0s autopkgtest [17:42:49]: starting date and time: 2024-03-22 17:42:49+0000 0s autopkgtest [17:42:49]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [17:42:49]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.e4it8803/out --timeout-copy=6000 -a i386 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:r-base --apt-upgrade r-cran-gparotation --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-59.secgroup --name adt-noble-i386-r-cran-gparotation-20240322-174249-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 127s autopkgtest [17:44:56]: testbed dpkg architecture: amd64 127s autopkgtest [17:44:56]: testbed apt version: 2.7.12 127s autopkgtest [17:44:56]: test architecture: i386 127s autopkgtest [17:44:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup 127s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 127s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB] 128s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [55.8 kB] 128s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 128s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3883 kB] 128s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [697 kB] 128s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [462 kB] 128s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B] 128s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [30.5 kB] 128s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6700 B] 128s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B] 128s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1286 kB] 128s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4250 kB] 128s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B] 128s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [26.8 kB] 128s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [93.7 kB] 128s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B] 131s Fetched 11.4 MB in 1s (7836 kB/s) 131s Reading package lists... 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 133s Calculating upgrade... 134s The following packages will be upgraded: 134s cloud-init fonts-ubuntu-console python3-markupsafe 134s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 134s Need to get 629 kB of archives. 134s After this operation, 11.3 kB disk space will be freed. 134s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB] 134s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 python3-markupsafe amd64 2.1.5-1build1 [12.6 kB] 134s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 cloud-init all 24.1.2-0ubuntu1 [597 kB] 134s Preconfiguring packages ... 134s Fetched 629 kB in 0s (24.1 MB/s) 134s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 71865 files and directories currently installed.) 134s Preparing to unpack .../fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ... 134s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ... 134s Preparing to unpack .../python3-markupsafe_2.1.5-1build1_amd64.deb ... 134s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ... 134s Preparing to unpack .../cloud-init_24.1.2-0ubuntu1_all.deb ... 135s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ... 135s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ... 135s Setting up cloud-init (24.1.2-0ubuntu1) ... 136s Setting up python3-markupsafe (2.1.5-1build1) ... 136s Processing triggers for man-db (2.12.0-3) ... 137s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 137s Reading package lists... 138s Building dependency tree... 138s Reading state information... 138s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 138s sh: Attempting to set up Debian/Ubuntu apt sources automatically 138s sh: Distribution appears to be Ubuntu 139s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s eatmydata is already the newest version (131-1). 140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 141s dbus is already the newest version (1.14.10-4ubuntu1). 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 141s rng-tools-debian is already the newest version (2.4). 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Reading package lists... 142s Building dependency tree... 142s Reading state information... 142s The following packages will be REMOVED: 142s cloud-init* python3-configobj* python3-debconf* 142s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 142s After this operation, 3256 kB disk space will be freed. 143s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 71864 files and directories currently installed.) 143s Removing cloud-init (24.1.2-0ubuntu1) ... 143s Removing python3-configobj (5.0.8-3) ... 143s Removing python3-debconf (1.5.86) ... 143s Processing triggers for man-db (2.12.0-3) ... 144s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 71475 files and directories currently installed.) 144s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 144s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 144s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 144s invoke-rc.d: policy-rc.d denied execution of try-restart. 144s Reading package lists... 145s Building dependency tree... 145s Reading state information... 145s linux-generic is already the newest version (6.8.0-11.11+1). 145s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 145s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 145s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 145s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 147s Reading package lists... 147s Reading package lists... 148s Building dependency tree... 148s Reading state information... 148s Calculating upgrade... 148s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 149s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s autopkgtest [17:45:18]: rebooting testbed after setup commands that affected boot 291s autopkgtest [17:47:40]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024 291s autopkgtest [17:47:40]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-gparotation 292s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-gparotation 2024.2-1-1 (dsc) [2135 B] 292s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-gparotation 2024.2-1-1 (tar) [311 kB] 292s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-gparotation 2024.2-1-1 (diff) [2472 B] 292s gpgv: Signature made Tue Feb 13 13:51:00 2024 UTC 292s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 292s gpgv: issuer "tille@debian.org" 292s gpgv: Can't check signature: No public key 292s dpkg-source: warning: cannot verify inline signature for ./r-cran-gparotation_2024.2-1-1.dsc: no acceptable signature found 293s autopkgtest [17:47:42]: testing package r-cran-gparotation version 2024.2-1-1 293s autopkgtest [17:47:42]: build not needed 294s autopkgtest [17:47:43]: test run-unit-test: preparing testbed 297s Note, using file '/tmp/autopkgtest.lANRY3/1-autopkgtest-satdep.dsc' to get the build dependencies 297s Reading package lists... 297s Building dependency tree... 297s Reading state information... 298s Starting pkgProblemResolver with broken count: 0 298s Starting 2 pkgProblemResolver with broken count: 0 298s Done 298s The following NEW packages will be installed: 298s build-essential cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu 298s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono g++ g++-13 298s g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-13 298s gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu libasan8 libatomic1 libblas3 298s libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libdatrie1 298s libdeflate0 libfontconfig1 libgcc-13-dev libgfortran5 libgomp1 298s libgraphite2-3 libharfbuzz0b libhwasan0 libice6 libisl23 libitm1 libjbig0 298s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 liblsan0 libmpc3 libnsl-dev 298s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 298s libpaper1 libpixman-1-0 libquadmath0 libsharpyuv0 libsm6 libstdc++-13-dev 298s libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 298s libubsan1 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 298s libxt6 linux-libc-dev r-base-core r-cran-gparotation rpcsvc-proto unzip 298s x11-common xdg-utils zip 299s 0 upgraded, 78 newly installed, 0 to remove and 0 not upgraded. 299s Need to get 105 MB of archives. 299s After this operation, 323 MB of additional disk space will be used. 299s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.39-0ubuntu2 [20.4 kB] 299s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB] 299s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB] 299s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-dev amd64 1.3.4+ds-1build1 [222 kB] 299s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl-dev amd64 1.3.0-3 [71.2 kB] 299s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu6 [68.5 kB] 299s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.39-0ubuntu2 [2126 kB] 299s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libisl23 amd64 0.26-3 [741 kB] 299s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libmpc3 amd64 1.3.1-1 [54.1 kB] 299s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.2 MB] 299s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-17ubuntu2 [1030 B] 299s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] 299s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] 299s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 14-20240303-1ubuntu1 [47.7 kB] 299s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240303-1ubuntu1 [147 kB] 299s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240303-1ubuntu1 [29.1 kB] 299s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240303-1ubuntu1 [10.4 kB] 299s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240303-1ubuntu1 [3026 kB] 299s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240303-1ubuntu1 [1310 kB] 299s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240303-1ubuntu1 [2732 kB] 299s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240303-1ubuntu1 [1172 kB] 299s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240303-1ubuntu1 [1629 kB] 299s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240303-1ubuntu1 [155 kB] 299s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-17ubuntu2 [2687 kB] 299s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [21.9 MB] 299s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-17ubuntu2 [477 kB] 299s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] 299s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] 299s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-17ubuntu2 [2340 kB] 299s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [12.5 MB] 299s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-17ubuntu2 [14.5 kB] 299s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] 299s Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] 299s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 299s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 299s Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 299s Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig-config amd64 2.15.0-1ubuntu1 [36.9 kB] 299s Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 libfontconfig1 amd64 2.15.0-1ubuntu1 [139 kB] 299s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig amd64 2.15.0-1ubuntu1 [180 kB] 299s Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.12.0-3 [238 kB] 299s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libpixman-1-0 amd64 0.42.2-1 [268 kB] 299s Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-render0 amd64 1.15-1 [16.3 kB] 299s Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-shm0 amd64 1.15-1 [5740 B] 299s Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB] 299s Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 libcairo2 amd64 1.18.0-1 [572 kB] 299s Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 libdatrie1 amd64 0.2.13-3 [20.9 kB] 299s Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate0 amd64 1.19-1 [43.7 kB] 299s Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran5 amd64 14-20240303-1ubuntu1 [924 kB] 