > y <- weightedMedian(x, w = c(NA, Inf, NA, Inf, NA), na.rm = FALSE)
213s > print(y)
213s [1] NA
213s > stopifnot(is.na(y))
213s > 
213s > x <- 1:10
213s > n <- length(x)
213s > 
213s > y1 <- median(x)                           # 5.5
213s > y2 <- weightedMedian(x)                   # 5.5
213s > stopifnot(all.equal(y1, y2))
213s > 
213s > 
213s > w <- rep(1, times = n)
213s > y1 <- weightedMedian(x, w)                 # 5.5 (default)
213s > y2a <- weightedMedian(x, ties = "weighted")  # 5.5 (default)
213s > y2b <- weightedMedian(x, ties = "min")       # 5
213s > y2c <- weightedMedian(x, ties = "max")       # 6
213s > stopifnot(all.equal(y2a, y1))
213s > 
213s > y3 <- weightedMedian(x, w)                # 5.5 (default)
213s > 
213s > 
213s > # Pull the median towards zero
213s > w[1] <- 5
213s > y1 <- weightedMedian(x, w)                # 3.5
213s > y <- c(rep(0, times = w[1]), x[-1])       # Only possible for integer weights
213s > y2 <- median(y)                           # 3.5
213s > stopifnot(all.equal(y1, y2))
213s > 
213s > # Put even more weight on the zero
213s > w[1] <- 8.5
213s > y <- weightedMedian(x, w)                # 2
213s > 
213s > # All weight on the first value
213s > w[1] <- Inf
213s > y <- weightedMedian(x, w)                # 1
213s > 
213s > # All weight on the last value
213s > w[1] <- 1
213s > w[n] <- Inf
213s > y <- weightedMedian(x, w)                # 10
213s > 
213s > # All weights set to zero
213s > w <- rep(0, times = n)
213s > y <- weightedMedian(x, w)                # NA
213s > 
213s > x <- 1:4
213s > w <- rep(1, times = 4)
213s > for (mode in c("integer", "double")) {
213s +   storage.mode(x) <- mode
213s +   for (ties in c("weighted", "mean", "min", "max")) {
213s +     cat(sprintf("ties = %s\n", ties))
213s +     y <- weightedMedian(x, w, ties = ties)
213s +   }
213s + }
213s ties = weighted
213s ties = mean
213s ties = min
213s ties = max
213s ties = weighted
213s ties = mean
213s ties = min
213s ties = max
213s > 
213s > set.seed(0x42)
213s > 
213s > y <- weightedMedian(x = double(0L))
213s > print(y)
213s [1] NA
213s > stopifnot(length(y) == 1L)
213s > stopifnot(is.na(y))
213s > 
213s > y <- weightedMedian(x = x[1])
213s > print(y)
213s [1] 1
213s > stopifnot(length(y) == 1L)
213s > stopifnot(all.equal(y, x[1]))
213s > 
213s > 
213s > n <- 1e3
213s > x <- runif(n)
213s > w <- runif(n, min = 0, max = 1)
213s > for (mode in c("integer", "double")) {
213s +   storage.mode(x) <- mode
213s +   for (ties in c("weighted", "mean", "min", "max")) {
213s +     y <- weightedMedian(x, w, ties = ties)
213s +     cat(sprintf("mode = %s, ties = %s, result = %g\n", mode, ties, y))
213s +   }
213s + }
213s mode = integer, ties = weighted, result = 0
213s mode = integer, ties = mean, result = 0
213s mode = integer, ties = min, result = 0
213s mode = integer, ties = max, result = 0
213s mode = double, ties = weighted, result = 0
213s mode = double, ties = mean, result = 0
213s mode = double, ties = min, result = 0
213s mode = double, ties = max, result = 0
213s > 
213s > 
213s > # A large vector
213s > n <- 1e5
213s > x <- runif(n)
213s > w <- runif(n, min = 0, max = 1)
213s > y <- weightedMedian(x, w)
213s > 
213s > y <- weightedMedian(x, w, ties = "min")
213s > 
213s > 
213s > # Single Number
213s > xs <- c(1, NA_integer_)
213s > ws <- c(1, NA_integer_)
213s > for (x in xs) {
213s +   for (w in ws) {
213s +     y <- weightedMedian(x = x, w = w)
213s +     if (is.na(w)) z <- NA_real_
213s +     else z <- x[1]
213s +     stopifnot(all.equal(y, z))
213s +   }
213s + }
213s > 
213s > ## Logical
213s > x1 <- c(TRUE, FALSE, TRUE)
213s > w0 <- c(0, 0, 0)
213s > stopifnot(!is.finite(weightedMedian(x1, w0)),
213s +           !is.infinite(weightedMedian(x1, w0)))
213s > 
213s > w1 <- c(1, 1, 1)
213s > stopifnot(weightedMedian(x1, w1) == 1)
213s > 
213s > w2 <- c(1, 2, 3)
213s > stopifnot(weightedMedian(x1, w2) == 1)
213s > 
213s > ### NA
213s > stopifnot(is.na(weightedMedian(c(TRUE, FALSE, NA),
213s +                                c(1, 2, 3))),
213s +           all.equal(weightedMedian(c(TRUE, FALSE, NA),
213s +                                    c(1, 2, 3),
213s +                                    na.rm = TRUE),
213s +                     weightedMedian(c(TRUE, FALSE),
213s +                                    c(1, 2))))
213s > ### Identical to as.integer()
213s > x <- rcauchy(100)
213s > w <- abs(rcauchy(100))
213s > stopifnot(all.equal(weightedMedian(x > 0, w),
213s +                     weightedMedian(as.integer(x > 0), w)))
213s > 
213s > 
213s > 
213s 
213s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
213s Copyright (C) 2025 The R Foundation for Statistical Computing
213s Platform: x86_64-pc-linux-gnu
213s 
213s R is free software and comes with ABSOLUTELY NO WARRANTY.
213s You are welcome to redistribute it under certain conditions.
213s Type 'license()' or 'licence()' for distribution details.
213s 
213s R is a collaborative project with many contributors.
213s Type 'contributors()' for more information and
213s 'citation()' on how to cite R or R packages in publications.
213s 
213s Type 'demo()' for some demos, 'help()' for on-line help, or
213s 'help.start()' for an HTML browser interface to help.
213s Type 'q()' to quit R.
213s 
213s > library("matrixStats")
213s > 
213s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
213s > # Subsetted tests
213s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
213s > source("utils/validateIndicesFramework.R")
213s > for (mode in c("numeric", "integer")) {
213s +   x <- runif(6, min = -6, max = 6)
213s +   w <- runif(6, min = 0, max = 6)
213s +   storage.mode(x) <- mode
213s +   storage.mode(w) <- mode
213s +   if (mode == "numeric") w[1] <- Inf
213s + 
213s +   for (idxs in index_cases) {
213s +     validateIndicesTestVector_w(x, w, idxs,
213s +                                 ftest = weightedMedian,
213s +                                 fsure = weightedMedian,
213s +                                 na.rm = TRUE)
213s +     validateIndicesTestVector_w(x, w, idxs,
213s +                                 ftest = weightedMedian,
213s +                                 fsure = weightedMedian,
213s +                                 na.rm = FALSE)
213s + 
213s +     for (ties in c("weighted", "mean", "min", "max")) {
213s +       validateIndicesTestVector_w(x, w, idxs,
213s +                                   ftest = weightedMedian,
213s +                                   fsure = weightedMedian,
213s +                                   na.rm = TRUE, ties = ties)
213s +       validateIndicesTestVector_w(x, w, idxs,
213s +                                   ftest = weightedMedian,
213s +                                   fsure = weightedMedian,
213s +                                   na.rm = FALSE, ties = ties)
213s +     }
213s +   }
213s + }
213s > 
213s 
213s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
213s Copyright (C) 2025 The R Foundation for Statistical Computing
213s Platform: x86_64-pc-linux-gnu
213s 
213s R is free software and comes with ABSOLUTELY NO WARRANTY.
213s You are welcome to redistribute it under certain conditions.
213s Type 'license()' or 'licence()' for distribution details.
213s 
213s R is a collaborative project with many contributors.
213s Type 'contributors()' for more information and
213s 'citation()' on how to cite R or R packages in publications.
213s 
213s Type 'demo()' for some demos, 'help()' for on-line help, or
213s 'help.start()' for an HTML browser interface to help.
213s Type 'q()' to quit R.
213s 
213s > library("matrixStats")
213s *** weightedVar() ...
213s - Zero elements
213s > 
213s > weightedVar_R <- function(x, w) {
213s +   mu <- weighted.mean(x, w = w)
213s +   sum(w * (x - mu) ^ 2) / (sum(w) - 1)
213s + }
213s > 
213s > 
213s > n <- 10
213s > x <- as.double(1:n)
213s > 
213s > message("*** weightedVar() ...")
213s > 
213s > message("- Zero elements")
213s > m0 <- var(integer(0))
213s > m1 <- weightedVar(integer(0), w = integer(0))
213s > str(list(m0 = m0, m1 = m1))
213s List of 2
213s  $ m0: num NA
213s  $ m1:- One elements
213s - Uniform weights (all w = 1)
213s - Uniform weights (all w = 3)
213s - Uniform weights on the first five elements
213s - Uniform weights on every second elements
213s - All weights are zero
213s - Infinite weight on first element
213s - Missing-value weight on first element
213s - Frequency weights
213s *** weightedVar() ... DONE
213s  int NA
213s > stopifnot(all.equal(m1, m0))
213s > 
213s > 
213s > message("- One elements")
213s > m0 <- var(1)
213s > m1 <- weightedVar(1)
213s > str(list(m0 = m0, m1 = m1))
213s List of 2
213s  $ m0: num NA
213s  $ m1: num NA
213s > stopifnot(all.equal(m1, m0))
213s > 
213s > 
213s > message("- Uniform weights (all w = 1)")
213s > m0 <- var(x)
213s > w <- rep(1, times = n)
213s > m1 <- weightedVar(x, w = w)
213s > str(list(m0 = m0, m1 = m1))
213s List of 2
213s  $ m0: num 9.17
213s  $ m1: num 9.17
213s > stopifnot(all.equal(m1, m0))
213s > 
213s > 
213s > message("- Uniform weights (all w = 3)")
213s > m0 <- var(rep(x, each = 3))
213s > w <- rep(3, times = n)
213s > m1 <- weightedVar(x, w = w)
213s > str(list(m0 = m0, m1 = m1))
213s List of 2
213s  $ m0: num 8.53
213s  $ m1: num 8.53
213s > stopifnot(all.equal(m1, m0))
213s > 
213s > 
213s > message("- Uniform weights on the first five elements")
213s > idxs <- 1:5
213s > m0 <- var(x[1:5])
213s > w <- rep(0, times = n)
213s > w[idxs] <- 1
213s > m1 <- weightedVar(x, w = w)
213s > str(list(m0 = m0, m1 = m1))
213s List of 2
213s  $ m0: num 2.5
213s  $ m1: num 2.5
213s > stopifnot(all.equal(m1, m0))
213s > 
213s > 
213s > message("- Uniform weights on every second elements")
213s > idxs <- seq(from = 1, to = n, by = 2)
213s > m0 <- var(x[idxs])
213s > w <- rep(0, times = n)
213s > w[idxs] <- 1
213s > m1 <- weightedVar(x, w = w)
213s > str(list(m0 = m0, m1 = m1))
213s List of 2
213s  $ m0: num 10
213s  $ m1: num 10
213s > stopifnot(all.equal(m1, m0))
213s > 
213s > 
213s > message("- All weights are zero")
213s > idxs <- integer(0L)
213s > m0 <- var(x[idxs])
213s > w <- rep(0, times = n)
213s > w[idxs] <- 1
213s > m1 <- weightedVar(x, w = w)
213s > str(list(m0 = m0, m1 = m1))
213s List of 2
213s  $ m0: num NA
213s  $ m1: num NA
213s > stopifnot(all.equal(m1, m0))
213s > 
213s > message("- Infinite weight on first element")
213s > idxs <- 1L
213s > m0 <- var(x[idxs])
213s > w <- rep(0, times = n)
213s > w[idxs] <- Inf
213s > m1 <- weightedVar(x, w = w)
213s > str(list(m0 = m0, m1 = m1))
213s List of 2
213s  $ m0: num NA
213s  $ m1: num NA
213s > stopifnot(all.equal(m1, m0))
213s > 
213s > message("- Missing-value weight on first element")
213s > idxs <- 1L
213s > w <- rep(1, times = n)
213s > w[idxs] <- NA_real_
213s > m1 <- weightedVar(x, w = w)
213s > str(list(m1 = m1))
213s List of 1
213s  $ m1: num NA
213s > stopifnot(identical(m1, NA_real_))
213s > 
213s > 
213s > message("- Frequency weights")
213s > 
213s > ## From https://en.wikipedia.org/wiki/Weighted_arithmetic_mean
213s > y <-  c(2, 2, 4, 5, 5, 5)
213s > x <- unique(y)
213s > w <- table(y)
213s > stopifnot(names(w) == x)
213s > 
213s > m0 <- weightedVar(x, w = w)
213s > m1 <- var(y)
213s > stopifnot(all.equal(m1, m0))
213s > m2 <- weightedVar(x, w = w)
213s > str(list(m0 = m0, m1 = m1, m2 = m2))
213s List of 3
213s  $ m0: num 2.17
213s  $ m1: num 2.17
213s  $ m2: num 2.17
213s > stopifnot(all.equal(m2, m0))
213s > 
213s > ## From https://github.com/HenrikBengtsson/matrixStats/issues/72
213s > large <- c(21, 8, 26, 1, 15, 33, 12, 25, 0, 84)
213s > years <- c(41706, 9301, 33678, 3082, 27040, 44188, 10049, 30591, 2275, 109831)
213s > 
213s > m0 <- weightedVar(large, w = years)
213s > m1 <- weightedVar(large, w = years)
213s > str(list(m0 = m0, m1 = m1))
213s List of 2
213s  $ m0: num 899
213s  $ m1: num 899
213s > stopifnot(all.equal(m1, m0))
213s > 
213s > message("*** weightedVar() ... DONE")
213s > 
213s 
213s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
213s Copyright (C) 2025 The R Foundation for Statistical Computing
213s Platform: x86_64-pc-linux-gnu
213s 
213s R is free software and comes with ABSOLUTELY NO WARRANTY.
213s You are welcome to redistribute it under certain conditions.
213s Type 'license()' or 'licence()' for distribution details.
213s 
213s R is a collaborative project with many contributors.
213s Type 'contributors()' for more information and
213s 'citation()' on how to cite R or R packages in publications.
213s 
213s Type 'demo()' for some demos, 'help()' for on-line help, or
213s 'help.start()' for an HTML browser interface to help.
213s Type 'q()' to quit R.