299s Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 libgraphite2-3 amd64 1.3.14-2 [83.1 kB] 299s Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 libharfbuzz0b amd64 8.3.0-2 [469 kB] 299s Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 299s Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libice6 amd64 2:1.0.10-1build2 [42.6 kB] 299s Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu1 [147 kB] 299s Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 299s Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.12.0-3 [2649 kB] 299s Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu1 [184 kB] 299s Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 libthai-data all 0.1.29-2 [158 kB] 299s Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 libthai0 amd64 0.1.29-2 [18.8 kB] 299s Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 libpango-1.0-0 amd64 1.51.0+ds-4 [228 kB] 299s Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 libpangoft2-1.0-0 amd64 1.51.0+ds-4 [42.1 kB] 299s Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 libpangocairo-1.0-0 amd64 1.51.0+ds-4 [29.0 kB] 299s Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper1 amd64 1.1.29 [13.4 kB] 299s Get:63 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper-utils amd64 1.1.29 [8658 B] 299s Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 libsharpyuv0 amd64 1.3.2-0.4 [15.6 kB] 299s Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 libsm6 amd64 2:1.2.3-1build2 [16.7 kB] 299s Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [984 kB] 299s Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 libjbig0 amd64 2.1-6.1ubuntu1 [29.3 kB] 299s Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 libwebp7 amd64 1.3.2-0.4 [230 kB] 299s Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 libtiff6 amd64 4.5.1+git230720-3ubuntu1 [232 kB] 299s Get:70 http://ftpmaster.internal/ubuntu noble/main amd64 libxft2 amd64 2.3.6-1 [44.5 kB] 299s Get:71 http://ftpmaster.internal/ubuntu noble/main amd64 libxss1 amd64 1:1.2.3-1build2 [8476 B] 299s Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 libtk8.6 amd64 8.6.13-2 [776 kB] 299s Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 libxt6 amd64 1:1.2.1-1.1 [173 kB] 299s Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 zip amd64 3.0-13 [176 kB] 299s Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 unzip amd64 6.0-28ubuntu3 [174 kB] 299s Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 299s Get:77 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-core amd64 4.3.2-1build1 [27.0 MB] 299s Get:78 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-gparotation all 2024.2-1-1 [407 kB] 300s Preconfiguring packages ... 300s Fetched 105 MB in 1s (129 MB/s) 300s Selecting previously unselected package libc-dev-bin. 300s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 71420 files and directories currently installed.) 300s Preparing to unpack .../00-libc-dev-bin_2.39-0ubuntu2_amd64.deb ... 300s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 300s Selecting previously unselected package linux-libc-dev:amd64. 300s Preparing to unpack .../01-linux-libc-dev_6.8.0-11.11_amd64.deb ... 300s Unpacking linux-libc-dev:amd64 (6.8.0-11.11) ... 300s Selecting previously unselected package libcrypt-dev:amd64. 300s Preparing to unpack .../02-libcrypt-dev_1%3a4.4.36-4_amd64.deb ... 300s Unpacking libcrypt-dev:amd64 (1:4.4.36-4) ... 300s Selecting previously unselected package libtirpc-dev:amd64. 300s Preparing to unpack .../03-libtirpc-dev_1.3.4+ds-1build1_amd64.deb ... 300s Unpacking libtirpc-dev:amd64 (1.3.4+ds-1build1) ... 300s Selecting previously unselected package libnsl-dev:amd64. 300s Preparing to unpack .../04-libnsl-dev_1.3.0-3_amd64.deb ... 300s Unpacking libnsl-dev:amd64 (1.3.0-3) ... 300s Selecting previously unselected package rpcsvc-proto. 300s Preparing to unpack .../05-rpcsvc-proto_1.4.2-0ubuntu6_amd64.deb ... 300s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 300s Selecting previously unselected package libc6-dev:amd64. 301s Preparing to unpack .../06-libc6-dev_2.39-0ubuntu2_amd64.deb ... 301s Unpacking libc6-dev:amd64 (2.39-0ubuntu2) ... 301s Selecting previously unselected package libisl23:amd64. 301s Preparing to unpack .../07-libisl23_0.26-3_amd64.deb ... 301s Unpacking libisl23:amd64 (0.26-3) ... 301s Selecting previously unselected package libmpc3:amd64. 301s Preparing to unpack .../08-libmpc3_1.3.1-1_amd64.deb ... 301s Unpacking libmpc3:amd64 (1.3.1-1) ... 301s Selecting previously unselected package cpp-13-x86-64-linux-gnu. 301s Preparing to unpack .../09-cpp-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 301s Unpacking cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 301s Selecting previously unselected package cpp-13. 301s Preparing to unpack .../10-cpp-13_13.2.0-17ubuntu2_amd64.deb ... 301s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 301s Selecting previously unselected package cpp-x86-64-linux-gnu. 301s Preparing to unpack .../11-cpp-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 301s Unpacking cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 301s Selecting previously unselected package cpp. 301s Preparing to unpack .../12-cpp_4%3a13.2.0-7ubuntu1_amd64.deb ... 301s Unpacking cpp (4:13.2.0-7ubuntu1) ... 301s Selecting previously unselected package libcc1-0:amd64. 301s Preparing to unpack .../13-libcc1-0_14-20240303-1ubuntu1_amd64.deb ... 301s Unpacking libcc1-0:amd64 (14-20240303-1ubuntu1) ... 301s Selecting previously unselected package libgomp1:amd64. 301s Preparing to unpack .../14-libgomp1_14-20240303-1ubuntu1_amd64.deb ... 301s Unpacking libgomp1:amd64 (14-20240303-1ubuntu1) ... 301s Selecting previously unselected package libitm1:amd64. 301s Preparing to unpack .../15-libitm1_14-20240303-1ubuntu1_amd64.deb ... 301s Unpacking libitm1:amd64 (14-20240303-1ubuntu1) ... 301s Selecting previously unselected package libatomic1:amd64. 301s Preparing to unpack .../16-libatomic1_14-20240303-1ubuntu1_amd64.deb ... 301s Unpacking libatomic1:amd64 (14-20240303-1ubuntu1) ... 301s Selecting previously unselected package libasan8:amd64. 301s Preparing to unpack .../17-libasan8_14-20240303-1ubuntu1_amd64.deb ... 301s Unpacking libasan8:amd64 (14-20240303-1ubuntu1) ... 301s Selecting previously unselected package liblsan0:amd64. 301s Preparing to unpack .../18-liblsan0_14-20240303-1ubuntu1_amd64.deb ... 301s Unpacking liblsan0:amd64 (14-20240303-1ubuntu1) ... 301s Selecting previously unselected package libtsan2:amd64. 301s Preparing to unpack .../19-libtsan2_14-20240303-1ubuntu1_amd64.deb ... 301s Unpacking libtsan2:amd64 (14-20240303-1ubuntu1) ... 301s Selecting previously unselected package libubsan1:amd64. 301s Preparing to unpack .../20-libubsan1_14-20240303-1ubuntu1_amd64.deb ... 301s Unpacking libubsan1:amd64 (14-20240303-1ubuntu1) ... 301s Selecting previously unselected package libhwasan0:amd64. 301s Preparing to unpack .../21-libhwasan0_14-20240303-1ubuntu1_amd64.deb ... 301s Unpacking libhwasan0:amd64 (14-20240303-1ubuntu1) ... 302s Selecting previously unselected package libquadmath0:amd64. 302s Preparing to unpack .../22-libquadmath0_14-20240303-1ubuntu1_amd64.deb ... 302s Unpacking libquadmath0:amd64 (14-20240303-1ubuntu1) ... 302s Selecting previously unselected package libgcc-13-dev:amd64. 302s Preparing to unpack .../23-libgcc-13-dev_13.2.0-17ubuntu2_amd64.deb ... 302s Unpacking libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ... 302s Selecting previously unselected package gcc-13-x86-64-linux-gnu. 302s Preparing to unpack .../24-gcc-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 302s Unpacking gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 302s Selecting previously unselected package gcc-13. 302s Preparing to unpack .../25-gcc-13_13.2.0-17ubuntu2_amd64.deb ... 302s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 302s Selecting previously unselected package gcc-x86-64-linux-gnu. 302s Preparing to unpack .../26-gcc-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 302s Unpacking gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 302s Selecting previously unselected package gcc. 302s Preparing to unpack .../27-gcc_4%3a13.2.0-7ubuntu1_amd64.deb ... 302s Unpacking gcc (4:13.2.0-7ubuntu1) ... 302s Selecting previously unselected package libstdc++-13-dev:amd64. 302s Preparing to unpack .../28-libstdc++-13-dev_13.2.0-17ubuntu2_amd64.deb ... 302s Unpacking libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ... 303s Selecting previously unselected package g++-13-x86-64-linux-gnu. 303s Preparing to unpack .../29-g++-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 303s Unpacking g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 303s Selecting previously unselected package g++-13. 303s Preparing to unpack .../30-g++-13_13.2.0-17ubuntu2_amd64.deb ... 303s Unpacking g++-13 (13.2.0-17ubuntu2) ... 303s Selecting previously unselected package g++-x86-64-linux-gnu. 303s Preparing to unpack .../31-g++-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 303s Unpacking g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 303s Selecting previously unselected package g++. 303s Preparing to unpack .../32-g++_4%3a13.2.0-7ubuntu1_amd64.deb ... 303s Unpacking g++ (4:13.2.0-7ubuntu1) ... 303s Selecting previously unselected package build-essential. 303s Preparing to unpack .../33-build-essential_12.10ubuntu1_amd64.deb ... 303s Unpacking build-essential (12.10ubuntu1) ... 303s Selecting previously unselected package fonts-dejavu-mono. 303s Preparing to unpack .../34-fonts-dejavu-mono_2.37-8_all.deb ... 303s Unpacking fonts-dejavu-mono (2.37-8) ... 303s Selecting previously unselected package fonts-dejavu-core. 303s Preparing to unpack .../35-fonts-dejavu-core_2.37-8_all.deb ... 303s Unpacking fonts-dejavu-core (2.37-8) ... 303s Selecting previously unselected package fontconfig-config. 303s Preparing to unpack .../36-fontconfig-config_2.15.0-1ubuntu1_amd64.deb ... 303s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 303s Selecting previously unselected package libfontconfig1:amd64. 303s Preparing to unpack .../37-libfontconfig1_2.15.0-1ubuntu1_amd64.deb ... 303s Unpacking libfontconfig1:amd64 (2.15.0-1ubuntu1) ... 303s Selecting previously unselected package fontconfig. 303s Preparing to unpack .../38-fontconfig_2.15.0-1ubuntu1_amd64.deb ... 303s Unpacking fontconfig (2.15.0-1ubuntu1) ... 303s Selecting previously unselected package libblas3:amd64. 303s Preparing to unpack .../39-libblas3_3.12.0-3_amd64.deb ... 303s Unpacking libblas3:amd64 (3.12.0-3) ... 303s Selecting previously unselected package libpixman-1-0:amd64. 303s Preparing to unpack .../40-libpixman-1-0_0.42.2-1_amd64.deb ... 303s Unpacking libpixman-1-0:amd64 (0.42.2-1) ... 304s Selecting previously unselected package libxcb-render0:amd64. 304s Preparing to unpack .../41-libxcb-render0_1.15-1_amd64.deb ... 304s Unpacking libxcb-render0:amd64 (1.15-1) ... 304s Selecting previously unselected package libxcb-shm0:amd64. 304s Preparing to unpack .../42-libxcb-shm0_1.15-1_amd64.deb ... 304s Unpacking libxcb-shm0:amd64 (1.15-1) ... 304s Selecting previously unselected package libxrender1:amd64. 304s Preparing to unpack .../43-libxrender1_1%3a0.9.10-1.1_amd64.deb ... 304s Unpacking libxrender1:amd64 (1:0.9.10-1.1) ... 304s Selecting previously unselected package libcairo2:amd64. 304s Preparing to unpack .../44-libcairo2_1.18.0-1_amd64.deb ... 304s Unpacking libcairo2:amd64 (1.18.0-1) ... 304s Selecting previously unselected package libdatrie1:amd64. 304s Preparing to unpack .../45-libdatrie1_0.2.13-3_amd64.deb ... 304s Unpacking libdatrie1:amd64 (0.2.13-3) ... 304s Selecting previously unselected package libdeflate0:amd64. 304s Preparing to unpack .../46-libdeflate0_1.19-1_amd64.deb ... 304s Unpacking libdeflate0:amd64 (1.19-1) ... 304s Selecting previously unselected package libgfortran5:amd64. 304s Preparing to unpack .../47-libgfortran5_14-20240303-1ubuntu1_amd64.deb ... 304s Unpacking libgfortran5:amd64 (14-20240303-1ubuntu1) ... 304s Selecting previously unselected package libgraphite2-3:amd64. 304s Preparing to unpack .../48-libgraphite2-3_1.3.14-2_amd64.deb ... 304s Unpacking libgraphite2-3:amd64 (1.3.14-2) ... 304s Selecting previously unselected package libharfbuzz0b:amd64. 304s Preparing to unpack .../49-libharfbuzz0b_8.3.0-2_amd64.deb ... 304s Unpacking libharfbuzz0b:amd64 (8.3.0-2) ... 304s Selecting previously unselected package x11-common. 304s Preparing to unpack .../50-x11-common_1%3a7.7+23ubuntu2_all.deb ... 304s Unpacking x11-common (1:7.7+23ubuntu2) ... 304s Selecting previously unselected package libice6:amd64. 304s Preparing to unpack .../51-libice6_2%3a1.0.10-1build2_amd64.deb ... 304s Unpacking libice6:amd64 (2:1.0.10-1build2) ... 304s Selecting previously unselected package libjpeg-turbo8:amd64. 304s Preparing to unpack .../52-libjpeg-turbo8_2.1.5-2ubuntu1_amd64.deb ... 304s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ... 304s Selecting previously unselected package libjpeg8:amd64. 304s Preparing to unpack .../53-libjpeg8_8c-2ubuntu11_amd64.deb ... 304s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 304s Selecting previously unselected package liblapack3:amd64. 304s Preparing to unpack .../54-liblapack3_3.12.0-3_amd64.deb ... 304s Unpacking liblapack3:amd64 (3.12.0-3) ... 304s Selecting previously unselected package liblerc4:amd64. 304s Preparing to unpack .../55-liblerc4_4.0.0+ds-4ubuntu1_amd64.deb ... 304s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu1) ... 304s Selecting previously unselected package libthai-data. 304s Preparing to unpack .../56-libthai-data_0.1.29-2_all.deb ... 304s Unpacking libthai-data (0.1.29-2) ... 304s Selecting previously unselected package libthai0:amd64. 304s Preparing to unpack .../57-libthai0_0.1.29-2_amd64.deb ... 304s Unpacking libthai0:amd64 (0.1.29-2) ... 304s Selecting previously unselected package libpango-1.0-0:amd64. 304s Preparing to unpack .../58-libpango-1.0-0_1.51.0+ds-4_amd64.deb ... 304s Unpacking libpango-1.0-0:amd64 (1.51.0+ds-4) ... 304s Selecting previously unselected package libpangoft2-1.0-0:amd64. 304s Preparing to unpack .../59-libpangoft2-1.0-0_1.51.0+ds-4_amd64.deb ... 304s Unpacking libpangoft2-1.0-0:amd64 (1.51.0+ds-4) ... 304s Selecting previously unselected package libpangocairo-1.0-0:amd64. 304s Preparing to unpack .../60-libpangocairo-1.0-0_1.51.0+ds-4_amd64.deb ... 304s Unpacking libpangocairo-1.0-0:amd64 (1.51.0+ds-4) ... 304s Selecting previously unselected package libpaper1:amd64. 304s Preparing to unpack .../61-libpaper1_1.1.29_amd64.deb ... 304s Unpacking libpaper1:amd64 (1.1.29) ... 304s Selecting previously unselected package libpaper-utils. 304s Preparing to unpack .../62-libpaper-utils_1.1.29_amd64.deb ... 304s Unpacking libpaper-utils (1.1.29) ... 304s Selecting previously unselected package libsharpyuv0:amd64. 304s Preparing to unpack .../63-libsharpyuv0_1.3.2-0.4_amd64.deb ... 304s Unpacking libsharpyuv0:amd64 (1.3.2-0.4) ... 304s Selecting previously unselected package libsm6:amd64. 304s Preparing to unpack .../64-libsm6_2%3a1.2.3-1build2_amd64.deb ... 304s Unpacking libsm6:amd64 (2:1.2.3-1build2) ... 304s Selecting previously unselected package libtcl8.6:amd64. 304s Preparing to unpack .../65-libtcl8.6_8.6.13+dfsg-2_amd64.deb ... 304s Unpacking libtcl8.6:amd64 (8.6.13+dfsg-2) ... 304s Selecting previously unselected package libjbig0:amd64. 304s Preparing to unpack .../66-libjbig0_2.1-6.1ubuntu1_amd64.deb ... 304s Unpacking libjbig0:amd64 (2.1-6.1ubuntu1) ... 305s Selecting previously unselected package libwebp7:amd64. 305s Preparing to unpack .../67-libwebp7_1.3.2-0.4_amd64.deb ... 305s Unpacking libwebp7:amd64 (1.3.2-0.4) ... 305s Selecting previously unselected package libtiff6:amd64. 305s Preparing to unpack .../68-libtiff6_4.5.1+git230720-3ubuntu1_amd64.deb ... 305s Unpacking libtiff6:amd64 (4.5.1+git230720-3ubuntu1) ... 305s Selecting previously unselected package libxft2:amd64. 305s Preparing to unpack .../69-libxft2_2.3.6-1_amd64.deb ... 305s Unpacking libxft2:amd64 (2.3.6-1) ... 305s Selecting previously unselected package libxss1:amd64. 305s Preparing to unpack .../70-libxss1_1%3a1.2.3-1build2_amd64.deb ... 305s Unpacking libxss1:amd64 (1:1.2.3-1build2) ... 305s Selecting previously unselected package libtk8.6:amd64. 305s Preparing to unpack .../71-libtk8.6_8.6.13-2_amd64.deb ... 305s Unpacking libtk8.6:amd64 (8.6.13-2) ... 305s Selecting previously unselected package libxt6:amd64. 305s Preparing to unpack .../72-libxt6_1%3a1.2.1-1.1_amd64.deb ... 305s Unpacking libxt6:amd64 (1:1.2.1-1.1) ... 305s Selecting previously unselected package zip. 305s Preparing to unpack .../73-zip_3.0-13_amd64.deb ... 305s Unpacking zip (3.0-13) ... 305s Selecting previously unselected package unzip. 305s Preparing to unpack .../74-unzip_6.0-28ubuntu3_amd64.deb ... 305s Unpacking unzip (6.0-28ubuntu3) ... 305s Selecting previously unselected package xdg-utils. 305s Preparing to unpack .../75-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 305s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 305s Selecting previously unselected package r-base-core. 305s Preparing to unpack .../76-r-base-core_4.3.2-1build1_amd64.deb ... 305s Unpacking r-base-core (4.3.2-1build1) ... 305s Selecting previously unselected package r-cran-gparotation. 305s Preparing to unpack .../77-r-cran-gparotation_2024.2-1-1_all.deb ... 305s Unpacking r-cran-gparotation (2024.2-1-1) ... 305s Setting up libgraphite2-3:amd64 (1.3.14-2) ... 305s Setting up libpixman-1-0:amd64 (0.42.2-1) ... 305s Setting up libsharpyuv0:amd64 (1.3.2-0.4) ... 305s Setting up libpaper1:amd64 (1.1.29) ... 306s 306s Creating config file /etc/papersize with new version 306s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu1) ... 306s Setting up libxrender1:amd64 (1:0.9.10-1.1) ... 306s Setting up libdatrie1:amd64 (0.2.13-3) ... 306s Setting up libxcb-render0:amd64 (1.15-1) ... 306s Setting up unzip (6.0-28ubuntu3) ... 306s Setting up x11-common (1:7.7+23ubuntu2) ... 306s Setting up libdeflate0:amd64 (1.19-1) ... 306s Setting up linux-libc-dev:amd64 (6.8.0-11.11) ... 306s Setting up libxcb-shm0:amd64 (1.15-1) ... 306s Setting up libpaper-utils (1.1.29) ... 306s Setting up libgomp1:amd64 (14-20240303-1ubuntu1) ... 306s Setting up libjbig0:amd64 (2.1-6.1ubuntu1) ... 306s Setting up zip (3.0-13) ... 306s Setting up libblas3:amd64 (3.12.0-3) ... 306s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 306s Setting up libtirpc-dev:amd64 (1.3.4+ds-1build1) ... 306s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 306s Setting up libquadmath0:amd64 (14-20240303-1ubuntu1) ... 306s Setting up fonts-dejavu-mono (2.37-8) ... 306s Setting up libmpc3:amd64 (1.3.1-1) ... 306s Setting up libatomic1:amd64 (14-20240303-1ubuntu1) ... 306s Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ... 306s Setting up fonts-dejavu-core (2.37-8) ... 306s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ... 306s Setting up libgfortran5:amd64 (14-20240303-1ubuntu1) ... 306s Setting up libwebp7:amd64 (1.3.2-0.4) ... 306s Setting up libubsan1:amd64 (14-20240303-1ubuntu1) ... 306s Setting up libnsl-dev:amd64 (1.3.0-3) ... 306s Setting up libhwasan0:amd64 (14-20240303-1ubuntu1) ... 306s Setting up libcrypt-dev:amd64 (1:4.4.36-4) ... 306s Setting up libasan8:amd64 (14-20240303-1ubuntu1) ... 306s Setting up libharfbuzz0b:amd64 (8.3.0-2) ... 306s Setting up libthai-data (0.1.29-2) ... 306s Setting up libxss1:amd64 (1:1.2.3-1build2) ... 306s Setting up libtsan2:amd64 (14-20240303-1ubuntu1) ... 306s Setting up libisl23:amd64 (0.26-3) ... 306s Setting up libc-dev-bin (2.39-0ubuntu2) ... 306s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 306s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 306s Setting up libcc1-0:amd64 (14-20240303-1ubuntu1) ... 306s Setting up liblsan0:amd64 (14-20240303-1ubuntu1) ... 306s Setting up libitm1:amd64 (14-20240303-1ubuntu1) ... 306s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 306s Setting up libice6:amd64 (2:1.0.10-1build2) ... 306s Setting up liblapack3:amd64 (3.12.0-3) ... 306s 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 306s Setting up cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 306s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 306s Setting up libthai0:amd64 (0.1.29-2) ... 306s Setting up libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ... 306s Setting up libtiff6:amd64 (4.5.1+git230720-3ubuntu1) ... 306s Setting up libc6-dev:amd64 (2.39-0ubuntu2) ... 306s Setting up libfontconfig1:amd64 (2.15.0-1ubuntu1) ... 306s Setting up libsm6:amd64 (2:1.2.3-1build2) ... 306s Setting up libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ... 306s Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 306s Setting up fontconfig (2.15.0-1ubuntu1) ... 308s Regenerating fonts cache... done. 308s Setting up libxft2:amd64 (2.3.6-1) ... 308s Setting up cpp-13 (13.2.0-17ubuntu2) ... 308s Setting up gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 308s Setting up libtk8.6:amd64 (8.6.13-2) ... 308s Setting up libpango-1.0-0:amd64 (1.51.0+ds-4) ... 308s Setting up libcairo2:amd64 (1.18.0-1) ... 308s Setting up gcc-13 (13.2.0-17ubuntu2) ... 308s Setting up libxt6:amd64 (1:1.2.1-1.1) ... 308s Setting up cpp (4:13.2.0-7ubuntu1) ... 308s Setting up libpangoft2-1.0-0:amd64 (1.51.0+ds-4) ... 308s Setting up libpangocairo-1.0-0:amd64 (1.51.0+ds-4) ... 308s Setting up g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 308s Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 308s Setting up gcc (4:13.2.0-7ubuntu1) ... 308s Setting up r-base-core (4.3.2-1build1) ... 309s 309s Creating config file /etc/R/Renviron with new version 309s Setting up r-cran-gparotation (2024.2-1-1) ... 309s Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 309s Setting up g++-13 (13.2.0-17ubuntu2) ... 309s Setting up g++ (4:13.2.0-7ubuntu1) ... 309s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 309s Setting up build-essential (12.10ubuntu1) ... 309s Processing triggers for libc-bin (2.39-0ubuntu2) ... 309s Processing triggers for man-db (2.12.0-3) ... 311s Processing triggers for install-info (7.1-3) ... 312s Reading package lists... 312s Building dependency tree... 312s Reading state information... 313s Starting pkgProblemResolver with broken count: 0 313s Starting 2 pkgProblemResolver with broken count: 0 313s Done 314s The following NEW packages will be installed: 314s autopkgtest-satdep 314s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 314s Need to get 0 B/704 B of archives. 314s After this operation, 0 B of additional disk space will be used. 314s Get:1 /tmp/autopkgtest.lANRY3/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [704 B] 314s Selecting previously unselected package autopkgtest-satdep. 314s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76485 files and directories currently installed.) 314s Preparing to unpack .../2-autopkgtest-satdep.deb ... 314s Unpacking autopkgtest-satdep (0) ... 314s Setting up autopkgtest-satdep (0) ... 317s (Reading database ... 76485 files and directories currently installed.) 317s Removing autopkgtest-satdep (0) ... 317s autopkgtest [17:48:06]: test run-unit-test: [----------------------- 317s BEGIN TEST Harman.R 317s 317s R version 4.3.2 (2023-10-31) -- "Eye Holes" 317s Copyright (C) 2023 The R Foundation for Statistical Computing 317s Platform: x86_64-pc-linux-gnu (64-bit) 317s 317s R is free software and comes with ABSOLUTELY NO WARRANTY. 317s You are welcome to redistribute it under certain conditions. 317s Type 'license()' or 'licence()' for distribution details. 317s 317s R is a collaborative project with many contributors. 317s Type 'contributors()' for more information and 317s 'citation()' on how to cite R or R packages in publications. 317s 317s Type 'demo()' for some demos, 'help()' for on-line help, or 317s 'help.start()' for an HTML browser interface to help. 317s Type 'q()' to quit R. 317s 317s > #Example from: Gradient Projection Algorithms and Software for 317s > # Arbitrary Rotation Criteria in Factor Analysis. 