213s 
213s > library("matrixStats")
213s > 
213s > fcns <- list(
213s +   weightedVar = weightedVar,
213s +   weightedSd  = weightedSd,
213s +   weightedMad = weightedMad
213s + )
213s > 
213s > for (name in names(fcns)) {
213s +   cat(sprintf("%s()...\n", name))
213s +   fcn <- fcns[[name]]
213s + 
213s +   for (mode in c("integer", "double")) {
213s +     cat("mode: ", mode, "\n", sep = "")
213s +     n <- 15L
213s +     x <- runif(n, min = -5, max = 5)
213s +     storage.mode(x) <- mode
213s +     str(x)
213s + 
213s +     for (add_na in c(FALSE, TRUE)) {
213s +       cat("add_na: ", add_na, "\n", sep = "")
213s +       if (add_na) {
213s +         x[c(5, 7)] <- NA
213s +       }
213s +       str(x)
213s + 
213s +       for (na.rm in c(FALSE, TRUE)) {
213s +         cat("na.rm: ", na.rm, "\n", sep = "")
213s + 
213s +         cat("Weights are not specified (all are 1)\n")
213s +         m1 <- fcn(x, na.rm = na.rm)
213s +         str(list(m1 = m1))
213s + 
213s +         cat("All weights are 1\n")
213s +         w <- rep(1, times = n)
213s +         m1 <- fcn(x, w, na.rm = na.rm)
213s +         str(list(m1 = m1))
213s + 
213s +         cat("First weight is 5\n")
213s +         # Pull the mean towards zero
213s +         w[1] <- 5
213s +         str(w)
213s +         m1 <- fcn(x, w, na.rm = na.rm)
213s +         str(list(m1 = m1))
213s + 
213s +         cat("All weights are 0\n")
213s +         # All weights set to zero
213s +         w <- rep(0, times = n)
213s +         m1 <- fcn(x, w, na.rm = na.rm)
213s +         str(list(m1 = m1))
213s + 
213s +         cat("First weight is 8.5\n")
213s +         # Put even more weight on the zero
213s +         w[1] <- 8.5
213s +         m1 <- fcn(x, w, na.rm = na.rm)
213s +         str(list(m1 = m1))
213s + 
213s +         cat("First weight is Inf\n")
213s +         # All weight on the first value
213s +         w[1] <- Inf
213s +         m1 <- fcn(x, w, na.rm = na.rm)
213s +         str(list(m1 = m1))
213s + 
213s +         cat("Last weight is Inf\n")
213s +         # All weight on the last value
213s +         w[1] <- 1
213s +         w[n] <- Inf
213s +         m1 <- fcn(x, w, na.rm = na.rm)
213s +         str(list(m1 = m1))
213s + 
213s +         cat("Last weight is NA\n")
213s +         # All weight on the last value
213s +         w[1] <- 1
213s +         w[n] <- NA_real_
213s +         m1 <- fcn(x, w, na.rm = na.rm)
213s +         str(list(m1 = m1))
213s +       } # for (na.rm ...)
213s +     } # for (add_na ...)
213s +   } # for (mode ...)
213s + 
213s +   cat(sprintf("%s()...DONE\n", name))
213s + } # for (name ...)
213s weightedVar()...
213s mode: integer
213s  int [1:15] 4 0 0 -3 1 -1 4 4 0 4 ...
213s add_na: FALSE
213s  int [1:15] 4 0 0 -3 1 -1 4 4 0 4 ...
213s na.rm: FALSE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num 5.54
213s All weights are 1
213s List of 1
213s  $ m1: num 5.54
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num 5.32
213s All weights are 0
213s List of 1
213s  $ m1: int NA
213s First weight is 8.5
213s List of 1
213s  $ m1: int NA
213s First weight is Inf
213s List of 1
213s  $ m1: int NA
213s Last weight is Inf
213s List of 1
213s  $ m1: int NA
213s Last weight is NA
213s List of 1
213s  $ m1: int NA
213s na.rm: TRUE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num 5.54
213s All weights are 1
213s List of 1
213s  $ m1: num 5.54
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num 5.32
213s All weights are 0
213s List of 1
213s  $ m1: int NA
213s First weight is 8.5
213s List of 1
213s  $ m1: int NA
213s First weight is Inf
213s List of 1
213s  $ m1: int NA
213s Last weight is Inf
213s List of 1
213s  $ m1: int NA
213s Last weight is NA
213s List of 1
213s  $ m1: int NA
213s add_na: TRUE
213s  int [1:15] 4 0 0 -3 NA -1 NA 4 0 4 ...
213s na.rm: FALSE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: int NA
213s All weights are 1
213s List of 1
213s  $ m1: int NA
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: int NA
213s All weights are 0
213s List of 1
213s  $ m1: int NA
213s First weight is 8.5
213s List of 1
213s  $ m1: int NA
213s First weight is Inf
213s List of 1
213s  $ m1: int NA
213s Last weight is Inf
213s List of 1
213s  $ m1: int NA
213s Last weight is NA
213s List of 1
213s  $ m1: int NA
213s na.rm: TRUE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num 5.94
213s All weights are 1
213s List of 1
213s  $ m1: num 5.94
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num 5.68
213s All weights are 0
213s List of 1
213s  $ m1: int NA
213s First weight is 8.5
213s List of 1
213s  $ m1: int NA
213s First weight is Inf
213s List of 1
213s  $ m1: int NA
213s Last weight is Inf
213s List of 1
213s  $ m1: int NA
213s Last weight is NA
213s List of 1
213s  $ m1: int NA
213s mode: double
213s  num [1:15] -3.225 0.941 -0.138 -0.544 0.131 ...
213s add_na: FALSE
213s  num [1:15] -3.225 0.941 -0.138 -0.544 0.131 ...
213s na.rm: FALSE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num 6.32
213s All weights are 1
213s List of 1
213s  $ m1: num 6.32
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num 6.02
213s All weights are 0
213s List of 1
213s  $ m1: num NA
213s First weight is 8.5
213s List of 1
213s  $ m1: num NA
213s First weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is NA
213s List of 1
213s  $ m1: num NA
213s na.rm: TRUE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num 6.32
213s All weights are 1
213s List of 1
213s  $ m1: num 6.32
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num 6.02
213s All weights are 0
213s List of 1
213s  $ m1: num NA
213s First weight is 8.5
213s List of 1
213s  $ m1: num NA
213s First weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is NA
213s List of 1
213s  $ m1: num NA
213s add_na: TRUE
213s  num [1:15] -3.225 0.941 -0.138 -0.544 NA ...
213s na.rm: FALSE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num NA
213s All weights are 1
213s List of 1
213s  $ m1: num NA
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num NA
213s All weights are 0
213s List of 1
213s  $ m1: num NA
213s First weight is 8.5
213s List of 1
213s  $ m1: num NA
213s First weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is NA
213s List of 1
213s  $ m1: num NA
213s na.rm: TRUE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num 7.24
213s All weights are 1
213s List of 1
213s  $ m1: num 7.24
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num 6.64
213s All weights are 0
213s List of 1
213s  $ m1: num NA
213s First weight is 8.5
213s List of 1
213s  $ m1: num NA
213s First weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is NA
213s List of 1
213s  $ m1: num NA
213s weightedVar()...DONE
213s weightedSd()...
213s mode: integer
213s  int [1:15] -4 -2 3 1 -1 0 3 -1 2 4 ...
213s add_na: FALSE
213s  int [1:15] -4 -2 3 1 -1 0 3 -1 2 4 ...
213s na.rm: FALSE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num 2.67
213s All weights are 1
213s List of 1
213s  $ m1: num 2.67
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num 2.89
213s All weights are 0
213s List of 1
213s  $ m1: num NA
213s First weight is 8.5
213s List of 1
213s  $ m1: num NA
213s First weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is NA
213s List of 1
213s  $ m1: num NA
213s na.rm: TRUE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num 2.67
213s All weights are 1
213s List of 1
213s  $ m1: num 2.67
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num 2.89
213s All weights are 0
213s List of 1
213s  $ m1: num NA
213s First weight is 8.5
213s List of 1
213s  $ m1: num NA
213s First weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is NA
213s List of 1
213s  $ m1: num NA
213s add_na: TRUE
213s  int [1:15] -4 -2 3 1 NA 0 NA -1 2 4 ...
213s na.rm: FALSE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num NA
213s All weights are 1
213s List of 1
213s  $ m1: num NA
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num NA
213s All weights are 0
213s List of 1
213s  $ m1: num NA
213s First weight is 8.5
213s List of 1
213s  $ m1: num NA
213s First weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is NA
213s List of 1
213s  $ m1: num NA
213s na.rm: TRUE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num 2.73
213s All weights are 1
213s List of 1
213s  $ m1: num 2.73
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num 2.9
213s All weights are 0
213s List of 1
213s  $ m1: num NA
213s First weight is 8.5
213s List of 1
213s  $ m1: num NA
213s First weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is NA
213s List of 1
213s  $ m1: num NA
213s mode: double
213s  num [1:15] 2.09 -2.74 4.24 3.56 -2.28 ...
213s add_na: FALSE
213s  num [1:15] 2.09 -2.74 4.24 3.56 -2.28 ...
213s na.rm: FALSE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num 2.96
213s All weights are 1
213s List of 1
213s  $ m1: num 2.96
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num 2.82
213s All weights are 0
213s List of 1
213s  $ m1: num NA
213s First weight is 8.5
213s List of 1
213s  $ m1: num NA
213s First weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is NA
213s List of 1
213s  $ m1: num NA
213s na.rm: TRUE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num 2.96
213s All weights are 1
213s List of 1
213s  $ m1: num 2.96
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num 2.82
213s All weights are 0
213s List of 1
213s  $ m1: num NA
213s First weight is 8.5
213s List of 1
213s  $ m1: num NA
213s First weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is NA
213s List of 1
213s  $ m1: num NA
213s add_na: TRUE
213s  num [1:15] 2.09 -2.74 4.24 3.56 NA ...
213s na.rm: FALSE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num NA
213s All weights are 1
213s List of 1
213s  $ m1: num NA
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num NA
213s All weights are 0
213s List of 1
213s  $ m1: num NA
213s First weight is 8.5
213s List of 1
213s  $ m1: num NA
213s First weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is NA
213s List of 1
213s  $ m1: num NA
213s na.rm: TRUE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num 3.12
213s All weights are 1
213s List of 1
213s  $ m1: num 3.12
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num 2.92
213s All weights are 0
213s List of 1
213s  $ m1: num NA
213s First weight is 8.5
213s List of 1
213s  $ m1: num NA
213s First weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is Inf
213s List of 1
213s  $ m1: num NA
213s Last weight is NA
213s List of 1
213s  $ m1: num NA
213s weightedSd()...DONE
213s weightedMad()...
213s mode: integer
213s  int [1:15] 0 -2 -4 2 -1 4 -4 4 0 3 ...
213s add_na: FALSE
213s  int [1:15] 0 -2 -4 2 -1 4 -4 4 0 3 ...
213s na.rm: FALSE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num 4.45
213s All weights are 1
213s List of 1
213s  $ m1: num 4.45
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num 2.97
213s All weights are 0
213s List of 1
213s  $ m1: int NA
213s First weight is 8.5
213s List of 1
213s  $ m1: int 0
213s First weight is Inf
213s List of 1
213s  $ m1: int 0
213s Last weight is Inf
213s List of 1
213s  $ m1: int 0
213s Last weight is NA
213s List of 1
213s  $ m1: int NA
213s na.rm: TRUE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num 4.45
213s All weights are 1
213s List of 1
213s  $ m1: num 4.45
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num 2.97
213s All weights are 0
213s List of 1
213s  $ m1: int NA
213s First weight is 8.5
213s List of 1
213s  $ m1: int 0
213s First weight is Inf
213s List of 1
213s  $ m1: int 0
213s Last weight is Inf
213s List of 1
213s  $ m1: int 0
213s Last weight is NA
213s List of 1
213s  $ m1: int NA
213s add_na: TRUE
213s  int [1:15] 0 -2 -4 2 NA 4 NA 4 0 3 ...
213s na.rm: FALSE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num NA
213s All weights are 1
213s List of 1
213s  $ m1: int NA
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: int NA
213s All weights are 0
213s List of 1
213s  $ m1: int NA
213s First weight is 8.5
213s List of 1
213s  $ m1: int 0
213s First weight is Inf
213s List of 1
213s  $ m1: int 0
213s Last weight is Inf
213s List of 1
213s  $ m1: int 0
213s Last weight is NA
213s List of 1
213s  $ m1: int NA
213s na.rm: TRUE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num 4.45
213s All weights are 1
213s List of 1
213s  $ m1: num 4.45
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num 2.97
213s All weights are 0
213s List of 1
213s  $ m1: int NA
213s First weight is 8.5
213s List of 1
213s  $ m1: int 0
213s First weight is Inf
213s List of 1
213s  $ m1: int 0
213s Last weight is Inf
213s List of 1
213s  $ m1: int 0
213s Last weight is NA
213s List of 1
213s  $ m1: int NA
213s mode: double
213s  num [1:15] 4.56 1.54 1.17 -2.07 1.08 ...
213s add_na: FALSE
213s  num [1:15] 4.56 1.54 1.17 -2.07 1.08 ...
213s na.rm: FALSE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num 2.55
213s All weights are 1
213s List of 1
213s  $ m1: num 2.55
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num 3.13
213s All weights are 0
213s List of 1
213s  $ m1: num NA
213s First weight is 8.5
213s List of 1
213s  $ m1: num 0
213s First weight is Inf
213s List of 1
213s  $ m1: num 0
213s Last weight is Inf
213s List of 1
213s  $ m1: num 0
213s Last weight is NA
213s List of 1
213s  $ m1: num NA
213s na.rm: TRUE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num 2.55
213s All weights are 1
213s List of 1
213s  $ m1: num 2.55
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num 3.13
213s All weights are 0
213s List of 1
213s  $ m1: num NA
213s First weight is 8.5
213s List of 1
213s  $ m1: num 0
213s First weight is Inf
213s List of 1
213s  $ m1: num 0
213s Last weight is Inf
213s List of 1
213s  $ m1: num 0
213s Last weight is NA
213s List of 1
213s  $ m1: num NA
213s add_na: TRUE
213s  num [1:15] 4.56 1.54 1.17 -2.07 NA ...
213s na.rm: FALSE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num NA
213s All weights are 1
213s List of 1
213s  $ m1: num NA
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num NA
213s All weights are 0
213s List of 1
213s  $ m1: num NA
213s First weight is 8.5
213s List of 1
213s  $ m1: num 0
213s First weight is Inf
213s List of 1
213s  $ m1: num 0
213s Last weight is Inf
213s List of 1
213s  $ m1: num 0
213s Last weight is NA
213s List of 1
213s  $ m1: num NA
213s na.rm: TRUE
213s Weights are not specified (all are 1)
213s List of 1
213s  $ m1: num 2.55
213s All weights are 1
213s List of 1
213s  $ m1: num 2.55
213s First weight is 5
213s  num [1:15] 5 1 1 1 1 1 1 1 1 1 ...
213s List of 1
213s  $ m1: num 3.16
213s All weights are 0
213s List of 1
213s  $ m1: num NA
213s First weight is 8.5
213s List of 1
213s  $ m1: num 0
213s First weight is Inf
213s List of 1
213s  $ m1: num 0
213s Last weight is Inf
213s List of 1
213s  $ m1: num 0
213s Last weight is NA
213s List of 1
213s  $ m1: num NA
213s weightedMad()...DONE
213s > 
213s 
213s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
213s Copyright (C) 2025 The R Foundation for Statistical Computing
213s Platform: x86_64-pc-linux-gnu
213s 
213s R is free software and comes with ABSOLUTELY NO WARRANTY.