317s > # by Coen A. Bernaards and Robert I. Jennrich 317s > # Website: http://www.stat.ucla.edu/research 317s > 317s > Sys.getenv("R_LIBS") 317s [1] "" 317s > library() 317s Packages in library ‘/usr/lib/R/site-library’: 317s 317s GPArotation Gradient Projection Factor Rotation 317s 317s Packages in library ‘/usr/lib/R/library’: 317s 317s base The R Base Package 317s compiler The R Compiler Package 317s datasets The R Datasets Package 317s graphics The R Graphics Package 317s grDevices The R Graphics Devices and Support for Colours 317s and Fonts 317s grid The Grid Graphics Package 317s methods Formal Methods and Classes 317s parallel Support for Parallel Computation in R 317s splines Regression Spline Functions and Classes 317s stats The R Stats Package 317s stats4 Statistical Functions using S4 Classes 317s tcltk Tcl/Tk Interface 317s tools Tools for Package Development 317s utils The R Utils Package 317s 317s Warning message: 317s In library() : library ‘/usr/local/lib/R/site-library’ contains no packages 317s > require("GPArotation") 317s Loading required package: GPArotation 317s > search() 317s [1] ".GlobalEnv" "package:GPArotation" "package:stats" 317s [4] "package:graphics" "package:grDevices" "package:utils" 317s [7] "package:datasets" "package:methods" "Autoloads" 317s [10] "package:base" 317s > Sys.info() 317s sysname 317s "Linux" 317s release 317s "6.8.0-11-generic" 317s version 317s "#11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024" 317s nodename 317s "autopkgtest" 317s machine 317s "x86_64" 317s login 317s "ubuntu" 317s user 317s "ubuntu" 317s effective_user 317s "ubuntu" 317s > 317s > 317s > fuzz <- 1e-5 # using eps=1e-5 these tests do not do better than this 317s > all.ok <- TRUE 317s > 317s > # quartimax (orthogonal) rotation of Harman's 8 physical variables. 317s > 317s > data("Harman", package="GPArotation") 317s > 317s > qHarman <- GPForth(Harman8, Tmat=diag(2), method="quartimax") 317s > qHarman2 <- quartimax(Harman8) 317s > 317s > if( fuzz < max(abs(qHarman$loadings - qHarman2$loadings))) { 317s + cat("Calculated value is not the same as test value in test Harman 1. Value:\n") 317s + print(qHarman$loadings, digits=18) 317s + cat("difference:\n") 317s + print(qHarman$loadings - qHarman2$loadings, digits=18) 317s + all.ok <- FALSE 317s + } 317s > 317s > #qHarman$Th - qHarman2$Th 317s > 317s > # with eps=1e-8 317s > # tst <- t(matrix(c( 317s > # 0.898754567491920398, 0.194823580226859222, 317s > # 0.933943406208487592, 0.129748657024604030, 317s > # 0.902131483644799892, 0.103864268239045668, 317s > # 0.876508251941102934, 0.171284220753554678, 317s > # 0.315572019798302239, 0.876476069451083251, 317s > # 0.251123191235179066, 0.773488941629975613, 317s > # 0.198007116064591759, 0.714678376605717203, 317s > # 0.307857241091366252, 0.659334451631046314 317s > # ), 2, 8)) 317s > 317s > # with eps=1e-5 317s > tst <- t(matrix(c( 317s + 0.898755404698461491, 0.194819718009510034, 317s + 0.933943963768413821, 0.129744643590955028, 317s + 0.902131929972106672, 0.103860391510923730, 317s + 0.876508987992224209, 0.171280454135453869, 317s + 0.315575786273609882, 0.876474713336210853, 317s + 0.251126515144778573, 0.773487862471829213, 317s + 0.198010187248201075, 0.714677525703678707, 317s + 0.307860074444663512, 0.659333128670876345 317s + ), 2, 8)) 317s > 317s > if( fuzz < max(abs(qHarman$loadings - tst ))) { 317s + cat("Calculated value is not the same as test value in test Harman 2. Value:\n") 317s + print(qHarman$loadings, digits=18) 317s + cat("difference:\n") 317s + print(qHarman$loadings - tst, digits=18) 317s + all.ok <- FALSE 317s + } 317s > 317s > # with eps=1e-8 317s > # tst <- t(matrix(c( 317s > # 0.790828307905322436, 0.612038060430562525, 317s > # -0.612038060430562525, 0.790828307905322214 317s > # ), 2, 2)) 317s > 317s > # with eps=1e-5 317s > tst <- t(matrix(c( 317s + 0.790830938007507367, 0.612034662000581764, 317s + -0.612034662000581764, 0.790830938007507145 317s + ), 2, 2)) 317s > 317s > if( fuzz < max(abs(qHarman$Th - tst ))) { 317s + cat("Calculated value is not the same as test value in test Harman 3. Value:\n") 317s + print(qHarman$Th, digits=18) 317s + cat("difference:\n") 317s + print(qHarman$Th - tst, digits=18) 317s + all.ok <- FALSE 317s + } 317s > 317s > 317s > 317s > 317s > 317s > # quartimin (oblique) rotation of Harman's 8 physical variables. 317s > 317s > qminHarman <- GPFoblq(Harman8, Tmat=diag(2), method="quartimin") 317s > qminHarman2 <- quartimin(Harman8) 317s > 317s > if( fuzz < max(abs(qminHarman$loadings - qminHarman2$loadings))) { 317s + cat("Calculated value is not the same as test value in test Harman 4. Value:\n") 317s + print(qminHarman$loadings, digits=18) 317s + cat("difference:\n") 317s + print(qminHarman$loadings - qminHarman2$loadings, digits=18) 317s + all.ok <- FALSE 317s + } 317s > 317s > 317s > # with eps=1e-8 317s > # tst <- t(matrix(c( 317s > # 0.8918217697289939627, 0.0560146456758183961, 317s > # 0.9536799985772628219, -0.0232460005406671701, 317s > # 0.9291498623396581280, -0.0465027396531852502, 317s > # 0.8766828510822184395, 0.0336582451338717017, 317s > # 0.0136988312985193428, 0.9250013826349388069, 317s > # -0.0172668087945964319, 0.8212535444941218010, 317s > # -0.0524468998178311899, 0.7649536381341245361, 317s > # 0.0858880630098148856, 0.6831160953442911854 317s > # ),2, 8)) 317s > 317s > # with eps=1e-5 317s > tst <- t(matrix(c( 317s + 0.8918219293548808047, 0.0560145122875230911, 317s + 0.9536799846795966928, -0.0232460559140742311, 317s + 0.9291497958388006406, -0.0465027685653178480, 317s + 0.8766829604751505967, 0.0336581364763500201, 317s + 0.0137008854716444972, 0.9250004106413580729, 317s + -0.0172649861805529957, 0.8212526839806429946, 317s + -0.0524452035885302342, 0.7649528396536503516, 317s + 0.0858895830186393733, 0.6831153711863455769 317s + ),2, 8)) 317s > 317s > if( fuzz < max(abs(qminHarman$loadings - tst ))) { 317s + cat("Calculated value is not the same as test value in test Harman 5. Value:\n") 317s + print(qminHarman$loadings, digits=18) 317s + cat("difference:\n") 317s + print(qminHarman$loadings - tst, digits=18) 317s + all.ok <- FALSE 317s + } 317s > 317s > 317s > # with eps=1e-8 317s > # tst <- t(matrix(c( 317s > # 1.000000000000000000, 0.472747617396915065, 317s > # 0.472747617396915065, 1.000000000000000000 317s > # ),2, 2)) 317s > 317s > # with eps=1e-5 317s > tst <- t(matrix(c( 317s + 1.000000000000000222, 0.472745958387102538, 317s + 0.472745958387102538, 1.000000000000000000 317s + ),2, 2)) 317s > 317s > if( fuzz < max(abs(qminHarman$Phi - tst ))) { 317s + cat("Calculated value is not the same as test value in test Harman 6. Value:\n") 317s + print(qminHarman$Phi, digits=18) 317s + cat("difference:\n") 317s + print(qminHarman$Phi - tst, digits=18) 317s + all.ok <- FALSE 317s + } 317s > 317s > 317s > # with eps=1e-8 317s > # tst <- t(matrix(c( 317s > # 0.878125245495924522, 0.836723841642554422, 317s > # -0.478430823863515542, 0.547625065922776710 317s > # ),2, 2)) 317s > 317s > # with eps=1e-5 317s > tst <- t(matrix(c( 317s + 0.878125280760480686, 0.836722770276292271, 317s + -0.478430759137962514, 0.547626702874473570 317s + ),2, 2)) 317s > 317s > if( fuzz < max(abs(qminHarman$Th - tst ))) { 317s + cat("Calculated value is not the same as test value in test Harman 7. Value:\n") 317s + print(qminHarman$Th, digits=18) 317s + cat("difference:\n") 317s + print(qminHarman$Th - tst, digits=18) 317s + all.ok <- FALSE 317s + } 317s > 317s > 317s > cat("tests completed.\n") 317s tests completed. 317s > 317s > if (! all.ok) stop("some tests FAILED") 317s > 317s > 317s BEGIN TEST Jennrich2002.R 317s 317s R version 4.3.2 (2023-10-31) -- "Eye Holes" 317s Copyright (C) 2023 The R Foundation for Statistical Computing 317s Platform: x86_64-pc-linux-gnu (64-bit) 317s 317s R is free software and comes with ABSOLUTELY NO WARRANTY. 317s You are welcome to redistribute it under certain conditions. 317s Type 'license()' or 'licence()' for distribution details. 317s 317s R is a collaborative project with many contributors. 317s Type 'contributors()' for more information and 317s 'citation()' on how to cite R or R packages in publications. 317s 317s Type 'demo()' for some demos, 'help()' for on-line help, or 317s 'help.start()' for an HTML browser interface to help. 317s Type 'q()' to quit R. 317s 317s > # test by William Revelle 317s > # from Jennrich, Psychometrika, 2002, solution for the Thurstone 20 box problem. # Specifying 27 elements to be 0 as discussed in that article (Table 1 at 317s > # page 12) and using vgQ.target as revised or vgQ.pst with a W matrix 317s > # and Target as specified does not yield the reported solution. 317s > # The solution is almost identical for the high loadings but differs slightly 317s > # for the small loadings. The two models have a factor congruence of .99 for 317s > # all three factors, but do not agree completely. 317s > 317s > # Jennrich (2002) apparently was using the oblique rotation option. 317s > # When running TargetQ the results are fine, or when running 317s > # the vgQ.pst function with GPFoblq. 317s > 317s > # This a good test case for both TargetQ 317s > # (It could also be adapted for pst but there is already a test for it.) 317s > 317s > require("GPArotation") 317s Loading required package: GPArotation 317s > data(Thurstone) #the 20 box problem 317s > 317s > #solution reported in Jennrich 2002 317s > 317s > browne <- t(matrix(c( 317s + 0.013, 0.994, 0.007, 317s + 0.991, 0.012, 0.001, 317s + 0.018, 0.003, 0.986, 317s + 0.772, 0.477, 0.002, 317s + 0.003, 0.393, 0.874, 317s + 0.409, 0.003, 0.816, 317s + 0.548, 0.730, -0.020, 317s + 0.023, 0.870, 0.405, 317s + 0.799, -0.024, 0.453, 317s + 0.664, 0.621, -0.005, 317s + -0.058, 0.915, 0.512, 317s + 0.639, -0.018, 0.644, 317s + 0.046, 0.980, -0.003, 317s + 0.971, -0.038, 0.060, 317s + -0.026, 0.025, 0.965, 317s + 0.380, 0.281, 0.726, 317s + 0.490, 0.652, 0.286, 317s + -0.025, 0.971, 0.019, 317s + 0.957, 0.061, -0.045, 317s + 0.028, 0.000, 0.976), 317s + 3,20,dimnames = list(c("B1", "B2", "B3"), NULL))) 317s > 317s > #a simplified target matrix, with NAs for ? and 0 for 0s. 317s > # (compare to pst appproach) 317s > Target <- t(matrix(c( 317s + 0, NA, 0, 317s + NA, 0, 0, 317s + 0, 0, NA, 317s + NA, NA, 0, 317s + 0, NA, NA, 317s + NA, 0, NA, 317s + NA, NA, 0, 317s + 0, NA, NA, 317s + NA, 0, NA, 317s + NA, NA, 0, 317s + 0, NA, NA, 317s + NA, 0, NA, 317s + 0, NA, 0, 317s + NA, 0, 0, 317s + 0, 0, NA, 317s + NA, NA, NA, 317s + NA, NA, NA, 317s + 0, NA, 0, 317s + NA, 0, 0, 317s + 0, 0, NA), 317s + 3, 20, dimnames = list(c("T1", "T2", "T3"), NULL))) 317s > 317s > v <- targetQ(box20,Target=Target)$loadings 317s > # THIS ONE WORKS 317s > #v <- GPFoblq(box20, method ="target", methodArgs = list(Target=Target))$loadings 317s > 317s > all.ok <- TRUE 317s > 317s > #slightly larger fuzz for comparison with published value. 317s > # note max(abs(v) - abs(browne))rather than max(abs(v - browne)) 317s > # as sign change is possible 317s > if( 10e-4 < max(abs(v) - abs(browne))) { 317s + cat("Calculated value is not the same as test value in Jennrich2002. Value:\n") 317s + print(v, digits=18) 317s + cat("difference:\n") 317s + print(v - browne, digits=18) 317s + all.ok <- FALSE 317s + } 317s > 317s > good <- t(matrix(c( 317s + 0.01324194563970146343, -0.99360765277094842407, 0.007265459960371034587, 317s + 0.99121314541487770544, -0.01178320700232154961, 0.000654586020267855506, 317s + 0.01798447315534307256, -0.00266076852016330911, 0.985581004768931734361, 317s + 0.77198435084052174915, -0.47723548341238952730, 0.001547735983967568618, 317s + 0.00334198654247502835, -0.39290416948063611180, 0.874043793719835537814, 317s + 0.40934347835281348349, -0.00274610551094590233, 0.815649888720176186041, 317s + 0.54757055519984310088, -0.72951044925148011977, -0.020211353947714422175, 317s + 0.02292379053779741716, -0.87011712730189194609, 0.404542252780873523577, 317s + 0.79911058029224457666, 0.02416810475294199623, 0.452727043944761764482, 317s + 0.66393502364020362538, -0.62149665012300570055, -0.005186928343372421146, 317s + -0.05839790682548451350, -0.91517931889838155524, 0.511521949806932663130, 317s + 0.63924406199386740735, 0.01841750353525576159, 0.643544196342115570886, 317s + 0.04597086497418309547, -0.97980801598321454193, -0.002918643110053173451, 317s + 0.97103389549392915558, 0.03847065084578840666, 0.060066450372699808913, 317s + -0.02622776344285615568, -0.02482060086975104718, 0.965272709232911085842, 317s + 0.37998105522582992233, -0.28073835673932595602, 0.726047993725112084107, 317s + 0.48985182554738604388, -0.65226812910595410866, 0.285738966726349907788, 317s + -0.02451057644240206557, -0.97122042802717223342, 0.019132901654980147277, 317s + 0.95708220223038309449, -0.06086293722346142188, -0.045050942196376064786, 317s + 0.02797903728304645954, 0.00036458752733534161, 0.976083771686937051726), 317s + 3,20,dimnames = list(c("B1", "B2", "B3"), NULL))) 317s > 317s > #tighter fuzz for numerical comparison with previous test value 317s > if( 10e-12 < max(abs(v - good))) { 317s + cat("Calculated value is not the same as previous test value. Value:\n") 317s + print(v, digits=18) 317s + cat("difference:\n") 317s + print(v - good, digits=18) 317s + all.ok <- FALSE 317s + } 317s > 317s > 317s > cat("tests completed.\n") 317s tests completed. 317s > 317s > 317s > if (! all.ok) stop("some tests FAILED") 317s > 317s BEGIN TEST KaiserNormalization.R 317s 317s R version 4.3.2 (2023-10-31) -- "Eye Holes" 317s Copyright (C) 2023 The R Foundation for Statistical Computing 317s Platform: x86_64-pc-linux-gnu (64-bit) 317s 317s R is free software and comes with ABSOLUTELY NO WARRANTY. 317s You are welcome to redistribute it under certain conditions. 317s Type 'license()' or 'licence()' for distribution details. 317s 317s R is a collaborative project with many contributors. 317s Type 'contributors()' for more information and 317s 'citation()' on how to cite R or R packages in publications. 317s 317s Type 'demo()' for some demos, 'help()' for on-line help, or 317s 'help.start()' for an HTML browser interface to help. 317s Type 'q()' to quit R. 317s 318s > # tests using normalization 318s > # All tests below use Kaiser normalization 318s > # A few other tests also use normalization when comparing varimax and Varimax 318s > 318s > # Following examples are from SPSS 318s > # See https://psych.unl.edu/psycrs/statpage/pc_rot.pdf 318s > 318s > Sys.getenv("R_LIBS") 318s [1] "" 318s > library() 318s Warning message: 318s In library() : library ‘/usr/local/lib/R/site-library’ contains no packages 318s Packages in library ‘/usr/lib/R/site-library’: 318s 318s GPArotation Gradient Projection Factor Rotation 318s 318s Packages in library ‘/usr/lib/R/library’: 318s 318s base The R Base Package 318s compiler The R Compiler Package 318s datasets The R Datasets Package 318s graphics The R Graphics Package 318s grDevices The R Graphics Devices and Support for Colours 318s and Fonts 318s grid The Grid Graphics Package 318s methods Formal Methods and Classes 318s parallel Support for Parallel Computation in R 318s splines Regression Spline Functions and Classes 318s stats The R Stats Package 318s stats4 Statistical Functions using S4 Classes 318s tcltk Tcl/Tk Interface 318s tools Tools for Package Development 318s utils The R Utils Package 318s 318s > require("GPArotation") 318s Loading required package: GPArotation 318s > search() 318s [1] ".GlobalEnv" "package:GPArotation" "package:stats" 318s [4] "package:graphics" "package:grDevices" "package:utils" 318s [7] "package:datasets" "package:methods" "Autoloads" 318s [10] "package:base" 318s > Sys.info() 318s sysname 318s "Linux" 318s release 318s "6.8.0-11-generic" 318s version 318s "#11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024" 318s nodename 318s "autopkgtest" 318s machine 318s "x86_64" 318s login 318s "ubuntu" 318s user 318s "ubuntu" 318s effective_user 318s "ubuntu" 318s > 318s > require("stats") 318s > require("GPArotation") 318s > 318s > fuzz <- 1e-3 #less strict; differences in 4rd decimal compared to SPSS 318s > all.ok <- TRUE 318s > 318s > # unrotated matrix 318s > L <- matrix(c(.758, .413, 1.164E-03, .693, .489, -.199, .362, .656, -.204, 318s + .826, 6.589E-02, .235, .540, -.510, .441, .654, -.335, .507, 318s + -.349, .539, .669, -.580, .450, .551), byrow=T, ncol=3) 318s > 318s > # quartimax, Kaiser normalization 318s > # uses the print command to get the right order of factors 318s > v <- print(quartimax(L, normalize = TRUE, eps = 1e-6))$loadings 318s Orthogonal rotation method Quartimax converged. 318s Loadings: 318s [,1] [,2] [,3] 318s [1,] 0.8134 0.2848 -0.0496 318s [2,] 0.8566 0.0828 -0.1355 318s [3,] 0.7459 -0.2036 0.0724 318s [4,] 0.5762 0.6342 -0.0875 318s [5,] -0.0613 0.8498 -0.1423 318s [6,] 0.1287 0.8826 -0.0385 318s [7,] 0.0204 -0.0415 0.9261 318s [8,] -0.1811 -0.2196 0.8726 318s 318s [,1] [,2] [,3] 318s SS loadings 2.337 2.083 1.675 318s Proportion Var 0.292 0.260 0.209 318s Cumulative Var 0.292 0.552 0.762 318s > 318s > tst <- matrix(c(.814, .285, -4.99E-02, .856, 8.321E-02, -.135, 318s + .746, -.203, 7.244E-02, .576, .634, -8.73E-02, 318s + -6.10E-02, .850, -.142, .129, .882, -3.86E-02, 318s + 2.063E-02, -4.15E-02, .927, -.181, -.220, .873), byrow=T, ncol=3) 318s > 318s > if( fuzz < max(abs(v - tst))) { 318s + cat("Calculated value is not the same as test value in test rotations 1. Value:\n") 318s + print(v, digits=18) 318s + cat("difference:\n") 318s + print(v - tst, digits=18) 318s + all.ok <- FALSE 318s + } 318s > 318s > # oblimin, Kaiser normalization 318s > # Pattern Matrix 318s > vw <- print(oblimin(L, normalize = TRUE, eps = 1e-7)) 318s Oblique rotation method Oblimin Quartimin converged. 318s Loadings: 318s [,1] [,2] [,3] 318s [1,] 0.7875 0.2396 -0.0133 318s [2,] 0.8484 0.0165 -0.1185 318s [3,] 0.7785 -0.2410 0.0683 318s [4,] 0.5085 0.6071 -0.0253 318s [5,] -0.1610 0.8569 -0.0728 318s [6,] 0.0327 0.8953 0.0397 318s [7,] 0.0740 0.0938 0.9481 318s [8,] -0.1130 -0.0860 0.8744 318s 318s [,1] [,2] [,3] 318s SS loadings 2.297 2.087 1.710 318s Proportion Var 0.287 0.261 0.214 318s Cumulative Var 0.287 0.548 0.762 318s 318s Phi: 318s [,1] [,2] [,3] 318s [1,] 1.0000 0.169 -0.0955 318s [2,] 0.1691 1.000 -0.2371 318s [3,] -0.0955 -0.237 1.0000 318s > v <- vw$loadings 318s > 318s > tst <- matrix(c(.241, .787, -1.36E-02, 1.783E-02, .848, -.119, 318s + -.240, .779, 6.824E-02, .608, .507, -2.52E-02, 318s + .858, -.163, -7.26E-02, .896, 3.050E-02, 3.954E-02, 318s + 9.405E-02, 7.397E-02, .949, -8.61E-02, -.113, .875), byrow=T, ncol=3) 318s > tst <- tst %*% matrix(c(0,1,0,1,0,0,0,0,1), 3) # Needed to line up factors correctly 318s > 318s > fuzz <- 3e-3 #less strict; differences in 4th decimal compared to SPSS; 0.003 or smaller diff 318s > 318s > if( fuzz < max(abs(v - tst))) { 318s + cat("Calculated value is not the same as test value in test rotations 1. Value:\n") 318s + print(v, digits=18) 318s + cat("difference:\n") 318s + print(v - tst, digits=18) 318s + all.ok <- FALSE 318s + } 318s > 318s > # oblimin, Kaiser normalization 318s > # Structure Matrix 318s > v <- vw$loadings %*% vw$Phi 318s > 318s > tst <- matrix(c(.379, .829, -.146, .191, .862, -.203, 318s + -.123, .731, .051, .701, .613, -.218, .847, -.010, -.261, 318s + .891, .180, -.176, -.118, .000, .919, -.313, -.211, .906), byrow=T, ncol=3) 318s > tst <- tst %*% matrix(c(0,1,0,1,0,0,0,0,1), 3) # Needed to line up factors correctly 318s > 318s > fuzz <- 4e-3 #less strict; differences in 4th decimal compared to SPSS; 0.004 or smaller diff 318s > 318s > if( fuzz < max(abs(v - tst))) { 318s + cat("Calculated value is not the same as test value in test rotations 1. Value:\n") 318s + print(v, digits=18) 318s + cat("difference:\n") 318s + print(v - tst, digits=18) 318s + all.ok <- FALSE 318s + } 318s > 318s > ################################################################# 318s > # 318s > # Confirmation that a row of zeroes will not break the normalization function 318s > # Normalizing with a column of zeroes was not affected 318s > # based on example from Kim-Laura Speck (25 October 2023) 318s > # Only affects Normalize=TRUE settings 318s > 318s > fuzz <- 1e-6 318s > 318s > D <- matrix(c(0,0,0, 1,2,3, 2,3,4, 5,2,5, 1,2,1, 3,4,5),ncol=3,byrow=T) 318s > set.seed(1000) #set seed becasuse some variance is observed in converged values 318s > v <- geominQ(D, normalize = TRUE, maxit = 10000)$loadings 318s > 318s > tst <- matrix(c( 318s + 0.00000000, 0.00000000, 0.00000000, 318s + -0.36979732, -0.13603325, 3.99622380, 318s + 0.03102554, 0.76678245, 4.68896063, 318s + 3.28926158, 0.01317821, 5.35447764, 318s + -0.02755956, 2.40311582, 0.06247234, 318s + 0.43184841, 1.66959816, 5.38169746), ncol = 3, byrow = TRUE) 318s > 318s > if( fuzz < max(abs(v - tst))) { 318s + cat("Calculated value is not the same as test value in test rotations 1. Value:\n") 318s + print(v, digits=18) 318s + cat("difference:\n") 318s + print(v - tst, digits=18) 318s + all.ok <- FALSE 318s + } 318s > 318s > 318s BEGIN TEST MASSoblimin.R 318s 318s R version 4.3.2 (2023-10-31) -- "Eye Holes" 318s Copyright (C) 2023 The R Foundation for Statistical Computing 318s Platform: x86_64-pc-linux-gnu (64-bit) 318s 318s R is free software and comes with ABSOLUTELY NO WARRANTY. 318s You are welcome to redistribute it under certain conditions. 318s Type 'license()' or 'licence()' for distribution details. 318s 318s R is a collaborative project with many contributors. 318s Type 'contributors()' for more information and 318s 'citation()' on how to cite R or R packages in publications. 318s 318s Type 'demo()' for some demos, 'help()' for on-line help, or 318s 'help.start()' for an HTML browser interface to help. 318s Type 'q()' to quit R. 318s 318s > 318s > Sys.getenv("R_LIBS") 318s [1] "" 318s > library() 318s Packages in library ‘/usr/lib/R/site-library’: 318s 318s GPArotation Gradient Projection Factor Rotation 318s 318s Packages in library ‘/usr/lib/R/library’: 318s 318s base The R Base Package 318s compiler The R Compiler Package 318s datasets The R Datasets Package 318s graphics The R Graphics Package 318s grDevices The R Graphics Devices and Support for Colours 318s and Fonts 318s grid The Grid Graphics Package 318s methods Formal Methods and Classes 318s parallel Support for Parallel Computation in R 318s splines Regression Spline Functions and Classes 318s stats The R Stats Package 318s stats4 Statistical Functions using S4 Classes 318s tcltk Tcl/Tk Interface 318s tools Tools for Package Development 318s utils The R Utils Package 318s 318s Warning message: 318s In library() : library ‘/usr/local/lib/R/site-library’ contains no packages 318s > require("GPArotation") 318s Loading required package: GPArotation 318s > search() 318s [1] ".GlobalEnv" "package:GPArotation" "package:stats" 318s [4] "package:graphics" "package:grDevices" "package:utils" 318s [7] "package:datasets" "package:methods" "Autoloads" 318s [10] "package:base" 318s > Sys.info() 318s sysname 318s "Linux" 318s release 318s "6.8.0-11-generic" 318s version 318s "#11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024" 318s nodename 318s "autopkgtest" 318s machine 318s "x86_64" 318s login 318s "ubuntu" 318s user 318s "ubuntu" 318s effective_user 318s "ubuntu" 318s > 318s > #require("stats") 318s > 318s > fuzz <- 1e-6 318s > all.ok <- TRUE 318s > 318s > 318s > # test MASS 4th ed. p 322-324 318s > 318s > data(ability.cov) 318s > ability.cov 318s $cov 318s general picture blocks maze reading vocab 318s general 24.641 5.991 33.520 6.023 20.755 29.701 318s picture 5.991 6.700 18.137 1.782 4.936 7.204 318s blocks 33.520 18.137 149.831 19.424 31.430 50.753 318s maze 6.023 1.782 19.424 12.711 4.757 9.075 318s reading 20.755 4.936 31.430 4.757 52.604 66.762 318s vocab 29.701 7.204 50.753 9.075 66.762 135.292 318s 318s $center 318s [1] 0 0 0 0 0 0 318s 318s $n.obs 318s [1] 112 318s 318s > ability.FA <- factanal(factors = 1, covmat=ability.cov) 318s > 318s > (ability.FA <- update(ability.FA, factors = 2)) 318s 318s Call: 318s factanal(factors = 2, covmat = ability.cov) 318s 318s Uniquenesses: 318s general picture blocks maze reading vocab 318s 0.455 0.589 0.218 0.769 0.052 0.334 318s 318s Loadings: 318s Factor1 Factor2 318s general 0.499 0.543 318s picture 0.156 0.622 318s blocks 0.206 0.860 318s maze 0.109 0.468 318s reading 0.956 0.182 318s vocab 0.785 0.225 318s 318s Factor1 Factor2 318s SS loadings 1.858 1.724 318s Proportion Var 0.310 0.287 318s Cumulative Var 0.310 0.597 318s 318s Test of the hypothesis that 2 factors are sufficient. 