213s You are welcome to redistribute it under certain conditions.
213s Type 'license()' or 'licence()' for distribution details.
213s 
213s R is a collaborative project with many contributors.
213s Type 'contributors()' for more information and
213s 'citation()' on how to cite R or R packages in publications.
213s 
213s Type 'demo()' for some demos, 'help()' for on-line help, or
213s 'help.start()' for an HTML browser interface to help.
213s Type 'q()' to quit R.
213s 
213s > library("matrixStats")
213s > 
213s > fcns <- list(
213s +   weightedVar = weightedVar,
213s +   weightedSd  = weightedSd,
213s +   weightedMad = weightedMad
213s + )
213s > 
213s > 
213s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
213s > # Subsetted tests
213s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
213s > source("utils/validateIndicesFramework.R")
213s > for (name in names(fcns)) {
213s +   cat(sprintf("subsetted tests on %s()...\n", name))
213s +   fcn <- fcns[[name]]
213s + 
213s +   for (mode in c("numeric", "integer")) {
213s +     x <- runif(6, min = -6, max = 6)
213s +     w <- runif(6, min = 0, max = 6)
213s +     storage.mode(x) <- mode
213s +     storage.mode(w) <- mode
213s +     if (mode == "numeric") w[1] <- Inf
213s + 
213s +     for (idxs in index_cases) {
213s +       validateIndicesTestVector_w(x, w, idxs,
213s +                                   ftest = fcn, fsure = fcn,
213s +                                   na.rm = TRUE)
213s +       validateIndicesTestVector_w(x, w, idxs,
213s +                                   ftest = fcn, fsure = fcn,
213s +                                   na.rm = FALSE)
213s +     }
213s +   }
213s +   cat(sprintf("%s()...DONE\n", name))
213s + }
213s subsetted tests on weightedVar()...
213s weightedVar()...DONE
213s subsetted tests on weightedSd()...
213s weightedSd()...DONE
213s subsetted tests on weightedMad()...
213s weightedMad()...DONE
213s > 
213s 
213s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
213s Copyright (C) 2025 The R Foundation for Statistical Computing
213s Platform: x86_64-pc-linux-gnu
213s 
213s R is free software and comes with ABSOLUTELY NO WARRANTY.
213s You are welcome to redistribute it under certain conditions.
213s Type 'license()' or 'licence()' for distribution details.
213s 
213s R is a collaborative project with many contributors.
213s Type 'contributors()' for more information and
213s 'citation()' on how to cite R or R packages in publications.
213s 
213s Type 'demo()' for some demos, 'help()' for on-line help, or
213s 'help.start()' for an HTML browser interface to help.
213s Type 'q()' to quit R.
213s 
213s > library("matrixStats")
213s > 
213s > x_OP_y_R <- function(x, y, OP, na.rm = FALSE) {
213s +   if (na.rm) {
213s +     xnok <- is.na(x)
213s +     ynok <- is.na(y)
213s +     anok <- xnok & ynok
213s +     unit <- switch(OP,
213s +       "+" = 0,
213s +       "-" = NA_real_,
213s +       "*" = 1,
213s +       "/" = NA_real_,
213s +       stop("Unknown 'OP' operator: ", OP)
213s +     )
213s +     x[xnok] <- unit
213s +     y[ynok] <- unit
213s +   }
213s + 
213s +   ans <- switch(OP,
213s +     "+" = x + y,
213s +     "-" = x - y,
213s +     "*" = x * y,
213s +     "/" = x / y,
213s +     stop("Unknown 'OP' operator: ", OP)
213s +   )
213s + 
213s +   if (na.rm) {
213s +     ans[anok] <- NA_real_
213s +   }
213s + 
213s +   ans
213s + } # x_OP_y_R()
213s > 
213s > 
213s > 
213s > t_tx_OP_y_R <- function(x, y, OP, na.rm = FALSE) {
213s +   t(x_OP_y_R(x = t(x), y = y, OP = OP, na.rm = na.rm))
213s + }
213s > 
213s > 
213s > 
213s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
213s > # No missing values
213s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
213s > x <- matrix(1:16, nrow = 4, ncol = 4)
213s > y <- 1:nrow(x)
213s > storage.mode(y) <- storage.mode(x)
213s > 
213s > for (OP in c("+", "-", "*", "/")) {
213s +   for (na.rm in c(FALSE, TRUE)) {
213s +     cat(sprintf("OP = '%s', na.rm = %s\n", OP, na.rm))
213s + 
213s +     a0 <- x_OP_y_R(x, y, OP, na.rm = na.rm)
213s +     a1 <- x_OP_y(x, y, OP, na.rm = na.rm)
213s +     str(a1)
213s +     stopifnot(all.equal(a1, a0))
213s + 
213s +     b0 <- t_tx_OP_y_R(x, y, OP, na.rm = na.rm)
213s +     b1 <- t_tx_OP_y(x, y, OP, na.rm = na.rm)
213s +     str(b1)
213s +     stopifnot(all.equal(b1, b0))
213s +   }
213s + }
213s OP = '+', na.rm = FALSE
213s  int [1:4, 1:4] 2 4 6 8 6 8 10 12 10 12 ...
213s  int [1:4, 1:4] 2 3 4 5 7 8 9 10 12 13 ...
213s OP = '+', na.rm = TRUE
213s  int [1:4, 1:4] 2 4 6 8 6 8 10 12 10 12 ...
213s  int [1:4, 1:4] 2 3 4 5 7 8 9 10 12 13 ...
213s OP = '-', na.rm = FALSE
213s  int [1:4, 1:4] 0 0 0 0 4 4 4 4 8 8 ...
213s  int [1:4, 1:4] 0 1 2 3 3 4 5 6 6 7 ...
213s OP = '-', na.rm = TRUE
213s  int [1:4, 1:4] 0 0 0 0 4 4 4 4 8 8 ...
213s  int [1:4, 1:4] 0 1 2 3 3 4 5 6 6 7 ...
213s OP = '*', na.rm = FALSE
213s  int [1:4, 1:4] 1 4 9 16 5 12 21 32 9 20 ...
213s  int [1:4, 1:4] 1 2 3 4 10 12 14 16 27 30 ...
213s OP = '*', na.rm = TRUE
213s  int [1:4, 1:4] 1 4 9 16 5 12 21 32 9 20 ...
213s  int [1:4, 1:4] 1 2 3 4 10 12 14 16 27 30 ...
213s OP = '/', na.rm = FALSE
213s  num [1:4, 1:4] 1 1 1 1 5 ...
213s  num [1:4, 1:4] 1 2 3 4 2.5 ...
213s OP = '/', na.rm = TRUE
213s  num [1:4, 1:4] 1 1 1 1 5 ...
213s  num [1:4, 1:4] 1 2 3 4 2.5 ...
213s > 
213s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
213s > # Missing values in x, y, or both.
213s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
213s > for (which in c("x", "y", "both")) {
213s +   x <- matrix(1:16, nrow = 4, ncol = 4)
213s +   y <- 1:nrow(x)
213s +   storage.mode(y) <- storage.mode(x)
213s + 
213s +   if (which == "x") {
213s +     x[3:6] <- NA_real_
213s +   } else if (which == "y") {
213s +     y[c(1, 3)] <- NA_real_
213s +   } else if (which == "both") {
213s +     x[3:6] <- NA_real_
213s +     y[c(1, 3)] <- NA_real_
213s +   }
213s + 
213s +   for (OP in c("+", "-", "*", "/")) {
213s +     for (na.rm in c(FALSE, TRUE)) {
213s +       cat(sprintf("OP = '%s', na.rm = %s\n", OP, na.rm))
213s +       a0 <- x_OP_y_R(x, y, OP, na.rm = na.rm)
213s +       a1 <- x_OP_y(x, y, OP, na.rm = na.rm)
213s +       str(a1)
213s +       stopifnot(all.equal(a1, a0))
213s + 
213s +       b0 <- t_tx_OP_y_R(x, y, OP, na.rm = na.rm)
213s +       b1 <- t_tx_OP_y(x, y, OP, na.rm = na.rm)
213s +       str(b1)
213s +       stopifnot(all.equal(b1, b0))
213s +     }
213s +   }
213s + }
213s OP = '+', na.rm = FALSE
213s  num [1:4, 1:4] 2 4 NA NA NA NA 10 12 10 12 ...
213s  num [1:4, 1:4] 2 3 NA NA NA NA 9 10 12 13 ...
213s OP = '+', na.rm = TRUE
213s  num [1:4, 1:4] 2 4 3 4 1 2 10 12 10 12 ...
213s  num [1:4, 1:4] 2 3 1 1 2 2 9 10 12 13 ...
213s OP = '-', na.rm = FALSE
213s  num [1:4, 1:4] 0 0 NA NA NA NA 4 4 8 8 ...
213s  num [1:4, 1:4] 0 1 NA NA NA NA 5 6 6 7 ...
213s OP = '-', na.rm = TRUE
213s  num [1:4, 1:4] 0 0 NA NA NA NA 4 4 8 8 ...
213s  num [1:4, 1:4] 0 1 NA NA NA NA 5 6 6 7 ...
213s OP = '*', na.rm = FALSE
213s  num [1:4, 1:4] 1 4 NA NA NA NA 21 32 9 20 ...
213s  num [1:4, 1:4] 1 2 NA NA NA NA 14 16 27 30 ...
213s OP = '*', na.rm = TRUE
213s  num [1:4, 1:4] 1 4 3 4 1 2 21 32 9 20 ...
213s  num [1:4, 1:4] 1 2 1 1 2 2 14 16 27 30 ...
213s OP = '/', na.rm = FALSE
213s  num [1:4, 1:4] 1 1 NA NA NA ...
213s  num [1:4, 1:4] 1 2 NA NA NA ...
213s OP = '/', na.rm = TRUE
213s  num [1:4, 1:4] 1 1 NA NA NA ...
213s  num [1:4, 1:4] 1 2 NA NA NA ...
213s OP = '+', na.rm = FALSE
213s  num [1:4, 1:4] NA 4 NA 8 NA 8 NA 12 NA 12 ...
213s  num [1:4, 1:4] NA NA NA NA 7 8 9 10 NA NA ...
213s OP = '+', na.rm = TRUE
213s  num [1:4, 1:4] 1 4 3 8 5 8 7 12 9 12 ...
213s  num [1:4, 1:4] 1 2 3 4 7 8 9 10 9 10 ...
213s OP = '-', na.rm = FALSE
213s  num [1:4, 1:4] NA 0 NA 0 NA 4 NA 4 NA 8 ...
213s  num [1:4, 1:4] NA NA NA NA 3 4 5 6 NA NA ...
213s OP = '-', na.rm = TRUE
213s  num [1:4, 1:4] NA 0 NA 0 NA 4 NA 4 NA 8 ...
213s  num [1:4, 1:4] NA NA NA NA 3 4 5 6 NA NA ...
213s OP = '*', na.rm = FALSE
213s  num [1:4, 1:4] NA 4 NA 16 NA 12 NA 32 NA 20 ...
213s  num [1:4, 1:4] NA NA NA NA 10 12 14 16 NA NA ...
213s OP = '*', na.rm = TRUE
213s  num [1:4, 1:4] 1 4 3 16 5 12 7 32 9 20 ...
213s  num [1:4, 1:4] 1 2 3 4 10 12 14 16 9 10 ...
213s OP = '/', na.rm = FALSE
213s  num [1:4, 1:4] NA 1 NA 1 NA 3 NA 2 NA 5 ...
213s  num [1:4, 1:4] NA NA NA NA 2.5 3 3.5 4 NA NA ...
213s OP = '/', na.rm = TRUE
213s  num [1:4, 1:4] NA 1 NA 1 NA 3 NA 2 NA 5 ...
213s  num [1:4, 1:4] NA NA NA NA 2.5 3 3.5 4 NA NA ...
213s OP = '+', na.rm = FALSE
213s  num [1:4, 1:4] NA 4 NA NA NA NA NA 12 NA 12 ...
213s  num [1:4, 1:4] NA NA NA NA NA NA 9 10 NA NA ...
213s OP = '+', na.rm = TRUE
213s  num [1:4, 1:4] 1 4 NA 4 NA 2 7 12 9 12 ...
213s  num [1:4, 1:4] 1 2 NA NA 2 2 9 10 9 10 ...
213s OP = '-', na.rm = FALSE
213s  num [1:4, 1:4] NA 0 NA NA NA NA NA 4 NA 8 ...
213s  num [1:4, 1:4] NA NA NA NA NA NA 5 6 NA NA ...
213s OP = '-', na.rm = TRUE
213s  num [1:4, 1:4] NA 0 NA NA NA NA NA 4 NA 8 ...
213s  num [1:4, 1:4] NA NA NA NA NA NA 5 6 NA NA ...
213s OP = '*', na.rm = FALSE
213s  num [1:4, 1:4] NA 4 NA NA NA NA NA 32 NA 20 ...
213s  num [1:4, 1:4] NA NA NA NA NA NA 14 16 NA NA ...
213s OP = '*', na.rm = TRUE
213s  num [1:4, 1:4] 1 4 NA 4 NA 2 7 32 9 20 ...
213s  num [1:4, 1:4] 1 2 NA NA 2 2 14 16 9 10 ...
213s OP = '/', na.rm = FALSE
213s  num [1:4, 1:4] NA 1 NA NA NA NA NA 2 NA 5 ...
213s  num [1:4, 1:4] NA NA NA NA NA NA 3.5 4 NA NA ...
213s OP = '/', na.rm = TRUE
213s  num [1:4, 1:4] NA 1 NA NA NA NA NA 2 NA 5 ...
213s  num [1:4, 1:4] NA NA NA NA NA NA 3.5 4 NA NA ...
213s > 
213s > 
213s > 
213s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
213s > # Length differences
213s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
213s > x <- matrix(1:8, nrow = 2, ncol = 4)
213s > y <- 1:ncol(x)
213s > storage.mode(y) <- storage.mode(x)
213s > 
213s > for (OP in c("+", "-", "*", "/")) {
213s +   for (na.rm in c(FALSE, TRUE)) {
213s +     cat(sprintf("OP = '%s', na.rm = %s\n", OP, na.rm))
213s + 
213s +     a0 <- x_OP_y_R(x, y, OP, na.rm = na.rm)
213s +     a1 <- x_OP_y(x, y, OP, na.rm = na.rm)
213s +     str(a1)
213s +     stopifnot(all.equal(a1, a0))
213s + 
213s +     b0 <- t_tx_OP_y_R(x, y, OP, na.rm = na.rm)
213s +     b1 <- t_tx_OP_y(x, y, OP, na.rm = na.rm)
213s +     str(b1)
213s +     stopifnot(all.equal(b1, b0))
213s +   }
213s + }
213s OP = '+', na.rm = FALSE
213s  int [1:2, 1:4] 2 4 6 8 6 8 10 12
213s  int [1:2, 1:4] 2 3 5 6 8 9 11 12
213s OP = '+', na.rm = TRUE
213s  int [1:2, 1:4] 2 4 6 8 6 8 10 12
213s  int [1:2, 1:4] 2 3 5 6 8 9 11 12
213s OP = '-', na.rm = FALSE
213s  int [1:2, 1:4] 0 0 0 0 4 4 4 4
213s  int [1:2, 1:4] 0 1 1 2 2 3 3 4
213s OP = '-', na.rm = TRUE
213s  int [1:2, 1:4] 0 0 0 0 4 4 4 4
213s  int [1:2, 1:4] 0 1 1 2 2 3 3 4
213s OP = '*', na.rm = FALSE
213s  int [1:2, 1:4] 1 4 9 16 5 12 21 32
214s  int [1:2, 1:4] 1 2 6 8 15 18 28 32
214s OP = '*', na.rm = TRUE
214s  int [1:2, 1:4] 1 4 9 16 5 12 21 32
214s  int [1:2, 1:4] 1 2 6 8 15 18 28 32
214s OP = '/', na.rm = FALSE
214s  num [1:2, 1:4] 1 1 1 1 5 ...
214s  num [1:2, 1:4] 1 2 1.5 2 1.67 ...
214s OP = '/', na.rm = TRUE
214s  num [1:2, 1:4] 1 1 1 1 5 ...
214s  num [1:2, 1:4] 1 2 1.5 2 1.67 ...
214s > 
214s > 
214s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
214s > # All missing values
214s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
214s > xs <- list(
214s +   A = matrix(1:2, nrow = 2, ncol = 2),
214s +   B = matrix(NA_integer_, nrow = 2, ncol = 2)
214s + )
214s > ys <- list(
214s +   A = 1L,
214s +   B = NA_integer_
214s + )
214s > 
214s > for (x in xs) {
214s +   for (y in ys) {
214s +     for (mode in c("logical", "integer", "double")) {
214s +       storage.mode(x) <- mode
214s +       storage.mode(y) <- mode
214s +       str(list(x = x, y = y))
214s + 
214s +       for (OP in c("+", "-", "*", "/")) {
214s +         for (na.rm in c(FALSE, TRUE)) {
214s +           cat(sprintf("mode = '%s', OP = '%s', na.rm = %s\n", mode, OP, na.rm))
214s +           suppressWarnings({
214s +             z0 <- x_OP_y_R(x, y, OP, na.rm = na.rm)
214s +             z <- x_OP_y(x, y, OP, na.rm = na.rm)
214s +           })
214s +           str(z)
214s +           stopifnot(all.equal(z, z0))
214s +         }
214s +       }
214s +     } # for (mode ...)
214s +   } # for (y ...)
214s + } # for (x ...)
214s List of 2
214s  $ x: logi [1:2, 1:2] TRUE TRUE TRUE TRUE
214s  $ y: logi TRUE
214s mode = 'logical', OP = '+', na.rm = FALSE
214s  int [1:2, 1:2] 2 2 2 2
214s mode = 'logical', OP = '+', na.rm = TRUE
214s  int [1:2, 1:2] 2 2 2 2
214s mode = 'logical', OP = '-', na.rm = FALSE
214s  int [1:2, 1:2] 0 0 0 0
214s mode = 'logical', OP = '-', na.rm = TRUE
214s  int [1:2, 1:2] 0 0 0 0
214s mode = 'logical', OP = '*', na.rm = FALSE
214s  int [1:2, 1:2] 1 1 1 1
214s mode = 'logical', OP = '*', na.rm = TRUE
214s  int [1:2, 1:2] 1 1 1 1
214s mode = 'logical', OP = '/', na.rm = FALSE
214s  num [1:2, 1:2] 1 1 1 1
214s mode = 'logical', OP = '/', na.rm = TRUE
214s  num [1:2, 1:2] 1 1 1 1
214s List of 2
214s  $ x: int [1:2, 1:2] 1 1 1 1
214s  $ y: int 1
214s mode = 'integer', OP = '+', na.rm = FALSE
214s  int [1:2, 1:2] 2 2 2 2
214s mode = 'integer', OP = '+', na.rm = TRUE
214s  int [1:2, 1:2] 2 2 2 2
214s mode = 'integer', OP = '-', na.rm = FALSE
214s  int [1:2, 1:2] 0 0 0 0
214s mode = 'integer', OP = '-', na.rm = TRUE
214s  int [1:2, 1:2] 0 0 0 0
214s mode = 'integer', OP = '*', na.rm = FALSE
214s  int [1:2, 1:2] 1 1 1 1
214s mode = 'integer', OP = '*', na.rm = TRUE
214s  int [1:2, 1:2] 1 1 1 1
214s mode = 'integer', OP = '/', na.rm = FALSE
214s  num [1:2, 1:2] 1 1 1 1
214s mode = 'integer', OP = '/', na.rm = TRUE
214s  num [1:2, 1:2] 1 1 1 1
214s List of 2
214s  $ x: num [1:2, 1:2] 1 1 1 1
214s  $ y: num 1
214s mode = 'double', OP = '+', na.rm = FALSE
214s  num [1:2, 1:2] 2 2 2 2
214s mode = 'double', OP = '+', na.rm = TRUE
214s  num [1:2, 1:2] 2 2 2 2
214s mode = 'double', OP = '-', na.rm = FALSE
214s  num [1:2, 1:2] 0 0 0 0
214s mode = 'double', OP = '-', na.rm = TRUE
214s  num [1:2, 1:2] 0 0 0 0
214s mode = 'double', OP = '*', na.rm = FALSE
214s  num [1:2, 1:2] 1 1 1 1
214s mode = 'double', OP = '*', na.rm = TRUE
214s  num [1:2, 1:2] 1 1 1 1
214s mode = 'double', OP = '/', na.rm = FALSE
214s  num [1:2, 1:2] 1 1 1 1
214s mode = 'double', OP = '/', na.rm = TRUE
214s  num [1:2, 1:2] 1 1 1 1
214s List of 2
214s  $ x: logi [1:2, 1:2] TRUE TRUE TRUE TRUE
214s  $ y: logi NA
214s mode = 'logical', OP = '+', na.rm = FALSE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'logical', OP = '+', na.rm = TRUE
214s  int [1:2, 1:2] 1 1 1 1
214s mode = 'logical', OP = '-', na.rm = FALSE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'logical', OP = '-', na.rm = TRUE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'logical', OP = '*', na.rm = FALSE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'logical', OP = '*', na.rm = TRUE
214s  int [1:2, 1:2] 1 1 1 1
214s mode = 'logical', OP = '/', na.rm = FALSE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'logical', OP = '/', na.rm = TRUE
214s  num [1:2, 1:2] NA NA NA NA
214s List of 2
214s  $ x: int [1:2, 1:2] 1 1 1 1
214s  $ y: int NA
214s mode = 'integer', OP = '+', na.rm = FALSE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'integer', OP = '+', na.rm = TRUE
214s  int [1:2, 1:2] 1 1 1 1
214s mode = 'integer', OP = '-', na.rm = FALSE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'integer', OP = '-', na.rm = TRUE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'integer', OP = '*', na.rm = FALSE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'integer', OP = '*', na.rm = TRUE
214s  int [1:2, 1:2] 1 1 1 1
214s mode = 'integer', OP = '/', na.rm = FALSE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'integer', OP = '/', na.rm = TRUE
214s  num [1:2, 1:2] NA NA NA NA
214s List of 2
214s  $ x: num [1:2, 1:2] 1 1 1 1
214s  $ y: num NA
214s mode = 'double', OP = '+', na.rm = FALSE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'double', OP = '+', na.rm = TRUE
214s  num [1:2, 1:2] 1 1 1 1
214s mode = 'double', OP = '-', na.rm = FALSE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'double', OP = '-', na.rm = TRUE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'double', OP = '*', na.rm = FALSE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'double', OP = '*', na.rm = TRUE
214s  num [1:2, 1:2] 1 1 1 1
214s mode = 'double', OP = '/', na.rm = FALSE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'double', OP = '/', na.rm = TRUE
214s  num [1:2, 1:2] NA NA NA NA
214s List of 2
214s  $ x: logi [1:2, 1:2] NA NA NA NA
214s  $ y: logi TRUE
214s mode = 'logical', OP = '+', na.rm = FALSE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'logical', OP = '+', na.rm = TRUE
214s  int [1:2, 1:2] 1 1 1 1
214s mode = 'logical', OP = '-', na.rm = FALSE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'logical', OP = '-', na.rm = TRUE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'logical', OP = '*', na.rm = FALSE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'logical', OP = '*', na.rm = TRUE
214s  int [1:2, 1:2] 1 1 1 1
214s mode = 'logical', OP = '/', na.rm = FALSE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'logical', OP = '/', na.rm = TRUE
214s  num [1:2, 1:2] NA NA NA NA
214s List of 2
214s  $ x: int [1:2, 1:2] NA NA NA NA
214s  $ y: int 1
214s mode = 'integer', OP = '+', na.rm = FALSE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'integer', OP = '+', na.rm = TRUE
214s  int [1:2, 1:2] 1 1 1 1
214s mode = 'integer', OP = '-', na.rm = FALSE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'integer', OP = '-', na.rm = TRUE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'integer', OP = '*', na.rm = FALSE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'integer', OP = '*', na.rm = TRUE
214s  int [1:2, 1:2] 1 1 1 1
214s mode = 'integer', OP = '/', na.rm = FALSE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'integer', OP = '/', na.rm = TRUE
214s  num [1:2, 1:2] NA NA NA NA
214s List of 2
214s  $ x: num [1:2, 1:2] NA NA NA NA
214s  $ y: num 1
214s mode = 'double', OP = '+', na.rm = FALSE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'double', OP = '+', na.rm = TRUE
214s  num [1:2, 1:2] 1 1 1 1
214s mode = 'double', OP = '-', na.rm = FALSE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'double', OP = '-', na.rm = TRUE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'double', OP = '*', na.rm = FALSE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'double', OP = '*', na.rm = TRUE
214s  num [1:2, 1:2] 1 1 1 1
214s mode = 'double', OP = '/', na.rm = FALSE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'double', OP = '/', na.rm = TRUE
214s  num [1:2, 1:2] NA NA NA NA
214s List of 2
214s  $ x: logi [1:2, 1:2] NA NA NA NA
214s  $ y: logi NA
214s mode = 'logical', OP = '+', na.rm = FALSE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'logical', OP = '+', na.rm = TRUE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'logical', OP = '-', na.rm = FALSE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'logical', OP = '-', na.rm = TRUE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'logical', OP = '*', na.rm = FALSE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'logical', OP = '*', na.rm = TRUE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'logical', OP = '/', na.rm = FALSE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'logical', OP = '/', na.rm = TRUE
214s  num [1:2, 1:2] NA NA NA NA
214s List of 2
214s  $ x: int [1:2, 1:2] NA NA NA NA
214s  $ y: int NA
214s mode = 'integer', OP = '+', na.rm = FALSE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'integer', OP = '+', na.rm = TRUE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'integer', OP = '-', na.rm = FALSE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'integer', OP = '-', na.rm = TRUE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'integer', OP = '*', na.rm = FALSE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'integer', OP = '*', na.rm = TRUE
214s  int [1:2, 1:2] NA NA NA NA
214s mode = 'integer', OP = '/', na.rm = FALSE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'integer', OP = '/', na.rm = TRUE
214s  num [1:2, 1:2] NA NA NA NA
214s List of 2
214s  $ x: num [1:2, 1:2] NA NA NA NA
214s  $ y: num NA
214s mode = 'double', OP = '+', na.rm = FALSE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'double', OP = '+', na.rm = TRUE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'double', OP = '-', na.rm = FALSE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'double', OP = '-', na.rm = TRUE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'double', OP = '*', na.rm = FALSE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'double', OP = '*', na.rm = TRUE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'double', OP = '/', na.rm = FALSE
214s  num [1:2, 1:2] NA NA NA NA
214s mode = 'double', OP = '/', na.rm = TRUE
214s  num [1:2, 1:2] NA NA NA NA
214s > 
214s 
214s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
214s Copyright (C) 2025 The R Foundation for Statistical Computing
214s Platform: x86_64-pc-linux-gnu
214s 
214s R is free software and comes with ABSOLUTELY NO WARRANTY.
214s You are welcome to redistribute it under certain conditions.
214s Type 'license()' or 'licence()' for distribution details.
214s 
214s R is a collaborative project with many contributors.
214s Type 'contributors()' for more information and
214s 'citation()' on how to cite R or R packages in publications.
214s 
214s Type 'demo()' for some demos, 'help()' for on-line help, or
214s 'help.start()' for an HTML browser interface to help.
214s Type 'q()' to quit R.
214s 
214s > library("matrixStats")
214s > 
214s > x_OP_y_R <- function(x, y, OP, na.rm = FALSE) {
214s +   if (na.rm) {
214s +     xnok <- is.na(x)
214s +     ynok <- is.na(y)
214s +     anok <- xnok & ynok
214s +     unit <- switch(OP,
214s +       "+" = 0,
214s +       "-" = NA_real_,
214s +       "*" = 1,
214s +       "/" = NA_real_,
214s +       stop("Unknown 'OP' operator: ", OP)
214s +     )
214s +     x[xnok] <- unit
214s +     y[ynok] <- unit
214s +   }
214s + 
214s +   ans <- switch(OP,
214s +     "+" = x + y,
214s +     "-" = x - y,
214s +     "*" = x * y,
214s +     "/" = x / y,
214s +     stop("Unknown 'OP' operator: ", OP)
214s +   )
214s + 
214s +   if (na.rm) {
214s +     ans[anok] <- NA_real_
214s +   }
214s + 
214s +   ans
214s + } # x_OP_y_R()
214s > 
214s > 
214s > t_tx_OP_y_R <- function(x, y, OP, na.rm = FALSE) {
214s +   t(x_OP_y_R(x = t(x), y = y, OP = OP, na.rm = na.rm))
214s + }
214s > 
214s > 
214s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
214s > # Subsetted tests
214s > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
214s > source("utils/validateIndicesFramework.R")
214s > for (OP in c("+", "-", "*", "/")) {
214s +   for (mode in c("numeric", "integer", "logical")) {
214s +     x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6L, ncol = 6L)
214s +     y <- runif(6, min = 0, max = 6)
214s +     storage.mode(x) <- mode
214s +     storage.mode(y) <- mode
214s +     if (mode == "numeric") y[1] <- Inf
214s + 
214s +     for (xrows in index_cases) {
214s +       for (xcols in index_cases) {
214s +         if (is.null(xrows)) xrows <- seq_len(nrow(x))
214s +         if (is.null(xcols)) xcols <- seq_len(ncol(x))
214s + 
214s +         for (yidxs in list(xrows, xcols)) {
214s +           for (na.rm in c(TRUE, FALSE)) {
214s + 
214s +             suppressWarnings({
214s +               actual <- tryCatch(
214s +                 x_OP_y(x, y, OP, xrows = xrows, xcols = xcols, yidxs = yidxs,
214s +                        na.rm = na.rm),
214s +                 error = function(c) "error"
214s +               )
214s + 
214s +               expect <- tryCatch(
214s +                 x_OP_y_R(x[xrows, xcols, drop = FALSE], y[yidxs], OP,
214s +                          na.rm = na.rm),
214s +                 error = function(c) "error"
214s +               )
214s +             })
214s +             stopifnot(all.equal(as.vector(actual), as.vector(expect)))
214s + 
214s +             suppressWarnings({
214s +               actual <- tryCatch(
214s +                 t_tx_OP_y(x, y, OP, xrows = xrows, xcols = xcols, yidxs = yidxs,
214s +                           na.rm = na.rm),
214s +                 error = function(c) "error"
214s +               )
214s + 
214s +               expect <- tryCatch(
214s +                 t_tx_OP_y_R(x[xrows, xcols, drop = FALSE], y[yidxs], OP,
214s +                             na.rm = na.rm),
214s +                 error = function(c) "error"
214s +               )
214s +             })
214s +             stopifnot(all.equal(as.vector(actual), as.vector(expect)))
214s +           }
214s +         }
214s +       }
214s +     }
214s +   }
214s + }
215s > 
215s 
215s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
215s Copyright (C) 2025 The R Foundation for Statistical Computing
215s Platform: x86_64-pc-linux-gnu
215s 
215s R is free software and comes with ABSOLUTELY NO WARRANTY.