318s The chi square statistic is 6.11 on 4 degrees of freedom. 318s The p-value is 0.191 318s > 318s > # ability.FA2 <- factanal(factors = 2, covmat = ability.cov) 318s > # max(abs(ability.FA2$loadings - ability.FA$loadings)) 318s > 318s > # summary(ability.FA) MASS ed.4 p 323 seems to be print not summary in R 2.0.1 318s > ability.FA 318s 318s Call: 318s factanal(factors = 2, covmat = ability.cov) 318s 318s Uniquenesses: 318s general picture blocks maze reading vocab 318s 0.455 0.589 0.218 0.769 0.052 0.334 318s 318s Loadings: 318s Factor1 Factor2 318s general 0.499 0.543 318s picture 0.156 0.622 318s blocks 0.206 0.860 318s maze 0.109 0.468 318s reading 0.956 0.182 318s vocab 0.785 0.225 318s 318s Factor1 Factor2 318s SS loadings 1.858 1.724 318s Proportion Var 0.310 0.287 318s Cumulative Var 0.310 0.597 318s 318s Test of the hypothesis that 2 factors are sufficient. 318s The chi square statistic is 6.11 on 4 degrees of freedom. 318s The p-value is 0.191 318s > 318s > # this is default varimax rotation. There are 3rd+ digit differences with MASS 318s > tst <- t(matrix(c( 318s + 0.499437829039896530, 0.54344904693111962, 318s + 0.156070079431279873, 0.62153798991197484, 318s + 0.205786989958578748, 0.85992588538426895, 318s + 0.108530754440558652, 0.46776101732283504, 318s + 0.956242470279811574, 0.18209631992182243, 318s + 0.784768183877880943, 0.22482213687364205 318s + ), 2, 6)) 318s > 318s > 318s > if( fuzz < max(abs(loadings(ability.FA) - tst))) { 318s + cat("Calculated value is not the same as test value in test 1. Value:\n") 318s + #print(loadings(ability.FA), digits=18) this truncates 318s + print(unclass(ability.FA$loadings), digits=18) 318s + cat("difference:\n") 318s + print(unclass(ability.FA$loadings) - tst, digits=18) 318s + all.ok <- FALSE 318s + } 318s > 318s > 318s > # differences with MASS here are a bit more than might be expected, 318s > # but there is already a difference before rotation. 318s > (oblirot <- oblimin(loadings(ability.FA))) 318s Oblique rotation method Oblimin Quartimin converged. 318s Loadings: 318s Factor1 Factor2 318s general 0.3864 0.4745 318s picture -0.0110 0.6459 318s blocks -0.0263 0.8961 318s maze -0.0180 0.4883 318s reading 0.9901 -0.0371 318s vocab 0.7906 0.0526 318s 318s Factor1 Factor2 318s SS loadings 1.825 1.757 318s Proportion Var 0.304 0.293 318s Cumulative Var 0.304 0.597 318s 318s Phi: 318s Factor1 Factor2 318s Factor1 1.000 0.465 318s Factor2 0.465 1.000 318s > 318s > obli2 <- factanal(factors = 2, covmat = ability.cov, rotation="oblimin") 318s > 318s > max(abs(loadings(oblirot) - loadings(obli2))) 318s [1] 2.38643e-06 318s > 318s > 318s > # factanal(factors = 2, covmat = ability.cov, scores = Bartlett, rotation="oblimin") 318s > 318s > 318s > tst <- t(matrix(c( 318s + 0.3863637969729337152, 0.4745113977203344047, 318s + -0.0110032278171669998, 0.6458708261423832253, 318s + -0.0262888675561207576, 0.8961123879025085781, 318s + -0.0180180060207963122, 0.4882918937716873575, 318s + 0.9900948712271664398, -0.0370729040114848238, 318s + 0.7905663749272058283, 0.0526099352008769991 318s + ), 2, 6)) 318s > 318s > if( fuzz < max(abs(loadings(oblirot) - tst ))) { 318s + cat("Calculated value is not the same as test value in test 2. Value:\n") 318s + print(loadings(oblirot), digits=18) 318s + cat("difference:\n") 318s + print(loadings(oblirot) - tst, digits=18) 318s + all.ok <- FALSE 318s + } 318s > 318s > cat("tests completed.\n") 318s tests completed. 318s > 318s > if (! all.ok) stop("some tests FAILED") 318s > 318s BEGIN TEST Revelle.R 318s 318s R version 4.3.2 (2023-10-31) -- "Eye Holes" 318s Copyright (C) 2023 The R Foundation for Statistical Computing 318s Platform: x86_64-pc-linux-gnu (64-bit) 318s 318s R is free software and comes with ABSOLUTELY NO WARRANTY. 318s You are welcome to redistribute it under certain conditions. 318s Type 'license()' or 'licence()' for distribution details. 318s 318s R is a collaborative project with many contributors. 318s Type 'contributors()' for more information and 318s 'citation()' on how to cite R or R packages in publications. 318s 318s Type 'demo()' for some demos, 'help()' for on-line help, or 318s 'help.start()' for an HTML browser interface to help. 318s Type 'q()' to quit R. 318s 318s > # This tests fix for an error caused by an exact initial setting. 318s > # (from William Revelle) 318s > 318s > require("GPArotation") 318s Loading required package: GPArotation 318s > 318s > f3 <- structure(c(0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 0, 1, 0,0), 318s + .Dim = c(6L, 3L), .Dimnames = list(NULL, c("PC1", "PC2", "PC3"))) 318s > 318s > f3 318s PC1 PC2 PC3 318s [1,] 0 0 1 318s [2,] 0 1 0 318s [3,] 1 0 0 318s [4,] 0 0 1 318s [5,] 0 1 0 318s [6,] 1 0 0 318s > 318s > # PC1 PC2 PC3 318s > #[1,] 0 0 1 318s > #[2,] 0 1 0 318s > #[3,] 1 0 0 318s > #[4,] 0 0 1 318s > #[5,] 0 1 0 318s > #[6,] 1 0 0 318s > 318s > # These previously gave object 'VgQt' not found 318s > GPForth(f3) 318s Orthogonal rotation method varimax converged. 318s Loadings: 318s PC1 PC2 PC3 318s [1,] 0 0 1 318s [2,] 0 1 0 318s [3,] 1 0 0 318s [4,] 0 0 1 318s [5,] 0 1 0 318s [6,] 1 0 0 318s 318s PC1 PC2 PC3 318s SS loadings 2.000 2.000 2.000 318s Proportion Var 0.333 0.333 0.333 318s Cumulative Var 0.333 0.667 1.000 318s > Varimax(f3) 318s Orthogonal rotation method varimax converged. 318s Loadings: 318s PC1 PC2 PC3 318s [1,] 0 0 1 318s [2,] 0 1 0 318s [3,] 1 0 0 318s [4,] 0 0 1 318s [5,] 0 1 0 318s [6,] 1 0 0 318s 318s PC1 PC2 PC3 318s SS loadings 2.000 2.000 2.000 318s Proportion Var 0.333 0.333 0.333 318s Cumulative Var 0.333 0.667 1.000 318s > 318s BEGIN TEST Thurstone.R 318s 318s R version 4.3.2 (2023-10-31) -- "Eye Holes" 318s Copyright (C) 2023 The R Foundation for Statistical Computing 318s Platform: x86_64-pc-linux-gnu (64-bit) 318s 318s R is free software and comes with ABSOLUTELY NO WARRANTY. 318s You are welcome to redistribute it under certain conditions. 318s Type 'license()' or 'licence()' for distribution details. 318s 318s R is a collaborative project with many contributors. 318s Type 'contributors()' for more information and 318s 'citation()' on how to cite R or R packages in publications. 318s 318s Type 'demo()' for some demos, 'help()' for on-line help, or 318s 'help.start()' for an HTML browser interface to help. 318s Type 'q()' to quit R. 318s 318s > #Example from: Gradient Projection Algorithms and Software for 318s > # Arbitrary Rotation Criteria in Factor Analysis. 318s > # by Coen A. Bernaards and Robert I. Jennrich 318s > # Website: http://www.stat.ucla.edu/research 318s > 318s > Sys.getenv("R_LIBS") 318s [1] "" 318s > library() 318s Packages in library ‘/usr/lib/R/site-library’: 318s 318s GPArotation Gradient Projection Factor Rotation 318s 318s Packages in library ‘/usr/lib/R/library’: 318s 318s base The R Base Package 318s compiler The R Compiler Package 318s datasets The R Datasets Package 318s graphics The R Graphics Package 318s grDevices The R Graphics Devices and Support for Colours 318s and Fonts 318s grid The Grid Graphics Package 318s methods Formal Methods and Classes 318s parallel Support for Parallel Computation in R 318s splines Regression Spline Functions and Classes 318s stats The R Stats Package 318s stats4 Statistical Functions using S4 Classes 318s tcltk Tcl/Tk Interface 318s tools Tools for Package Development 318s utils The R Utils Package 318s 318s Warning message: 318s In library() : library ‘/usr/local/lib/R/site-library’ contains no packages 318s > require("GPArotation") 318s Loading required package: GPArotation 318s > search() 318s [1] ".GlobalEnv" "package:GPArotation" "package:stats" 318s [4] "package:graphics" "package:grDevices" "package:utils" 318s [7] "package:datasets" "package:methods" "Autoloads" 318s [10] "package:base" 318s > Sys.info() 318s sysname 318s "Linux" 318s release 318s "6.8.0-11-generic" 318s version 318s "#11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024" 318s nodename 318s "autopkgtest" 318s machine 318s "x86_64" 318s login 318s "ubuntu" 318s user 318s "ubuntu" 318s effective_user 318s "ubuntu" 318s > 318s > data("Thurstone", package="GPArotation") 318s > if (!exists("box20")) stop("Test data not found. Testing stopped.") 318s > 318s > fuzz <- 1e-5 318s > all.ok <- TRUE 318s > 318s > # Thurstone's box problem. (1947, p. 136) 318s > # The matrix box20 is the initial loading matrix from Thurstone's box problem. 318s > 318s > # This takes a lot of iterations to converge at a higher tolerance 318s > qbox20 <- quartimax(box20, eps=1e-5) 318s > qbox20G <- GPForth(box20, Tmat=diag(1,3), method="quartimax", eps=1e-5) 318s > 318s > if( fuzz < max(abs(qbox20$loadings - qbox20G$loadings))) { 318s + cat("Calculated value is not the same as test value in test Thurstone 1. Value:\n") 318s + print(qbox20$loadings - qbox20G$loadings, digits=18) 318s + cat("difference:\n") 318s + print(qbox20$loadings - tst, digits=18) 318s + all.ok <- FALSE 318s + } 318s > 318s > #qbox20$Th - qbox20G$Th 318s > 318s > # These values compare with those in: 318s > # http://www.stat.ucla.edu/research/web.pdf 318s > tst <- t(matrix(c( 318s + 0.0104916072210123716, -0.993396087928394733, -0.089861775335686706, 318s + 0.1584646383898045685, -0.167305085570175344, -0.967087879524061056, 318s + 0.9822741057703969769, -0.094961339079248266, -0.081938545344928893, 318s + 0.1249962020162782989, -0.597065497283680413, -0.789290657131387352, 318s + 0.8695614167874907707, -0.471622450093366785, -0.090438968384549553, 318s + 0.8757114893176747294, -0.141012080768234127, -0.452333925937943637, 318s + 0.0679423211019681700, -0.811411071716238719, -0.588554936857709099, 318s + 0.4066768108416509708, -0.907862149146695163, -0.115673202040957226, 318s + 0.5770808894249742638, -0.142370726163931066, -0.806527261406603468, 318s + 0.1012712863762783577, -0.723336747696182614, -0.694640249329106285, 318s + 0.5000928657774492692, -0.949746569049947253, -0.046846346456817907, 318s + 0.7412589798326677526, -0.140350561965914555, -0.663578062154924320, 318s + 0.0055655501003109590, -0.983847100401775698, -0.120037109608235590, 318s + 0.2142330103903098415, -0.119429100752156334, -0.947421187831809397, 318s + 0.9550804066106526324, -0.108275659756619305, -0.039227521113362487, 318s + 0.7823218737697450464, -0.405437596810190704, -0.439275358874331168, 318s + 0.3626971102221024923, -0.753122462957226402, -0.546281394544768872, 318s + 0.0162483298780003657, -0.966230359337758582, -0.052114148464710915, 318s + 0.1076692386876715729, -0.206734953950642314, -0.934620775424686911, 318s + 0.9744239420161749932, -0.092650552854598708, -0.090828719474599584 318s + ), 3, 20)) 318s > 318s > if( fuzz < max(abs(qbox20$loadings - tst ))) { 318s + cat("Calculated value is not the same as test value in test Thurstone 2. Value:\n") 318s + print(qbox20$loadings, digits=18) 318s + cat("difference:\n") 318s + print(qbox20$loadings - tst, digits=18) 318s + all.ok <- FALSE 318s + } 318s > 318s > tst <- t(matrix(c( 318s + 0.57232345894276127, -0.60751194947821441, -0.55079496147384377, 318s + 0.60249460283341838, 0.76716797198365361, -0.22012168525406509, 318s + 0.55627880770383020, -0.20587018726291534, 0.80509089803322043 318s + ), 3, 3)) 318s > 318s > if( fuzz < max(abs(qbox20$Th - tst ))) { 318s + cat("Calculated value is not the same as test value in test Thurstone 3. Value:\n") 318s + print(qbox20$Th, digits=18) 318s + cat("difference:\n") 318s + print(qbox20$Th - tst, digits=18) 318s + all.ok <- FALSE 318s + } 318s > 318s > 318s > # sorted absolute loading plots. 