215s You are welcome to redistribute it under certain conditions.
215s Type 'license()' or 'licence()' for distribution details.
215s 
215s R is a collaborative project with many contributors.
215s Type 'contributors()' for more information and
215s 'citation()' on how to cite R or R packages in publications.
215s 
215s Type 'demo()' for some demos, 'help()' for on-line help, or
215s 'help.start()' for an HTML browser interface to help.
215s Type 'q()' to quit R.
215s 
216s > ## These tests need to be last of all tests, otherwise
216s > ## covr::package_coverage() gives an error.
216s > cat("1. Loading package\n")
216s 1. Loading package
216s > loadNamespace("matrixStats")
216s <environment: namespace:matrixStats>
216s > stopifnot("matrixStats" %in% loadedNamespaces())
216s > 
216s > cat("2. Unloading package\n")
216s 2. Unloading package
216s > unloadNamespace("matrixStats")
216s > stopifnot(!"matrixStats" %in% loadedNamespaces())
216s > 
216s > if (FALSE) {
216s +   ## 'covr' gives "Error in library("matrixStats") :
216s +   ## there is no package called 'matrixStats'" here, cf.
216s +   ## https://travis-ci.org/HenrikBengtsson/matrixStats/builds/48015577
216s + 
216s +   cat("3. Attaching package\n")
216s +   library("matrixStats")
216s +   stopifnot("package:matrixStats" %in% search())
216s + 
216s +   cat("4. Detaching package\n")
216s +   detach("package:matrixStats")
216s +   stopifnot(!"package:matrixStats" %in% search())
216s +   stopifnot("matrixStats" %in% loadedNamespaces())
216s + 
216s +   cat("5. Unloading package\n")
216s +   unloadNamespace("matrixStats")
216s +   stopifnot(!"matrixStats" %in% loadedNamespaces())
216s + 
216s +   cat("6. Attaching package (again)\n")
216s +   library("matrixStats")
216s +   stopifnot("package:matrixStats" %in% search())
216s + 
216s +   cat("7. Detaching package (again)\n")
216s +   detach("package:matrixStats")
216s +   stopifnot(!"package:matrixStats" %in% search())
216s +   stopifnot("matrixStats" %in% loadedNamespaces())
216s + }
216s > 
216s > cat("7. DONE\n")
216s 7. DONE
216s > 
216s autopkgtest [05:30:05]: test run-unit-test: -----------------------]
216s autopkgtest [05:30:05]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
216s run-unit-test        PASS
217s autopkgtest [05:30:06]: test pkg-r-autopkgtest: preparing testbed
236s Creating nova instance adt-resolute-amd64-r-cran-matrixstats-20260210-052629-juju-7f2275-prod-proposed-migration-environment-2-bcb2911b-cc5a-4553-b510-6a8e48ee2fa6 from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)...
305s autopkgtest [05:31:34]: testbed dpkg architecture: amd64
306s autopkgtest [05:31:35]: testbed apt version: 3.1.14
306s autopkgtest [05:31:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup
306s autopkgtest [05:31:35]: testbed release detected to be: resolute
307s autopkgtest [05:31:36]: updating testbed package index (apt update)
307s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB]
307s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
307s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
307s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
307s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [178 kB]
307s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1727 kB]
308s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [31.1 kB]
308s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [266 kB]
308s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [219 kB]
308s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6184 B]
308s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B]
308s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [792 kB]
308s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1787 kB]
308s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [32.5 kB]
309s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [26.4 kB]
309s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [5020 B]
309s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [996 B]
309s Fetched 5197 kB in 2s (2919 kB/s)
310s Reading package lists...
310s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease
310s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
310s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
310s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
311s Reading package lists...
311s Reading package lists...
311s Building dependency tree...
311s Reading state information...
311s Calculating upgrade...
311s The following package was automatically installed and is no longer required:
311s   libpython3.13
311s Use 'sudo apt autoremove' to remove it.
311s The following NEW packages will be installed:
311s   gcc-16-base libpython3.14 libpython3.14-minimal libpython3.14-stdlib
311s   linux-headers-6.19.0-3 linux-headers-6.19.0-3-generic
311s   linux-image-6.19.0-3-generic linux-modules-6.19.0-3-generic
311s   linux-tools-6.19.0-3 linux-tools-6.19.0-3-generic
311s The following packages will be upgraded:
311s   3cpio amd64-microcode apt bpftool busybox-initramfs busybox-static
311s   cryptsetup-bin dash dbus dbus-bin dbus-daemon dbus-session-bus-common
311s   dbus-system-bus-common dbus-user-session debianutils dmsetup dracut-install
311s   ethtool findutils gir1.2-girepository-3.0 gir1.2-glib-2.0 hwdata iproute2
311s   iptables less libapt-pkg7.0 libatomic1 libattr1 libbpf1 libbrotli1 libbsd0
311s   libcryptsetup12 libdbus-1-3 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common
311s   libdrm2 libevent-core-2.1-7t64 libgcc-s1 libgdbm-compat4t64 libgdbm6t64
311s   libgirepository-2.0-0 libglib2.0-0t64 libglib2.0-data libgpm2 libgudev-1.0-0
311s   libidn2-0 libip4tc2 libip6tc2 libjansson4 libkeyutils1 liblsof0
311s   libmaxminddb0 libnetfilter-conntrack3 libnpth0t64 libonig5 libpcap0.8t64
311s   libpci3 libsensors-config libsensors5 libstdc++6 libusb-1.0-0 libwrap0
311s   libxau6 libxkbcommon0 libxtables12 linux-generic linux-headers-generic
311s   linux-headers-virtual linux-image-generic linux-image-virtual linux-perf
311s   linux-tools-common linux-virtual lsof man-db mawk patch pciutils pnp.ids
311s   pollinate python3-linkify-it python3-markdown-it python3-referencing sed
311s   shared-mime-info tar tcpdump ubuntu-kernel-accessories ubuntu-standard wget
312s 91 upgraded, 10 newly installed, 0 to remove and 0 not upgraded.
312s Need to get 237 MB of archives.
312s After this operation, 339 MB of additional disk space will be used.
312s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 debianutils amd64 5.23.2build1 [93.3 kB]
312s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 dash amd64 0.5.12-12ubuntu3 [96.0 kB]
312s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB]
312s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB]
312s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB]
312s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB]
312s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-16-base amd64 16-20260208-1ubuntu1 [59.7 kB]
312s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1 amd64 16-20260208-1ubuntu1 [80.3 kB]
312s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libbsd0 amd64 0.12.2-2build2 [42.3 kB]
312s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB]
312s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6 amd64 16-20260208-1ubuntu1 [844 kB]
312s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB]
312s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB]
313s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-system-bus-common all 1.16.2-2ubuntu3 [55.8 kB]
313s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-session-bus-common all 1.16.2-2ubuntu3 [54.4 kB]
313s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-user-session amd64 1.16.2-2ubuntu3 [9696 B]
313s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-daemon amd64 1.16.2-2ubuntu3 [119 kB]
313s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-bin amd64 1.16.2-2ubuntu3 [40.1 kB]
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313s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libdbus-1-3 amd64 1.16.2-2ubuntu3 [185 kB]
313s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB]
313s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB]
313s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 ethtool amd64 1:6.15-3build1 [318 kB]
313s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-3.0 amd64 2.87.2-2 [25.2 kB]
313s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-2.0-0 amd64 2.87.2-2 [76.1 kB]
313s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1 amd64 16-20260208-1ubuntu1 [11.4 kB]
313s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-glib-2.0 amd64 2.87.2-2 [182 kB]
319s dpkg-preconfigure: unable to re-open stdin: No such file or directory
319s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-0t64 amd64 2.87.2-2 [1613 kB]
319s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libbpf1 amd64 1:1.6.2-1build1 [184 kB]
319s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 iptables amd64 1.8.11-2ubuntu3 [381 kB]
319s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libip4tc2 amd64 1.8.11-2ubuntu3 [24.2 kB]
319s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libip6tc2 amd64 1.8.11-2ubuntu3 [24.4 kB]
319s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libnetfilter-conntrack3 amd64 1.1.1-1 [47.5 kB]
319s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libxtables12 amd64 1.8.11-2ubuntu3 [36.6 kB]
319s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 iproute2 amd64 6.18.0-1ubuntu1 [1178 kB]
319s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB]
319s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libcryptsetup12 amd64 2:2.8.0-1ubuntu3 [283 kB]
319s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-data all 2.87.2-2 [58.2 kB]
319s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libidn2-0 amd64 2.3.8-4build1 [67.6 kB]
319s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB]
319s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB]
319s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB]
319s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 shared-mime-info amd64 2.4-5build3 [476 kB]
319s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB]
319s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B]
319s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB]
319s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm6t64 amd64 1.26-1build1 [36.5 kB]
319s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB]
319s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libjansson4 amd64 2.14-2build4 [33.2 kB]
319s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 lsof amd64 4.99.4+dfsg-2build2 [239 kB]
319s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsof0 amd64 4.99.4+dfsg-2build2 [56.5 kB]
319s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB]
319s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcap0.8t64 amd64 1.10.5-2ubuntu3 [154 kB]
319s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 pciutils amd64 1:3.14.0-1build2 [95.5 kB]
319s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libpci3 amd64 1:3.14.0-1build2 [38.1 kB]
319s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B]
319s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB]
319s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libusb-1.0-0 amd64 2:1.0.29-2build1 [56.9 kB]
319s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxau6 amd64 1:1.0.11-1build2 [7502 B]
319s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxkbcommon0 amd64 1.13.1-1 [159 kB]
319s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 man-db amd64 2.13.1-1build1 [1392 kB]
319s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 tcpdump amd64 4.99.5-2ubuntu3 [477 kB]
319s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 wget amd64 1.25.0-2ubuntu4 [353 kB]
319s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-standard amd64 1.564 [13.3 kB]
319s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 3cpio amd64 0.14.0-1ubuntu1 [285 kB]
319s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 bpftool amd64 7.7.0+6.19.0-3.3 [1229 kB]
319s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB]
319s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 cryptsetup-bin amd64 2:2.8.0-1ubuntu3 [228 kB]
319s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 dracut-install amd64 109-11ubuntu1 [45.8 kB]
319s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 hwdata all 0.394-1build1 [1566 B]
319s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 pnp.ids all 0.394-1build1 [29.6 kB]
319s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libbrotli1 amd64 1.2.0-3 [343 kB]
319s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB]
319s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10build2 [93.1 kB]
319s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm-compat4t64 amd64 1.26-1build1 [6796 B]
319s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libgudev-1.0-0 amd64 1:238-7build1 [15.9 kB]
319s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B]
319s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libonig5 amd64 6.9.10-1build1 [174 kB]
319s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB]
319s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB]
319s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14 amd64 3.14.2-1 [2568 kB]
319s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 libwrap0 amd64 7.6.q-36build2 [48.5 kB]
319s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-modules-6.19.0-3-generic amd64 6.19.0-3.3 [171 MB]
319s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-6.19.0-3-generic amd64 6.19.0-3.3+1 [16.8 MB]
319s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB]
319s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-generic amd64 6.19.0-3.3 [1698 B]
319s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-generic amd64 6.19.0-3.3 [12.2 kB]
319s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-virtual amd64 6.19.0-3.3 [1700 B]
319s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-virtual amd64 6.19.0-3.3 [12.1 kB]
319s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-virtual amd64 6.19.0-3.3 [1646 B]
319s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3 all 6.19.0-3.3 [14.9 MB]
319s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3-generic amd64 6.19.0-3.3 [4330 kB]
319s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-generic amd64 6.19.0-3.3 [12.0 kB]
319s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-perf amd64 6.19.0-3.3 [4480 kB]
319s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-common all 6.19.0-3.3 [345 kB]
319s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3 amd64 6.19.0-3.3 [1455 kB]
319s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3-generic amd64 6.19.0-3.3 [1612 B]
319s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB]
319s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB]
319s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB]
319s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-kernel-accessories amd64 1.564 [13.1 kB]
319s Fetched 237 MB in 5s (49.0 MB/s)
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319s Preparing to unpack .../debianutils_5.23.2build1_amd64.deb ...
319s Unpacking debianutils (5.23.2build1) over (5.23.2) ...
319s Setting up debianutils (5.23.2build1) ...
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319s Preparing to unpack .../dash_0.5.12-12ubuntu3_amd64.deb ...
319s Unpacking dash (0.5.12-12ubuntu3) over (0.5.12-12ubuntu2) ...
319s Setting up dash (0.5.12-12ubuntu3) ...
319s (Reading database ... 
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319s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ...
319s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ...
319s Setting up findutils (4.10.0-3build2) ...
319s (Reading database ... 
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319s Preparing to unpack .../sed_4.9-2build3_amd64.deb ...
319s Unpacking sed (4.9-2build3) over (4.9-2build2) ...
319s Setting up sed (4.9-2build3) ...
319s (Reading database ... 
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319s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ...
319s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ...
319s Setting up tar (1.35+dfsg-3.1build2) ...
319s (Reading database ... 
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319s Preparing to unpack .../libattr1_1%3a2.5.2-3build2_amd64.deb ...
319s Unpacking libattr1:amd64 (1:2.5.2-3build2) over (1:2.5.2-3build1) ...
319s Setting up libattr1:amd64 (1:2.5.2-3build2) ...
319s Selecting previously unselected package gcc-16-base:amd64.
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319s Preparing to unpack .../gcc-16-base_16-20260208-1ubuntu1_amd64.deb ...
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319s (Reading database ... 
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319s Preparing to unpack .../libgcc-s1_16-20260208-1ubuntu1_amd64.deb ...
319s Unpacking libgcc-s1:amd64 (16-20260208-1ubuntu1) over (15.2.0-12ubuntu1) ...
319s Setting up libgcc-s1:amd64 (16-20260208-1ubuntu1) ...
319s (Reading database ... 
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319s Preparing to unpack .../00-libbsd0_0.12.2-2build2_amd64.deb ...
319s Unpacking libbsd0:amd64 (0.12.2-2build2) over (0.12.2-2build1) ...
319s Preparing to unpack .../01-mawk_1.3.4.20260129-1_amd64.deb ...
319s Unpacking mawk (1.3.4.20260129-1) over (1.3.4.20250131-2) ...
319s Preparing to unpack .../02-libstdc++6_16-20260208-1ubuntu1_amd64.deb ...