318s > sal <- abs(c(loadings(qbox20)))[order(abs(c(loadings(qbox20))))] 318s > plot(seq(length(sal)), sal) 319s > 319s > 319s > #compare quartimax rotation of the initial loading matrix box20. 319s > 319s > if( fuzz < max(abs(loadings(qbox20) - box20 %*% qbox20$Th ))) { 319s + cat("Calculated value is not the same as test value in test Thurstone 4. Value:\n") 319s + print(loadings(qbox20), digits=18) 319s + cat("difference:\n") 319s + print(loadings(qbox20) - box20 %*% qbox20$Th, digits=18) 319s + all.ok <- FALSE 319s + } 319s > 319s > 319s > 319s > qminbox20G <- GPFoblq(box20, Tmat=diag(1,3), method="quartimin", eps=1e-5) 319s > qminbox20 <- quartimin(box20, eps=1e-5) 319s > 319s > if( fuzz < max(abs(loadings(qminbox20) - qminbox20G$loadings))) { 319s + cat("Calculated value is not the same as test value in test Thurstone 5. Value:\n") 319s + print(qminbox20G$loadings , digits=18) 319s + cat("difference:\n") 319s + print(loadings(qminbox20) - qminbox20G$loadings, digits=18) 319s + all.ok <- FALSE 319s + } 319s > 319s > #qminbox20$Th - quartimin(box20)$Th 319s > 319s > # These values compare with those in: 319s > # http://www.stat.ucla.edu/research/web.pdf 319s > tst <- t(matrix(c( 319s + -0.099561899210599963, -1.0236437309424475384, 0.017110338313848200, 319s + -0.007103778102200991, 0.0427848301281630802, -1.009962780073245581, 319s + 1.012864497258948226, 0.0331727792925069487, 0.050367710973030555, 319s + -0.054843850612513692, -0.4493155290974688021, -0.772334543778026350, 319s + 0.856287122381722998, -0.3740197232441037078, 0.069350368268248391, 319s + 0.835580575619599641, 0.0487450425576793633, -0.360381644212301344, 319s + -0.102893671454670210, -0.7226715938020771279, -0.537456650126404090, 319s + 0.322103633211960838, -0.8816846447967544576, 0.031159743715387874, 319s + 0.462799683447739529, 0.0852338438217692257, -0.783762970578423479, 319s + -0.076585435689138226, -0.6043060025891554554, -0.658295846696152820, 319s + 0.427772530893690217, -0.9288687512327726825, 0.122866182561916254, 319s + 0.659408232467282085, 0.0772080094990600374, -0.607348040513722709, 319s + -0.108761719100651882, -1.0079608432113262850, -0.017378089000366713, 319s + 0.059518597564186392, 0.0955950614351480238, -0.986779686330629513, 319s + 0.989890866913205381, 0.0071520817823045348, 0.094691644950703049, 319s + 0.713733277219835149, -0.2427293600063723522, -0.328268187306521242, 319s + 0.220344503737931546, -0.6353746612195683152, -0.459661643730432223, 319s + -0.084703580704062989, -1.0022284232457450148, 0.055740317456252478, 319s + -0.059151779416785115, -0.0113377397453605679, -0.976867596293413132, 319s + 1.003360458549731771, 0.0365098037316876067, 0.039427150580815938 319s + ), 3, 20)) 319s > 319s > if( fuzz < max(abs(qminbox20G$loadings - tst ))) { 319s + cat("Calculated value is not the same as test value in test Thurstone 6. Value:\n") 319s + print(qminbox20G$loadings, digits=18) 319s + cat("difference:\n") 319s + print(qminbox20G$loadings - tst, digits=18) 319s + all.ok <- FALSE 319s + } 319s > 319s > tst <- t(matrix(c( 319s + 1.00000000000000000, -0.25676300454795098, -0.32155119431295237, 319s + -0.25676300454795098, 1.00000000000000000, 0.33656790396842257, 319s + -0.32155119431295237, 0.33656790396842257, 1.00000000000000000 319s + ), 3, 3)) 319s > 319s > if( fuzz < max(abs(qminbox20G$Phi - tst ))) { 319s + cat("Calculated value is not the same as test value in test Thurstone 7. Value:\n") 319s + print(qminbox20G$Phi, digits=18) 319s + cat("difference:\n") 319s + print(qminbox20G$Phi - tst, digits=18) 319s + all.ok <- FALSE 319s + } 319s > 319s > 319s > #To fuzz precision the rotated loading matrix and the factor cor- 319s > #relation matrix phi are identical to those produced using the oblique GP 319s > #algorithm with exact derivatives. 319s > 319s > if( fuzz < max(abs(qminbox20G$Phi - 319s + t(qminbox20G$Th )%*% qminbox20G$Th ))) { 319s + cat("Calculated value is not the same as test value in test Thurstone 8. Value:\n") 319s + print(qminbox20G$Phi, digits=18) 319s + cat("difference:\n") 319s + print(qminbox20G$Phi - 319s + t(qminbox20G$Th )%*% qminbox20G$Th, digits=18) 319s + all.ok <- FALSE 319s + } 319s > 319s > #compare quartimin rotation of the initial loading matrix box20. 319s > if( fuzz < max(abs(qminbox20G$loadings - box20 %*% solve(t(qminbox20G$Th))))) { 319s + cat("Calculated value is not the same as test value in test Thurstone 9. Value:\n") 319s + print(qminbox20G$loadings, digits=18) 319s + cat("difference:\n") 319s + print(qminbox20G$loadings - box20 %*% solve(t(qminbox20G$Th)), digits=18) 319s + all.ok <- FALSE 319s + } 319s > 319s > data("box26", package="GPArotation") 319s Warning message: 319s In data("box26", package = "GPArotation") : data set ‘box26’ not found 319s > if (!exists("box26")) stop("Test data box26 not found. Testing stopped.") 319s > 319s > qbox26 <- GPForth(box26, Tmat=diag(1,3), method="quartimax", eps=1e-5) 319s > 319s > tst <- t(matrix(c( 319s + 0.6245197355925140581, -0.2708954695931116152, 0.7151983951389878635, 319s + 0.7386116884036847408, 0.6266342260884526505, -0.0617439911892987553, 319s + 0.7803093788467402314, -0.3830982859243221017, -0.4578886072022986253, 319s + 0.8540550453155928423, 0.2886436985992582027, 0.4062915145925659610, 319s + 0.8810593765418006651, -0.4428658074662961130, 0.1233946983666596581, 319s + 0.9084731768740617053, 0.1540526132602804965, -0.3723026715563940159, 319s + 0.8150592858039771293, 0.0441965358534676597, 0.5600768044145943980, 319s + 0.8466584455973064083, 0.4551177395514792168, 0.1889929089788950356, 319s + 0.8156808837280125069, -0.4090629943132625956, 0.3690652552112651530, 319s + 0.9629492340906220527, -0.4781483041690369196, -0.0866081507974762743, 319s + 0.8731366884896356595, 0.3451069860590937899, -0.2914969834947889749, 319s + 0.8921854600753849063, -0.0276323108621970258, -0.4257376659710629951, 319s + -0.0938760381595044741, -0.7873218033841372643, 0.6012450975895150540, 319s + 0.0938760381595044741, 0.7873218033841372643, -0.6012450975895150540, 319s + -0.0986092863860908303, 0.1513605567468480073, 0.9692559984337008050, 319s + 0.0986092863860908303, -0.1513605567468480073, -0.9692559984337008050, 319s + -0.0189573629854957251, 0.9527983290277913797, 0.2944078167958268377, 319s + 0.0189573629854957251, -0.9527983290277913797, -0.2944078167958268377, 319s + 0.8394181189595459891, 0.3631767908642606346, 0.3398717995655929913, 319s + 0.8703065201362156778, -0.4691145408161159214, 0.0770980453920554615, 319s + 0.9141063746617547059, 0.1583184861345137973, -0.3535658252020681958, 319s + 0.8348118627305495254, 0.3535663452183119837, 0.3271666140872500073, 319s + 0.8541352373790773722, -0.4476738735312740247, 0.0569042988261160704, 319s + 0.9034738474019414767, 0.1663655738425987851, -0.3227406124130587362, 319s + 0.9861758757457432800, 0.0103496363116840455, 0.0635926656567585569, 319s + 0.9643516568468981642, 0.0660181478622221818, -0.0304218028637989850 319s + ), 3, 26)) 319s > 319s > if( fuzz < max(abs(qbox26$loadings - tst ))) { 319s + cat("Calculated value is not the same as test value in test Thurstone 10. Value:\n") 319s + print(qbox26$loadings, digits=18) 319s + cat("difference:\n") 319s + print(qbox26$loadings - tst, digits=18) 319s + all.ok <- FALSE 319s + } 319s > 319s > 319s > 319s > tst <- t(matrix(c( 319s + 0.9996572020207266096, 0.0216275672176080257, 0.0147555679097727491, 319s + -0.0158190757965277796, 0.9480178905874908635, -0.3178235925273457108, 319s + -0.0208622934749700742, 0.3174812237948764770, 0.9480350400953921897 319s + ), 3, 3)) 319s > 319s > if( fuzz < max(abs(qbox26$Th - tst ))) { 319s + cat("Calculated value is not the same as test value in test Thurstone 11. Value:\n") 319s + print(qbox26$Th, digits=18) 319s + cat("difference:\n") 319s + print(qbox26$Th - tst, digits=18) 319s + all.ok <- FALSE 319s + } 319s > 319s > 319s > qminbox26 <- GPFoblq(box26, Tmat=diag(1,3), method="quartimin", eps=1e-5) 319s > 319s > tst <- t(matrix(c( 319s + 0.6088436426802223966, -0.2567107018725688361, 0.7213648290819488773, 319s + 0.7318447535507376367, 0.6298398026581654152, -0.0549983771960348838, 319s + 0.7973321695017724364, -0.3855960314746548212, -0.4504478973568259437, 319s + 0.8392144987741166906, 0.2994932968625432235, 0.4143558581243267924, 319s + 0.8833452352200144020, -0.4361046712803113290, 0.1319331147095905710, 319s + 0.9161366872228343672, 0.1535557844336666034, -0.3638337328539109072, 319s + 0.7993355454002614158, 0.0571270784641514026, 0.5678963531379384033, 319s + 0.8354288250614068101, 0.4626764152757318893, 0.1968789749765105790, 319s + 0.8109923806202916641, -0.3989909333845649830, 0.3770226870580207779, 319s + 0.9712737747877250305, -0.4740722765307348041, -0.0773243882106463137, 319s + 0.8761501947960563808, 0.3456235893514668089, -0.2834183138879167174, 319s + 0.9036601763684347643, -0.0290211959776035672, -0.4173652812159966974, 319s + -0.0995525797764766768, -0.7788574612781464790, 0.6007791331268093060, 319s + 0.0995525797764766768, 0.7788574612781464790, -0.6007791331268093060, 319s + -0.1264036712449473909, 0.1653130238928011975, 0.9684661160120416890, 319s + 0.1264036712449473909, -0.1653130238928011975, -0.9684661160120416890, 319s + -0.0392946742598458687, 0.9571059478962877787, 0.2939285303852590125, 319s + 0.0392946742598458687, -0.9571059478962877787, -0.2939285303852590125, 319s + 0.8253744379910458173, 0.3729516010405902748, 0.3477554718030251846, 319s + 0.8741734789142978634, -0.4631063486451737488, 0.0855349365396926159, 319s + 0.9212130243051569467, 0.1581334796580046720, -0.3450412531516501846, 319s + 0.8212340853954427367, 0.3631252613622908965, 0.3350076577679809153, 319s + 0.8582635618771776720, -0.4420579024138228674, 0.0651757040961165046, 319s + 0.9096561314838297330, 0.1665824736284239604, -0.3143133889989875307, 319s + 0.9840845767693481294, 0.0168070160966761091, 0.0729425956763933708, 319s + 0.9640420478016114014, 0.0709475796833391181, -0.0213192081807395371 319s + ), 3, 26)) 319s > 319s > if( fuzz < max(abs(qminbox26$loadings - tst ))) { 319s + cat("Calculated value is not the same as test value in test Thurstone 12. Value:\n") 319s + print(qminbox26$loadings, digits=18) 319s + cat("difference:\n") 319s + print(qminbox26$loadings - tst, digits=18) 319s + all.ok <- FALSE 319s + } 319s > 319s > 319s > 319s > tst <- t(matrix(c( 319s + 1.000000000000000 , 0.00767934084449363279, 0.0170654511973979163, 319s + 0.00767934084449363279, 1.000000000000000 , -0.0144994900961642244, 319s + 0.01706545119739791630, -0.01449949009616422445, 1.000000000000000 319s + ), 3, 3)) 319s > 319s > if( fuzz < max(abs(qminbox26$Phi - tst ))) { 319s + cat("Calculated value is not the same as test value in test Thurstone 13. Value:\n") 319s + print(qminbox26$Phi, digits=18) 319s + cat("difference:\n") 319s + print(qminbox26$Phi - tst, digits=18) 319s + all.ok <- FALSE 319s + } 319s > 319s > 319s > 319s > tst <- t(matrix(c( 319s + 0.9993401424148040668, 0.0347479564402226465, 0.0408645923859655008, 319s + -0.0179660947915933414, 0.9476477730670300748, -0.3324117322929439067, 319s + -0.0315673755054017430, 0.3174212937474846785, 0.9422486536594960604 319s + ), 3, 3)) 319s > 319s > if( fuzz < max(abs(qminbox26$Th - tst ))) { 319s + cat("Calculated value is not the same as test value in test Thurstone 14. Value:\n") 319s + print(qminbox26$Th, digits=18) 319s + cat("difference:\n") 319s + print(qminbox26$Th - tst, digits=18) 319s + all.ok <- FALSE 319s + } 319s > 319s > 319s > 319s > cat("tests completed.\n") 319s tests completed. 319s > 319s > if (! all.ok) stop("some tests FAILED") 319s > 319s > 319s > cat("tests completed.\n") 319s tests completed. 319s > 319s > if (! all.ok) stop("some tests FAILED") 319s > 319s > 319s BEGIN TEST WansbeekMeijer.R 319s 319s R version 4.3.2 (2023-10-31) -- "Eye Holes" 319s Copyright (C) 2023 The R Foundation for Statistical Computing 319s Platform: x86_64-pc-linux-gnu (64-bit) 319s 319s R is free software and comes with ABSOLUTELY NO WARRANTY. 