319s Unpacking libstdc++6:amd64 (16-20260208-1ubuntu1) over (15.2.0-12ubuntu1) ...
319s Preparing to unpack .../03-libapt-pkg7.0_3.1.15_amd64.deb ...
319s Unpacking libapt-pkg7.0:amd64 (3.1.15) over (3.1.14) ...
319s Preparing to unpack .../04-apt_3.1.15_amd64.deb ...
319s Unpacking apt (3.1.15) over (3.1.14) ...
319s Preparing to unpack .../05-dbus-system-bus-common_1.16.2-2ubuntu3_all.deb ...
319s Unpacking dbus-system-bus-common (1.16.2-2ubuntu3) over (1.16.2-2ubuntu2) ...
319s Preparing to unpack .../06-dbus-session-bus-common_1.16.2-2ubuntu3_all.deb ...
319s Unpacking dbus-session-bus-common (1.16.2-2ubuntu3) over (1.16.2-2ubuntu2) ...
319s Preparing to unpack .../07-dbus-user-session_1.16.2-2ubuntu3_amd64.deb ...
319s Unpacking dbus-user-session (1.16.2-2ubuntu3) over (1.16.2-2ubuntu2) ...
319s Preparing to unpack .../08-dbus-daemon_1.16.2-2ubuntu3_amd64.deb ...
319s Unpacking dbus-daemon (1.16.2-2ubuntu3) over (1.16.2-2ubuntu2) ...
319s Preparing to unpack .../09-dbus-bin_1.16.2-2ubuntu3_amd64.deb ...
319s Unpacking dbus-bin (1.16.2-2ubuntu3) over (1.16.2-2ubuntu2) ...
319s Preparing to unpack .../10-dbus_1.16.2-2ubuntu3_amd64.deb ...
319s Unpacking dbus (1.16.2-2ubuntu3) over (1.16.2-2ubuntu2) ...
319s Preparing to unpack .../11-libdbus-1-3_1.16.2-2ubuntu3_amd64.deb ...
319s Unpacking libdbus-1-3:amd64 (1.16.2-2ubuntu3) over (1.16.2-2ubuntu2) ...
319s Preparing to unpack .../12-libdevmapper1.02.1_2%3a1.02.205-2ubuntu3_amd64.deb ...
319s Unpacking libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) over (2:1.02.205-2ubuntu2) ...
319s Preparing to unpack .../13-dmsetup_2%3a1.02.205-2ubuntu3_amd64.deb ...
319s Unpacking dmsetup (2:1.02.205-2ubuntu3) over (2:1.02.205-2ubuntu2) ...
319s Preparing to unpack .../14-ethtool_1%3a6.15-3build1_amd64.deb ...
319s Unpacking ethtool (1:6.15-3build1) over (1:6.15-3) ...
319s Preparing to unpack .../15-gir1.2-girepository-3.0_2.87.2-2_amd64.deb ...
319s Unpacking gir1.2-girepository-3.0:amd64 (2.87.2-2) over (2.86.3-4) ...
319s Preparing to unpack .../16-libgirepository-2.0-0_2.87.2-2_amd64.deb ...
319s Unpacking libgirepository-2.0-0:amd64 (2.87.2-2) over (2.86.3-4) ...
319s Preparing to unpack .../17-libatomic1_16-20260208-1ubuntu1_amd64.deb ...
319s Unpacking libatomic1:amd64 (16-20260208-1ubuntu1) over (15.2.0-12ubuntu1) ...
319s Preparing to unpack .../18-gir1.2-glib-2.0_2.87.2-2_amd64.deb ...
319s Unpacking gir1.2-glib-2.0:amd64 (2.87.2-2) over (2.86.3-4) ...
319s Preparing to unpack .../19-libglib2.0-0t64_2.87.2-2_amd64.deb ...
319s Unpacking libglib2.0-0t64:amd64 (2.87.2-2) over (2.86.3-4) ...
319s Preparing to unpack .../20-libbpf1_1%3a1.6.2-1build1_amd64.deb ...
319s Unpacking libbpf1:amd64 (1:1.6.2-1build1) over (1:1.6.2-1) ...
319s Preparing to unpack .../21-iptables_1.8.11-2ubuntu3_amd64.deb ...
319s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ...
319s Preparing to unpack .../22-libip4tc2_1.8.11-2ubuntu3_amd64.deb ...
319s Unpacking libip4tc2:amd64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ...
319s Preparing to unpack .../23-libip6tc2_1.8.11-2ubuntu3_amd64.deb ...
319s Unpacking libip6tc2:amd64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ...
319s Preparing to unpack .../24-libnetfilter-conntrack3_1.1.1-1_amd64.deb ...
319s Unpacking libnetfilter-conntrack3:amd64 (1.1.1-1) over (1.1.0-1build1) ...
319s Preparing to unpack .../25-libxtables12_1.8.11-2ubuntu3_amd64.deb ...
319s Unpacking libxtables12:amd64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ...
319s Preparing to unpack .../26-iproute2_6.18.0-1ubuntu1_amd64.deb ...
319s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ...
319s Preparing to unpack .../27-less_668-1build1_amd64.deb ...
319s Unpacking less (668-1build1) over (668-1) ...
319s Preparing to unpack .../28-libcryptsetup12_2%3a2.8.0-1ubuntu3_amd64.deb ...
319s Unpacking libcryptsetup12:amd64 (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ...
319s Preparing to unpack .../29-libglib2.0-data_2.87.2-2_all.deb ...
319s Unpacking libglib2.0-data (2.87.2-2) over (2.86.3-4) ...
319s Preparing to unpack .../30-libidn2-0_2.3.8-4build1_amd64.deb ...
319s Unpacking libidn2-0:amd64 (2.3.8-4build1) over (2.3.8-4) ...
319s Preparing to unpack .../31-libkeyutils1_1.6.3-6ubuntu3_amd64.deb ...
319s Unpacking libkeyutils1:amd64 (1.6.3-6ubuntu3) over (1.6.3-6ubuntu2) ...
319s Preparing to unpack .../32-python3-linkify-it_2.0.3-1ubuntu3_all.deb ...
319s Unpacking python3-linkify-it (2.0.3-1ubuntu3) over (2.0.3-1ubuntu2) ...
319s Preparing to unpack .../33-python3-markdown-it_3.0.0-3build1_all.deb ...
319s Unpacking python3-markdown-it (3.0.0-3build1) over (3.0.0-3) ...
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319s Unpacking shared-mime-info (2.4-5build3) over (2.4-5build2) ...
319s Preparing to unpack .../35-busybox-static_1%3a1.37.0-7ubuntu1_amd64.deb ...
319s Unpacking busybox-static (1:1.37.0-7ubuntu1) over (1:1.37.0-4ubuntu1) ...
319s Preparing to unpack .../36-libdrm-common_2.4.131-1_all.deb ...
319s Unpacking libdrm-common (2.4.131-1) over (2.4.129-1) ...
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319s Unpacking libdrm2:amd64 (2.4.131-1) over (2.4.129-1) ...
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319s Unpacking libgdbm6t64:amd64 (1.26-1build1) over (1.26-1) ...
319s Preparing to unpack .../39-libgpm2_1.20.7-12build1_amd64.deb ...
319s Unpacking libgpm2:amd64 (1.20.7-12build1) over (1.20.7-12) ...
319s Preparing to unpack .../40-libjansson4_2.14-2build4_amd64.deb ...
319s Unpacking libjansson4:amd64 (2.14-2build4) over (2.14-2build3) ...
319s Preparing to unpack .../41-lsof_4.99.4+dfsg-2build2_amd64.deb ...
319s Unpacking lsof (4.99.4+dfsg-2build2) over (4.99.4+dfsg-2build1) ...
319s Preparing to unpack .../42-liblsof0_4.99.4+dfsg-2build2_amd64.deb ...
319s Unpacking liblsof0 (4.99.4+dfsg-2build2) over (4.99.4+dfsg-2build1) ...
319s Preparing to unpack .../43-libmaxminddb0_1.12.2-1build2_amd64.deb ...
319s Unpacking libmaxminddb0:amd64 (1.12.2-1build2) over (1.12.2-1build1) ...
319s Preparing to unpack .../44-libpcap0.8t64_1.10.5-2ubuntu3_amd64.deb ...
319s Unpacking libpcap0.8t64:amd64 (1.10.5-2ubuntu3) over (1.10.5-2ubuntu2) ...
319s Preparing to unpack .../45-pciutils_1%3a3.14.0-1build2_amd64.deb ...
319s Unpacking pciutils (1:3.14.0-1build2) over (1:3.14.0-1build1) ...
319s Preparing to unpack .../46-libpci3_1%3a3.14.0-1build2_amd64.deb ...
319s Unpacking libpci3:amd64 (1:3.14.0-1build2) over (1:3.14.0-1build1) ...
319s Preparing to unpack .../47-libsensors-config_1%3a3.6.2-2build1_all.deb ...
319s Unpacking libsensors-config (1:3.6.2-2build1) over (1:3.6.2-2) ...
319s Preparing to unpack .../48-libsensors5_1%3a3.6.2-2build1_amd64.deb ...
319s Unpacking libsensors5:amd64 (1:3.6.2-2build1) over (1:3.6.2-2) ...
319s Preparing to unpack .../49-libusb-1.0-0_2%3a1.0.29-2build1_amd64.deb ...
319s Unpacking libusb-1.0-0:amd64 (2:1.0.29-2build1) over (2:1.0.29-2) ...
319s Preparing to unpack .../50-libxau6_1%3a1.0.11-1build2_amd64.deb ...
319s Unpacking libxau6:amd64 (1:1.0.11-1build2) over (1:1.0.11-1build1) ...
319s Preparing to unpack .../51-libxkbcommon0_1.13.1-1_amd64.deb ...
319s Unpacking libxkbcommon0:amd64 (1.13.1-1) over (1.12.3-1) ...
319s Preparing to unpack .../52-man-db_2.13.1-1build1_amd64.deb ...
319s Unpacking man-db (2.13.1-1build1) over (2.13.1-1) ...
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319s Unpacking ubuntu-standard (1.564) over (1.563) ...
319s Preparing to unpack .../56-3cpio_0.14.0-1ubuntu1_amd64.deb ...
319s Unpacking 3cpio (0.14.0-1ubuntu1) over (0.13.1-1ubuntu1) ...
319s Preparing to unpack .../57-bpftool_7.7.0+6.19.0-3.3_amd64.deb ...
319s Unpacking bpftool (7.7.0+6.19.0-3.3) over (7.7.0+6.18.0-9.9) ...
320s Preparing to unpack .../58-busybox-initramfs_1%3a1.37.0-7ubuntu1_amd64.deb ...
320s Unpacking busybox-initramfs (1:1.37.0-7ubuntu1) over (1:1.37.0-4ubuntu1) ...
320s Preparing to unpack .../59-cryptsetup-bin_2%3a2.8.0-1ubuntu3_amd64.deb ...
320s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ...
320s Preparing to unpack .../60-dracut-install_109-11ubuntu1_amd64.deb ...
320s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ...
320s Preparing to unpack .../61-hwdata_0.394-1build1_all.deb ...
320s Unpacking hwdata (0.394-1build1) over (0.394-1) ...
320s Preparing to unpack .../62-pnp.ids_0.394-1build1_all.deb ...
320s Unpacking pnp.ids (0.394-1build1) over (0.394-1) ...
320s Preparing to unpack .../63-libbrotli1_1.2.0-3_amd64.deb ...
320s Unpacking libbrotli1:amd64 (1.2.0-3) over (1.1.0-2build6) ...
320s Preparing to unpack .../64-libdrm-amdgpu1_2.4.131-1_amd64.deb ...
320s Unpacking libdrm-amdgpu1:amd64 (2.4.131-1) over (2.4.129-1) ...
320s Preparing to unpack .../65-libevent-core-2.1-7t64_2.1.12-stable-10build2_amd64.deb ...
320s Unpacking libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build2) over (2.1.12-stable-10build1) ...
320s Preparing to unpack .../66-libgdbm-compat4t64_1.26-1build1_amd64.deb ...
320s Unpacking libgdbm-compat4t64:amd64 (1.26-1build1) over (1.26-1) ...
320s Preparing to unpack .../67-libgudev-1.0-0_1%3a238-7build1_amd64.deb ...
320s Unpacking libgudev-1.0-0:amd64 (1:238-7build1) over (1:238-7) ...
320s Preparing to unpack .../68-libnpth0t64_1.8-3build1_amd64.deb ...
320s Unpacking libnpth0t64:amd64 (1.8-3build1) over (1.8-3) ...
320s Preparing to unpack .../69-libonig5_6.9.10-1build1_amd64.deb ...
320s Unpacking libonig5:amd64 (6.9.10-1build1) over (6.9.10-1) ...
320s Selecting previously unselected package libpython3.14-minimal:amd64.
320s Preparing to unpack .../70-libpython3.14-minimal_3.14.2-1_amd64.deb ...
320s Unpacking libpython3.14-minimal:amd64 (3.14.2-1) ...
320s Selecting previously unselected package libpython3.14-stdlib:amd64.
320s Preparing to unpack .../71-libpython3.14-stdlib_3.14.2-1_amd64.deb ...
320s Unpacking libpython3.14-stdlib:amd64 (3.14.2-1) ...
320s Selecting previously unselected package libpython3.14:amd64.
320s Preparing to unpack .../72-libpython3.14_3.14.2-1_amd64.deb ...
320s Unpacking libpython3.14:amd64 (3.14.2-1) ...
320s Preparing to unpack .../73-libwrap0_7.6.q-36build2_amd64.deb ...
320s Unpacking libwrap0:amd64 (7.6.q-36build2) over (7.6.q-36build1) ...
320s Selecting previously unselected package linux-modules-6.19.0-3-generic.
320s Preparing to unpack .../74-linux-modules-6.19.0-3-generic_6.19.0-3.3_amd64.deb ...
320s Unpacking linux-modules-6.19.0-3-generic (6.19.0-3.3) ...
321s Selecting previously unselected package linux-image-6.19.0-3-generic.
321s Preparing to unpack .../75-linux-image-6.19.0-3-generic_6.19.0-3.3+1_amd64.deb ...
321s Unpacking linux-image-6.19.0-3-generic (6.19.0-3.3+1) ...
321s Preparing to unpack .../76-amd64-microcode_3.20251202.1ubuntu1_amd64.deb ...
321s Unpacking amd64-microcode (3.20251202.1ubuntu1) over (3.20250708.1ubuntu1) ...
321s Preparing to unpack .../77-linux-generic_6.19.0-3.3_amd64.deb ...
321s Unpacking linux-generic (6.19.0-3.3) over (6.18.0-9.9+1) ...
321s Preparing to unpack .../78-linux-image-generic_6.19.0-3.3_amd64.deb ...
321s Unpacking linux-image-generic (6.19.0-3.3) over (6.18.0-9.9+1) ...
321s Preparing to unpack .../79-linux-virtual_6.19.0-3.3_amd64.deb ...
321s Unpacking linux-virtual (6.19.0-3.3) over (6.18.0-9.9+1) ...
321s Preparing to unpack .../80-linux-image-virtual_6.19.0-3.3_amd64.deb ...
321s Unpacking linux-image-virtual (6.19.0-3.3) over (6.18.0-9.9+1) ...
321s Preparing to unpack .../81-linux-headers-virtual_6.19.0-3.3_amd64.deb ...
321s Unpacking linux-headers-virtual (6.19.0-3.3) over (6.18.0-9.9+1) ...
321s Selecting previously unselected package linux-headers-6.19.0-3.
321s Preparing to unpack .../82-linux-headers-6.19.0-3_6.19.0-3.3_all.deb ...
321s Unpacking linux-headers-6.19.0-3 (6.19.0-3.3) ...
322s Selecting previously unselected package linux-headers-6.19.0-3-generic.
322s Preparing to unpack .../83-linux-headers-6.19.0-3-generic_6.19.0-3.3_amd64.deb ...
322s Unpacking linux-headers-6.19.0-3-generic (6.19.0-3.3) ...
323s Preparing to unpack .../84-linux-headers-generic_6.19.0-3.3_amd64.deb ...
323s Unpacking linux-headers-generic (6.19.0-3.3) over (6.18.0-9.9+1) ...
323s Preparing to unpack .../85-linux-perf_6.19.0-3.3_amd64.deb ...
323s Unpacking linux-perf (6.19.0-3.3) over (6.18.0-9.9) ...
323s Preparing to unpack .../86-linux-tools-common_6.19.0-3.3_all.deb ...
323s Unpacking linux-tools-common (6.19.0-3.3) over (6.18.0-9.9) ...
323s Selecting previously unselected package linux-tools-6.19.0-3.
323s Preparing to unpack .../87-linux-tools-6.19.0-3_6.19.0-3.3_amd64.deb ...
323s Unpacking linux-tools-6.19.0-3 (6.19.0-3.3) ...
323s Selecting previously unselected package linux-tools-6.19.0-3-generic.
323s Preparing to unpack .../88-linux-tools-6.19.0-3-generic_6.19.0-3.3_amd64.deb ...
323s Unpacking linux-tools-6.19.0-3-generic (6.19.0-3.3) ...
323s Preparing to unpack .../89-patch_2.8-2build1_amd64.deb ...
323s Unpacking patch (2.8-2build1) over (2.8-2) ...
323s Preparing to unpack .../90-pollinate_4.33-4ubuntu5_all.deb ...
323s Unpacking pollinate (4.33-4ubuntu5) over (4.33-4ubuntu4) ...
323s Preparing to unpack .../91-python3-referencing_0.36.2-1ubuntu2_all.deb ...
323s Unpacking python3-referencing (0.36.2-1ubuntu2) over (0.36.2-1ubuntu1) ...
323s Preparing to unpack .../92-ubuntu-kernel-accessories_1.564_amd64.deb ...
323s Unpacking ubuntu-kernel-accessories (1.564) over (1.563) ...
323s Setting up libip4tc2:amd64 (1.8.11-2ubuntu3) ...
323s Setting up 3cpio (0.14.0-1ubuntu1) ...
323s Setting up libxau6:amd64 (1:1.0.11-1build2) ...
323s Setting up libnpth0t64:amd64 (1.8-3build1) ...
323s Setting up libkeyutils1:amd64 (1.6.3-6ubuntu3) ...
323s Setting up ubuntu-kernel-accessories (1.564) ...
323s Setting up libgpm2:amd64 (1.20.7-12build1) ...
323s Setting up libgdbm6t64:amd64 (1.26-1build1) ...
323s Setting up linux-modules-6.19.0-3-generic (6.19.0-3.3) ...
324s Setting up libgdbm-compat4t64:amd64 (1.26-1build1) ...
324s Setting up bpftool (7.7.0+6.19.0-3.3) ...
324s Setting up libip6tc2:amd64 (1.8.11-2ubuntu3) ...
324s Setting up liblsof0 (4.99.4+dfsg-2build2) ...
324s Setting up libmaxminddb0:amd64 (1.12.2-1build2) ...
324s Setting up libbrotli1:amd64 (1.2.0-3) ...
324s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ...
324s Setting up libsensors-config (1:3.6.2-2build1) ...
324s Setting up less (668-1build1) ...
324s Setting up linux-headers-6.19.0-3 (6.19.0-3.3) ...
324s Setting up libidn2-0:amd64 (2.3.8-4build1) ...
324s Setting up amd64-microcode (3.20251202.1ubuntu1) ...
324s amd64-microcode: microcode will be updated at next boot
324s Setting up man-db (2.13.1-1build1) ...
324s Updating database of manual pages ...
326s man-db.service is a disabled or a static unit not running, not starting it.
326s Setting up libjansson4:amd64 (2.14-2build4) ...
326s Setting up libglib2.0-data (2.87.2-2) ...
326s Setting up pollinate (4.33-4ubuntu5) ...
336s Setting up busybox-static (1:1.37.0-7ubuntu1) ...
336s Setting up libwrap0:amd64 (7.6.q-36build2) ...
336s Setting up linux-image-6.19.0-3-generic (6.19.0-3.3+1) ...
338s I: /boot/vmlinuz is now a symlink to vmlinuz-6.19.0-3-generic
338s I: /boot/initrd.img is now a symlink to initrd.img-6.19.0-3-generic
338s Setting up libdbus-1-3:amd64 (1.16.2-2ubuntu3) ...
338s Setting up libatomic1:amd64 (16-20260208-1ubuntu1) ...
338s Setting up patch (2.8-2build1) ...
338s Setting up libsensors5:amd64 (1:3.6.2-2build1) ...
338s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ...
338s Setting up libxtables12:amd64 (1.8.11-2ubuntu3) ...
338s Setting up lsof (4.99.4+dfsg-2build2) ...
338s Setting up libpci3:amd64 (1:3.14.0-1build2) ...
338s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ...
338s Setting up dracut-install (109-11ubuntu1) ...
338s Setting up dmsetup (2:1.02.205-2ubuntu3) ...
338s Setting up libnetfilter-conntrack3:amd64 (1.1.1-1) ...
338s Setting up pnp.ids (0.394-1build1) ...
338s Setting up dbus-session-bus-common (1.16.2-2ubuntu3) ...
338s Setting up python3-linkify-it (2.0.3-1ubuntu3) ...
338s Setting up libpcap0.8t64:amd64 (1.10.5-2ubuntu3) ...
338s Setting up libcryptsetup12:amd64 (2:2.8.0-1ubuntu3) ...
338s Setting up mawk (1.3.4.20260129-1) ...
338s Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build2) ...
338s Setting up libusb-1.0-0:amd64 (2:1.0.29-2build1) ...
338s Setting up linux-image-virtual (6.19.0-3.3) ...
338s Setting up dbus-system-bus-common (1.16.2-2ubuntu3) ...
338s Setting up libbsd0:amd64 (0.12.2-2build2) ...
338s Setting up libdrm-common (2.4.131-1) ...
338s Setting up libstdc++6:amd64 (16-20260208-1ubuntu1) ...
338s Setting up dbus-bin (1.16.2-2ubuntu3) ...
338s Setting up libonig5:amd64 (6.9.10-1build1) ...
338s Setting up libbpf1:amd64 (1:1.6.2-1build1) ...
338s Setting up ethtool (1:6.15-3build1) ...
338s Setting up python3-referencing (0.36.2-1ubuntu2) ...
338s Setting up libxkbcommon0:amd64 (1.13.1-1) ...
338s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ...
338s Setting up linux-headers-6.19.0-3-generic (6.19.0-3.3) ...
338s Setting up tcpdump (4.99.5-2ubuntu3) ...
338s Setting up linux-image-generic (6.19.0-3.3) ...
338s Setting up wget (1.25.0-2ubuntu4) ...
338s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ...
338s Setting up iptables (1.8.11-2ubuntu3) ...
338s Setting up iproute2 (6.18.0-1ubuntu1) ...
338s Setting up linux-headers-generic (6.19.0-3.3) ...
338s Setting up dbus-daemon (1.16.2-2ubuntu3) ...
338s Setting up hwdata (0.394-1build1) ...
338s Setting up dbus-user-session (1.16.2-2ubuntu3) ...
338s Setting up libglib2.0-0t64:amd64 (2.87.2-2) ...
338s No schema files found: doing nothing.
338s Setting up dbus (1.16.2-2ubuntu3) ...
338s A reboot is required to replace the running dbus-daemon.
338s Please reboot the system when convenient.
338s Setting up shared-mime-info (2.4-5build3) ...
339s Setting up gir1.2-glib-2.0:amd64 (2.87.2-2) ...
339s Setting up pciutils (1:3.14.0-1build2) ...
339s Setting up python3-markdown-it (3.0.0-3build1) ...
339s Setting up libdrm2:amd64 (2.4.131-1) ...
339s Setting up libpython3.14:amd64 (3.14.2-1) ...
339s Setting up libapt-pkg7.0:amd64 (3.1.15) ...
339s Setting up linux-tools-common (6.19.0-3.3) ...
339s Setting up libgudev-1.0-0:amd64 (1:238-7build1) ...
339s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ...
339s Setting up apt (3.1.15) ...
340s Setting up linux-headers-virtual (6.19.0-3.3) ...
340s Setting up linux-generic (6.19.0-3.3) ...
340s Setting up libgirepository-2.0-0:amd64 (2.87.2-2) ...
340s Setting up linux-tools-6.19.0-3 (6.19.0-3.3) ...
340s Setting up ubuntu-standard (1.564) ...
340s Setting up gir1.2-girepository-3.0:amd64 (2.87.2-2) ...
340s Setting up linux-virtual (6.19.0-3.3) ...
340s Setting up linux-perf (6.19.0-3.3) ...
340s Setting up linux-tools-6.19.0-3-generic (6.19.0-3.3) ...
340s Processing triggers for debianutils (5.23.2build1) ...
340s Processing triggers for install-info (7.2-5) ...
340s Processing triggers for initramfs-tools (0.150ubuntu7) ...
340s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic
344s Processing triggers for libc-bin (2.42-2ubuntu4) ...
344s Processing triggers for linux-image-6.19.0-3-generic (6.19.0-3.3+1) ...
344s /etc/kernel/postinst.d/initramfs-tools:
344s update-initramfs: Generating /boot/initrd.img-6.19.0-3-generic
348s /etc/kernel/postinst.d/zz-update-grub:
348s Sourcing file `/etc/default/grub'
348s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
348s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg'
348s Generating grub configuration file ...
348s Found linux image: /boot/vmlinuz-6.19.0-3-generic
348s Found initrd image: /boot/initrd.img-6.19.0-3-generic
349s Found linux image: /boot/vmlinuz-6.18.0-9-generic
349s Found initrd image: /boot/initrd.img-6.18.0-9-generic
349s Warning: os-prober will not be executed to detect other bootable partitions.
349s Systems on them will not be added to the GRUB boot configuration.
349s Check GRUB_DISABLE_OS_PROBER documentation entry.
349s Adding boot menu entry for UEFI Firmware Settings ...
349s done
349s autopkgtest [05:32:18]: upgrading testbed (apt dist-upgrade and autopurge)
349s Reading package lists...
350s Building dependency tree...
350s Reading state information...
350s Calculating upgrade...
350s The following package was automatically installed and is no longer required:
350s   libpython3.13
350s Use 'sudo apt autoremove' to remove it.
350s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
350s Reading package lists...
350s Building dependency tree...
350s Reading state information...
350s Solving dependencies...
350s The following packages will be REMOVED:
350s   libpython3.13*
350s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded.
350s After this operation, 7599 kB disk space will be freed.
350s (Reading database ... 
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(Reading database ... 125273 files and directories currently installed.)
350s Removing libpython3.13:amd64 (3.13.11-1) ...
350s Processing triggers for libc-bin (2.42-2ubuntu4) ...
351s autopkgtest [05:32:20]: rebooting testbed after setup commands that affected boot
381s Reading package lists...
381s Building dependency tree...
381s Reading state information...
381s Solving dependencies...
382s The following NEW packages will be installed:
382s   build-essential cpp cpp-15 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu
382s   dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
382s   fonts-glyphicons-halflings fonts-mathjax g++ g++-15 g++-15-x86-64-linux-gnu
382s   g++-x86-64-linux-gnu gcc gcc-15 gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu
382s   gfortran gfortran-15 gfortran-15-x86-64-linux-gnu gfortran-x86-64-linux-gnu
382s   icu-devtools libasan8 libblas-dev libblas3 libbz2-dev libc-dev-bin libc6-dev
382s   libcairo2 libcc1-0 libcrypt-dev libdatrie1 libdeflate-dev libdeflate0
382s   libfontconfig1 libgcc-15-dev libgfortran-15-dev libgfortran5 libgomp1
382s   libgraphite2-3 libharfbuzz0b libhwasan0 libice6 libicu-dev libisl23 libitm1
382s   libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev
382s   libjs-bootstrap libjs-highlight.js libjs-jquery libjs-jquery-datatables
382s   libjs-mathjax liblapack-dev liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3
382s   libncurses-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
382s   libpaper-utils libpaper2 libpcre2-16-0 libpcre2-32-0 libpcre2-dev
382s   libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev libquadmath0
382s   libreadline-dev libsharpyuv0 libsm6 libstdc++-15-dev libtcl8.6 libthai-data
382s   libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1 libwebp7
382s   libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 libzstd-dev
382s   linux-libc-dev node-normalize.css pkg-r-autopkgtest pkgconf pkgconf-bin
382s   r-base-core r-base-dev r-cran-base64enc r-cran-cli r-cran-commonmark
382s   r-cran-evaluate r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gtable
382s   r-cran-highr r-cran-isoband r-cran-knitr r-cran-labeling r-cran-lifecycle
382s   r-cran-markdown r-cran-matrixstats r-cran-r6 r-cran-rcolorbrewer
382s   r-cran-rlang r-cran-s7 r-cran-scales r-cran-vctrs r-cran-viridislite
382s   r-cran-withr r-cran-xfun r-cran-yaml rpcsvc-proto unzip x11-common xdg-utils
382s   zip zlib1g-dev
382s 0 upgraded, 138 newly installed, 0 to remove and 0 not upgraded.
382s Need to get 179 MB of archives.
382s After this operation, 567 MB of additional disk space will be used.
382s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libc-dev-bin amd64 2.42-2ubuntu4 [23.3 kB]
382s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-libc-dev amd64 6.19.0-3.3 [1846 kB]
382s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libcrypt-dev amd64 1:4.5.1-1 [122 kB]
382s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 rpcsvc-proto amd64 1.4.3-1build1 [68.3 kB]
382s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libc6-dev amd64 2.42-2ubuntu4 [2207 kB]
382s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1build1 [691 kB]
382s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB]
382s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [12.9 MB]
382s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-12ubuntu1 [1034 B]
382s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B]
382s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB]
382s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 16-20260208-1ubuntu1 [51.2 kB]
382s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 16-20260208-1ubuntu1 [162 kB]
382s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 16-20260208-1ubuntu1 [30.2 kB]
382s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 16-20260208-1ubuntu1 [3182 kB]
383s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 16-20260208-1ubuntu1 [1392 kB]
383s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 16-20260208-1ubuntu1 [2838 kB]
383s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 16-20260208-1ubuntu1 [1238 kB]
383s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 16-20260208-1ubuntu1 [1729 kB]
383s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 16-20260208-1ubuntu1 [155 kB]
383s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-12ubuntu1 [2866 kB]
383s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [25.4 MB]
385s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-12ubuntu1 [530 kB]
385s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B]
385s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B]
385s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-12ubuntu1 [2553 kB]
385s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [14.4 MB]
385s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-12ubuntu1 [25.3 kB]
385s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B]
385s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B]
385s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu2 [5256 B]
385s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 dctrl-tools amd64 2.24-3build4 [104 kB]
385s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB]
385s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB]
385s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB]
385s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB]
385s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.17.1-3ubuntu1 [180 kB]
385s Get:38 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB]
385s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB]
386s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 16-20260208-1ubuntu1 [957 kB]
386s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran-15-dev amd64 15.2.0-12ubuntu1 [973 kB]
386s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [13.6 MB]
386s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15 amd64 15.2.0-12ubuntu1 [18.1 kB]
386s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1014 B]
386s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran amd64 4:15.2.0-4ubuntu1 [1172 B]
386s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 icu-devtools amd64 78.2-1ubuntu1 [214 kB]
386s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB]
386s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas-dev amd64 3.12.1-7ubuntu1 [235 kB]
386s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libbz2-dev amd64 1.0.8-6build2 [36.2 kB]
386s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB]
386s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2ubuntu1 [16.2 kB]
386s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2ubuntu1 [5808 B]
386s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB]
386s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB]
386s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB]
386s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2build1 [51.6 kB]
386s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate-dev amd64 1.23-2build1 [58.8 kB]
386s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB]
386s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.2-1 [519 kB]
386s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB]
386s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1build1 [44.0 kB]
386s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 libicu-dev amd64 78.2-1ubuntu1 [12.5 MB]
386s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu3 [156 kB]
386s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8-dev amd64 2.1.5-4ubuntu3 [300 kB]
386s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu12 [2142 B]
386s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8-dev amd64 8c-2ubuntu12 [1480 B]
386s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-dev amd64 8c-2ubuntu12 [1480 B]
386s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB]
386s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-highlight.js all 10.7.3+dfsg-2 [144 kB]
386s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB]
386s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB]
386s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB]
386s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack-dev amd64 3.12.1-7ubuntu1 [5433 kB]
386s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB]
386s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libncurses-dev amd64 6.6+20251231-1 [389 kB]
386s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.30-1 [155 kB]
386s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.30-1 [19.2 kB]
386s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.57.0-1 [241 kB]
386s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.57.0-1 [53.3 kB]
386s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.57.0-1 [29.0 kB]
386s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3build1 [17.3 kB]
386s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3build1 [15.6 kB]
386s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-16-0 amd64 10.46-1 [243 kB]
386s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-32-0 amd64 10.46-1 [230 kB]
386s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-posix3 amd64 10.46-1 [7354 B]
387s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-dev amd64 10.46-1 [832 kB]
387s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 libpkgconf3 amd64 1.8.1-4build1 [32.8 kB]
387s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu2 [898 kB]
387s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 libpng-dev amd64 1.6.54-1 [273 kB]
387s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 libreadline-dev amd64 8.3-3 [189 kB]
387s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB]
387s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1build1 [16.9 kB]
387s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1build1 [1003 kB]
387s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB]
387s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB]
387s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB]
387s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build2 [45.1 kB]
387s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build4 [7084 B]
387s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB]
387s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB]
387s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 libzstd-dev amd64 1.5.7+dfsg-3 [376 kB]
387s Get:102 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-normalize.css all 8.0.1-5.1 [10.4 kB]
387s Get:103 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu3 [175 kB]
387s Get:104 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-29ubuntu1 [180 kB]
387s Get:105 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB]
387s Get:106 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.2-1ubuntu2 [28.8 MB]
387s Get:107 http://ftpmaster.internal/ubuntu resolute/main amd64 liblzma-dev amd64 5.8.2-2 [179 kB]
387s Get:108 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf-bin amd64 1.8.1-4build1 [21.7 kB]
387s Get:109 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf amd64 1.8.1-4build1 [16.8 kB]
387s Get:110 http://ftpmaster.internal/ubuntu resolute/main amd64 libtirpc-dev amd64 1.3.6+ds-1 [195 kB]
387s Get:111 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-dev all 4.5.2-1ubuntu2 [1880 B]
387s Get:112 http://ftpmaster.internal/ubuntu resolute/universe amd64 pkg-r-autopkgtest all 20250812 [6158 B]
387s Get:113 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-base64enc amd64 0.1-3-3build1 [28.5 kB]
387s Get:114 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB]
387s Get:115 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-commonmark amd64 1.9.5-1 [138 kB]
387s Get:116 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-evaluate all 1.0.5-1 [117 kB]
387s Get:117 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB]
387s Get:118 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB]
387s Get:119 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rlang amd64 1.1.5-3 [1721 kB]
387s Get:120 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB]
387s Get:121 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB]
387s Get:122 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB]
387s Get:123 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-s7 amd64 0.2.0-1 [328 kB]
387s Get:124 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB]
387s Get:125 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB]
387s Get:126 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB]
387s Get:127 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-viridislite all 0.4.3-1 [1088 kB]
387s Get:128 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-scales all 1.4.0-1 [725 kB]
387s Get:129 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB]
387s Get:130 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB]
388s Get:131 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB]
388s Get:132 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xfun amd64 0.55+dfsg-1 [587 kB]
388s Get:133 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB]
388s Get:134 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB]
388s Get:135 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB]
388s Get:136 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-knitr all 1.51+dfsg-1 [847 kB]
388s Get:137 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-markdown all 1.13-1 [162 kB]
388s Get:138 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrixstats amd64 1.5.0-1 [542 kB]
388s Preconfiguring packages ...
388s Fetched 179 MB in 6s (28.4 MB/s)
388s Selecting previously unselected package libc-dev-bin.
388s (Reading database ... 
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(Reading database ... 125269 files and directories currently installed.)
388s Preparing to unpack .../000-libc-dev-bin_2.42-2ubuntu4_amd64.deb ...
388s Unpacking libc-dev-bin (2.42-2ubuntu4) ...
388s Selecting previously unselected package linux-libc-dev:amd64.
388s Preparing to unpack .../001-linux-libc-dev_6.19.0-3.3_amd64.deb ...
388s Unpacking linux-libc-dev:amd64 (6.19.0-3.3) ...
388s Selecting previously unselected package libcrypt-dev:amd64.
388s Preparing to unpack .../002-libcrypt-dev_1%3a4.5.1-1_amd64.deb ...
388s Unpacking libcrypt-dev:amd64 (1:4.5.1-1) ...
388s Selecting previously unselected package rpcsvc-proto.
388s Preparing to unpack .../003-rpcsvc-proto_1.4.3-1build1_amd64.deb ...
388s Unpacking rpcsvc-proto (1.4.3-1build1) ...
388s Selecting previously unselected package libc6-dev:amd64.
388s Preparing to unpack .../004-libc6-dev_2.42-2ubuntu4_amd64.deb ...
388s Unpacking libc6-dev:amd64 (2.42-2ubuntu4) ...
388s Selecting previously unselected package libisl23:amd64.
388s Preparing to unpack .../005-libisl23_0.27-1build1_amd64.deb ...
388s Unpacking libisl23:amd64 (0.27-1build1) ...
388s Selecting previously unselected package libmpc3:amd64.
388s Preparing to unpack .../006-libmpc3_1.3.1-2_amd64.deb ...
388s Unpacking libmpc3:amd64 (1.3.1-2) ...
388s Selecting previously unselected package cpp-15-x86-64-linux-gnu.
388s Preparing to unpack .../007-cpp-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ...
388s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
389s Selecting previously unselected package cpp-15.
389s Preparing to unpack .../008-cpp-15_15.2.0-12ubuntu1_amd64.deb ...
389s Unpacking cpp-15 (15.2.0-12ubuntu1) ...
389s Selecting previously unselected package cpp-x86-64-linux-gnu.
389s Preparing to unpack .../009-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ...
389s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
389s Selecting previously unselected package cpp.
389s Preparing to unpack .../010-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ...
389s Unpacking cpp (4:15.2.0-4ubuntu1) ...
389s Selecting previously unselected package libcc1-0:amd64.
389s Preparing to unpack .../011-libcc1-0_16-20260208-1ubuntu1_amd64.deb ...
389s Unpacking libcc1-0:amd64 (16-20260208-1ubuntu1) ...
389s Selecting previously unselected package libgomp1:amd64.
389s Preparing to unpack .../012-libgomp1_16-20260208-1ubuntu1_amd64.deb ...
389s Unpacking libgomp1:amd64 (16-20260208-1ubuntu1) ...
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392s Setting up libgraphite2-3:amd64 (1.3.14-11ubuntu1) ...
392s Setting up libpixman-1-0:amd64 (0.46.4-1) ...
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392s Setting up libzstd-dev:amd64 (1.5.7+dfsg-3) ...
392s Setting up libjs-mathjax (2.7.9+dfsg-1build1) ...
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392s Setting up unzip (6.0-29ubuntu1) ...
392s Setting up x11-common (1:7.7+24ubuntu1) ...
392s Setting up libdeflate0:amd64 (1.23-2build1) ...
392s Setting up linux-libc-dev:amd64 (6.19.0-3.3) ...
392s Setting up libxcb-shm0:amd64 (1.17.0-2ubuntu1) ...
392s Setting up libgomp1:amd64 (16-20260208-1ubuntu1) ...
392s Setting up libjbig0:amd64 (2.1-6.1ubuntu3) ...
392s Setting up libpcre2-16-0:amd64 (10.46-1) ...
392s Setting up zip (3.0-15ubuntu3) ...
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392s Setting up libblas3:amd64 (3.12.1-7ubuntu1) ...
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392s Setting up libtcl8.6:amd64 (8.6.17+dfsg-1build1) ...
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392s Setting up pkgconf-bin (1.8.1-4build1) ...
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392s Setting up libgfortran5:amd64 (16-20260208-1ubuntu1) ...
392s Setting up libwebp7:amd64 (1.5.0-0.1build1) ...
392s Setting up liblzma-dev:amd64 (5.8.2-2) ...
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392s Setting up libjs-highlight.js (10.7.3+dfsg-2) ...
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392s Setting up libasan8:amd64 (16-20260208-1ubuntu1) ...
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393s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
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393s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode
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393s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
393s Setting up libgcc-15-dev:amd64 (15.2.0-12ubuntu1) ...
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393s Setting up gcc-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
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393s Setting up libbz2-dev:amd64 (1.0.8-6build2) ...
393s Setting up cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
393s Setting up gfortran-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
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395s Regenerating fonts cache... done.
395s Setting up libjpeg-turbo8-dev:amd64 (2.1.5-4ubuntu3) ...
395s Setting up libxft2:amd64 (2.3.6-1build2) ...
395s Setting up libncurses-dev:amd64 (6.6+20251231-1) ...
395s Setting up libpcre2-dev:amd64 (10.46-1) ...
395s Setting up gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
395s Setting up libtk8.6:amd64 (8.6.17-1) ...
395s Setting up libpango-1.0-0:amd64 (1.57.0-1) ...
395s Setting up libreadline-dev:amd64 (8.3-3) ...
395s Setting up gfortran-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
395s Setting up libcairo2:amd64 (1.18.4-3) ...
395s Setting up gcc-15 (15.2.0-12ubuntu1) ...
395s Setting up libstdc++-15-dev:amd64 (15.2.0-12ubuntu1) ...
395s Setting up libxt6t64:amd64 (1:1.2.1-1.3) ...
395s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu2) ...
395s Setting up cpp (4:15.2.0-4ubuntu1) ...
395s Setting up libpangoft2-1.0-0:amd64 (1.57.0-1) ...
395s Setting up libjpeg8-dev:amd64 (8c-2ubuntu12) ...
395s Setting up gfortran-15 (15.2.0-12ubuntu1) ...
395s Setting up libpangocairo-1.0-0:amd64 (1.57.0-1) ...
395s Setting up g++-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
395s Setting up libpng-dev:amd64 (1.6.54-1) ...
395s Setting up libjpeg-dev:amd64 (8c-2ubuntu12) ...
395s Setting up gcc (4:15.2.0-4ubuntu1) ...
395s Setting up r-base-core (4.5.2-1ubuntu2) ...
395s Creating config file /etc/R/Renviron with new version
395s Setting up r-cran-labeling (0.4.3-1) ...
395s Setting up r-cran-farver (2.1.2-1) ...
395s Setting up r-cran-viridislite (0.4.3-1) ...
395s Setting up g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
395s Setting up r-cran-commonmark (1.9.5-1) ...
395s Setting up r-cran-r6 (2.6.1-1) ...
395s Setting up g++-15 (15.2.0-12ubuntu1) ...
395s Setting up r-cran-rlang (1.1.5-3) ...
395s Setting up r-cran-matrixstats (1.5.0-1) ...
395s Setting up r-cran-xfun (0.55+dfsg-1) ...
395s Setting up r-cran-withr (3.0.2+dfsg-1) ...
395s Setting up r-cran-base64enc (0.1-3-3build1) ...
395s Setting up r-cran-yaml (2.3.10-1) ...
395s Setting up r-cran-evaluate (1.0.5-1) ...
395s Setting up r-cran-highr (0.11+dfsg-1) ...
395s Setting up r-cran-glue (1.8.0-1) ...
395s Setting up r-cran-cli (3.6.4-1) ...
395s Setting up gfortran (4:15.2.0-4ubuntu1) ...
395s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
395s 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
395s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
395s 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
395s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ...
395s Setting up r-cran-markdown (1.13-1) ...
395s Setting up r-cran-s7 (0.2.0-1) ...
395s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ...
395s Setting up r-cran-isoband (0.2.7-1) ...
395s Setting up r-cran-scales (1.4.0-1) ...
395s Setting up r-cran-gtable (0.3.6+dfsg-1) ...
395s Setting up r-cran-knitr (1.51+dfsg-1) ...
395s Setting up g++ (4:15.2.0-4ubuntu1) ...
395s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
395s Setting up build-essential (12.12ubuntu2) ...
395s Setting up r-cran-vctrs (0.6.5-1) ...
395s Setting up r-base-dev (4.5.2-1ubuntu2) ...
395s Setting up r-cran-ggplot2 (4.0.2+dfsg-1) ...
395s Setting up pkg-r-autopkgtest (20250812) ...
395s Processing triggers for libc-bin (2.42-2ubuntu4) ...
395s Processing triggers for man-db (2.13.1-1build1) ...
396s Processing triggers for install-info (7.2-5) ...
397s autopkgtest [05:33:06]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
397s autopkgtest [05:33:06]: test pkg-r-autopkgtest: [-----------------------
398s Test: Try to load the R library matrixStats
398s 
398s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
398s Copyright (C) 2025 The R Foundation for Statistical Computing
398s Platform: x86_64-pc-linux-gnu
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 
398s > library('matrixStats')
398s > 
398s autopkgtest [05:33:07]: test pkg-r-autopkgtest: -----------------------]
398s autopkgtest [05:33:07]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
398s pkg-r-autopkgtest    PASS
399s autopkgtest [05:33:08]: @@@@@@@@@@@@@@@@@@@@ summary
399s run-unit-test        PASS
399s pkg-r-autopkgtest    PASS