319s You are welcome to redistribute it under certain conditions. 319s Type 'license()' or 'licence()' for distribution details. 319s 319s R is a collaborative project with many contributors. 319s Type 'contributors()' for more information and 319s 'citation()' on how to cite R or R packages in publications. 319s 319s Type 'demo()' for some demos, 'help()' for on-line help, or 319s 'help.start()' for an HTML browser interface to help. 319s Type 'q()' to quit R. 319s 319s > Sys.getenv("R_LIBS") 319s [1] "" 319s > library() 319s Packages in library ‘/usr/lib/R/site-library’: 319s 319s GPArotation Gradient Projection Factor Rotation 319s 319s Packages in library ‘/usr/lib/R/library’: 319s 319s base The R Base Package 319s compiler The R Compiler Package 319s datasets The R Datasets Package 319s graphics The R Graphics Package 319s grDevices The R Graphics Devices and Support for Colours 319s and Fonts 319s grid The Grid Graphics Package 319s methods Formal Methods and Classes 319s parallel Support for Parallel Computation in R 319s splines Regression Spline Functions and Classes 319s stats The R Stats Package 319s stats4 Statistical Functions using S4 Classes 319s tcltk Tcl/Tk Interface 319s tools Tools for Package Development 319s utils The R Utils Package 319s 319s Warning message: 319s In library() : library ‘/usr/local/lib/R/site-library’ contains no packages 319s > require("GPArotation") 319s Loading required package: GPArotation 319s > search() 319s [1] ".GlobalEnv" "package:GPArotation" "package:stats" 319s [4] "package:graphics" "package:grDevices" "package:utils" 319s [7] "package:datasets" "package:methods" "Autoloads" 319s [10] "package:base" 319s > Sys.info() 319s sysname 319s "Linux" 319s release 319s "6.8.0-11-generic" 319s version 319s "#11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024" 319s nodename 319s "autopkgtest" 319s machine 319s "x86_64" 319s login 319s "ubuntu" 319s user 319s "ubuntu" 319s effective_user 319s "ubuntu" 319s > 319s > fuzz <- 1e-6 319s > all.ok <- TRUE 319s > 319s > data(WansbeekMeijer, package="GPArotation") 319s > 319s > fa.none <- factanal(factors=2, covmat=NetherlandsTV, rotation="none") 319s > 319s > tst <- t(matrix(c( 319s + 0.6972803, -0.3736554, 319s + 0.7774628, -0.3184149, 319s + 0.6832300, -0.3620428, 319s + 0.6612198, 0.2361132, 319s + 0.6972393, 0.3026050, 319s + 0.7100285, 0.4059509, 319s + 0.6353584, 0.3526947 319s + ), 2, 7)) 319s > 319s > if( fuzz < max(abs(fa.none$loadings - tst))) { 319s + cat("Calculated value is not the same as test value in test WansbeekMeijer 1. Value:\n") 319s + print(fa.none$loadings, digits=18) 319s + cat("difference:\n") 319s + print(fa.none$loadings - tst, digits=18) 319s + all.ok <- FALSE 319s + } 319s > 319s > 319s > 319s > fa.varimax <- GPFoblq(fa.none$loadings, method="varimax", normalize=TRUE) 319s > 319s > # with eps=1e-8 319s > # tst <- t(matrix(c( 319s > # 0.229695829694226694, -0.757005882905721683, 319s > # 0.325474298411086493, -0.774533969509160203, 319s > # 0.227951538606475851, -0.738861531224136225, 319s > # 0.634850649690308022, -0.299876110481063607, 319s > # 0.707312661165822032, -0.278246783076943283, 319s > # 0.789359884149245072, -0.214120439603779994, 319s > # 0.698885205896135120, -0.199081171877497243 319s > # ), 2, 7)) 319s > 319s > # with eps=1e-5 319s > tst <- t(matrix(c( 319s + 0.229698038368303409, -0.757005212686898243, 319s + 0.325476558225504142, -0.774533019824047542, 319s + 0.227953694341768043, -0.738860866094951829, 319s + 0.634851524619887475, -0.299874258087383661, 319s + 0.707313472988376213, -0.278244719250824557, 319s + 0.789360508873491518, -0.214118136377292989, 319s + 0.698885786741510029, -0.199079132641678647 319s + ), 2, 7)) 319s > 319s > if( fuzz < max(abs(fa.varimax$loadings - tst))) { 319s + cat("Calculated value is not the same as test value in test WansbeekMeijer 2. Value:\n") 319s + print(fa.varimax$loadings, digits=18) 319s + cat("difference:\n") 319s + print(fa.varimax$loadings - tst, digits=18) 319s + all.ok <- FALSE 319s + } 319s > 319s > 319s > 319s > fa.oblimin <- GPFoblq(fa.none$loadings, method="oblimin", normalize=TRUE) 319s > 319s > # with eps=1e-8 319s > # tst <- t(matrix(c( 319s > # -0.0244898894997362740, -0.8055076884898763057, 319s > # 0.0821776433220552660, -0.7883517482514345032, 319s > # -0.0194442483441249758, -0.7847120136813017233, 319s > # 0.6350106056917923514, -0.1038114236654337219, 319s > # 0.7293893902400611085, -0.0495156037400738894, 319s > # 0.8517915457391848078, 0.0588983480418694277, 319s > # 0.7504355940804637859, 0.0408946221245683056 319s > # ), 2, 7)) 319s > 319s > # with eps=1e-5 319s > tst <- t(matrix(c( 319s + -0.0244886312423446446, -0.8055069385602275922, 319s + 0.0821788889356081659, -0.7883509906546982693, 319s + -0.0194430219824419312, -0.7847112821295906260, 319s + 0.6350108529538124325, -0.1038111848933331444, 319s + 0.7293895650539216069, -0.0495153948664520185, 319s + 0.8517915670863017708, 0.0588984825074335624, 319s + 0.7504356301074717184, 0.0408947509009953206 319s + ), 2, 7)) 319s > 319s > if( fuzz < max(abs(fa.oblimin$loadings - tst))) { 319s + cat("Calculated value is not the same as test value in test WansbeekMeijer 3. Value:\n") 319s + print(fa.oblimin$loadings, digits=18) 319s + cat("difference:\n") 319s + print(fa.oblimin$loadings - tst, digits=18) 319s + all.ok <- FALSE 319s + } 319s > 319s > 319s > cat("tests completed.\n") 319s tests completed. 319s > 319s > if (! all.ok) stop("some tests FAILED") 319s > 319s > 319s BEGIN TEST print-GPArotation.R 319s 319s R version 4.3.2 (2023-10-31) -- "Eye Holes" 319s Copyright (C) 2023 The R Foundation for Statistical Computing 319s Platform: x86_64-pc-linux-gnu (64-bit) 319s 319s R is free software and comes with ABSOLUTELY NO WARRANTY. 319s You are welcome to redistribute it under certain conditions. 319s Type 'license()' or 'licence()' for distribution details. 319s 319s R is a collaborative project with many contributors. 319s Type 'contributors()' for more information and 319s 'citation()' on how to cite R or R packages in publications. 319s 319s Type 'demo()' for some demos, 'help()' for on-line help, or 319s 'help.start()' for an HTML browser interface to help. 319s Type 'q()' to quit R. 319s 319s > # testing that the print.GPArotation output is identical 319s > # for 2 runs of quartimin rotation, that have 2 319s > # different looking loadings matrices wrt sign and order 319s > # the print.GPArotation should look identical 319s > 319s > 319s > Sys.getenv("R_LIBS") 319s [1] "" 319s > library() 319s Packages in library ‘/usr/lib/R/site-library’: 319s 319s GPArotation Gradient Projection Factor Rotation 319s 319s Packages in library ‘/usr/lib/R/library’: 319s 319s base The R Base Package 319s compiler The R Compiler Package 319s datasets The R Datasets Package 319s graphics The R Graphics Package 319s grDevices The R Graphics Devices and Support for Colours 319s and Fonts 319s grid The Grid Graphics Package 319s methods Formal Methods and Classes 319s parallel Support for Parallel Computation in R 319s splines Regression Spline Functions and Classes 319s stats The R Stats Package 319s stats4 Statistical Functions using S4 Classes 319s tcltk Tcl/Tk Interface 319s tools Tools for Package Development 319s utils The R Utils Package 319s 319s Warning message: 319s In library() : library ‘/usr/local/lib/R/site-library’ contains no packages 319s > require("GPArotation") 319s Loading required package: GPArotation 319s > search() 319s [1] ".GlobalEnv" "package:GPArotation" "package:stats" 319s [4] "package:graphics" "package:grDevices" "package:utils" 319s [7] "package:datasets" "package:methods" "Autoloads" 319s [10] "package:base" 319s > Sys.info() 319s sysname 319s "Linux" 319s release 319s "6.8.0-11-generic" 319s version 319s "#11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024" 319s nodename 319s "autopkgtest" 319s machine 319s "x86_64" 319s login 319s "ubuntu" 319s user 319s "ubuntu" 319s effective_user 319s "ubuntu" 319s > 319s > require("stats") 319s > require("GPArotation") 319s > 319s > athl <- matrix(c( 319s + .73, -.07, .50, .82, -.01, .27, .77, -.46, -.22, .78, .17, .03, 319s + .77, .41, .13, .81, -.01, .27, .71, -.45, -.30, .82, .12, -.11, 319s + .66, -.15, -.45, .39, .76, -.40), byrow=T, ncol =3) 319s > ## z1 gives the results that have the right ordering and sign of the factors 319s > ## z2 is a random other order and sign 319s > set.seed(238) 319s > z1 <- quartimin(athl, Tmat = Random.Start(3)) 319s > head(z1$loadings) 319s [,1] [,2] [,3] 319s [1,] -0.9451409 0.05346419 0.180327102 319s [2,] -0.7725340 -0.14313505 -0.011868009 319s [3,] -0.1322889 -0.86168891 0.128470606 319s [4,] -0.5377313 -0.20500970 -0.287529554 319s [5,] -0.6888492 0.05547964 -0.440716643 319s [6,] -0.7665208 -0.13863386 -0.009868994 319s > set.seed(46) 319s > z2 <- quartimin(athl, Tmat = Random.Start(3)) 319s > head(z2$loadings) 319s [,1] [,2] [,3] 319s [1,] -0.9451416 -0.180326159 0.05346510 319s [2,] -0.7725340 0.011869079 -0.14313424 319s [3,] -0.1322881 -0.128469679 -0.86168934 319s [4,] -0.5377307 0.287530600 -0.20500891 319s [5,] -0.6888486 0.440717717 0.05548088 319s [6,] -0.7665208 0.009870051 -0.13863307 319s > 319s > 319s > #> z1 319s > #Oblique rotation method Quartimin converged. 319s > #Loadings: 319s > # [,1] [,2] [,3] 319s > # [1,] 0.9451 -0.0535 -0.18033 319s > # [2,] 0.7725 0.1431 0.01187 319s > # [3,] 0.1323 0.8617 -0.12847 319s > # [4,] 0.5377 0.2050 0.28753 319s > # [5,] 0.6888 -0.0555 0.44072 319s > # [6,] 0.7665 0.1386 0.00987 319s > # [7,] 0.0150 0.8967 -0.08931 319s > # [8,] 0.4047 0.3792 0.32647 319s > # [9,] -0.1056 0.7915 0.24071 319s > #[10,] -0.0155 -0.0165 0.94994 319s > # 319s > # [,1] [,2] [,3] 319s > #SS loadings 3.034 2.405 1.401 319s > #Proportion Var 0.303 0.240 0.140 319s > #Cumulative Var 0.303 0.544 0.684 319s > # 319s > #Phi: 319s > # [,1] [,2] [,3] 319s > #[1,] 1.000 0.554 0.259 319s > #[2,] 0.554 1.000 0.186 319s > #[3,] 0.259 0.186 1.000 319s > #> z2 319s > #Oblique rotation method Quartimin converged. 319s > #Loadings: 319s > # [,1] [,2] [,3] 319s > # [1,] 0.9451 -0.0535 -0.18033 319s > # [2,] 0.7725 0.1431 0.01187 319s > # [3,] 0.1323 0.8617 -0.12847 319s > # [4,] 0.5377 0.2050 0.28753 319s > # [5,] 0.6888 -0.0555 0.44072 319s > # [6,] 0.7665 0.1386 0.00987 319s > # [7,] 0.0150 0.8967 -0.08930 319s > # [8,] 0.4047 0.3792 0.32647 319s > # [9,] -0.1056 0.7915 0.24071 319s > #[10,] -0.0155 -0.0165 0.94994 319s > # 319s > # [,1] [,2] [,3] 319s > #SS loadings 3.034 2.405 1.401 319s > #Proportion Var 0.303 0.240 0.140 319s > #Cumulative Var 0.303 0.544 0.684 319s > # 319s > #Phi: 319s > # [,1] [,2] [,3] 319s > #[1,] 1.000 0.554 0.259 319s > #[2,] 0.554 1.000 0.186 319s > #[3,] 0.259 0.186 1.000 319s > 319s BEGIN TEST rotations.R 319s 319s R version 4.3.2 (2023-10-31) -- "Eye Holes" 319s Copyright (C) 2023 The R Foundation for Statistical Computing 319s Platform: x86_64-pc-linux-gnu (64-bit) 319s 319s R is free software and comes with ABSOLUTELY NO WARRANTY. 319s You are welcome to redistribute it under certain conditions. 319s Type 'license()' or 'licence()' for distribution details. 319s 319s R is a collaborative project with many contributors. 319s Type 'contributors()' for more information and 319s 'citation()' on how to cite R or R packages in publications. 319s 319s Type 'demo()' for some demos, 'help()' for on-line help, or 319s 'help.start()' for an HTML browser interface to help. 319s Type 'q()' to quit R. 319s 319s > # Tests here only compare against values computed previously with this code, 319s > # to ensure there was no accidental change. It would be better to have 319s > # comparisons with known correct values. 319s > 319s > # Test for oblimax is commented out as it appears to be unstable. 319s > 319s > 319s > Sys.getenv("R_LIBS") 319s [1] "" 319s > library() 319s Packages in library ‘/usr/lib/R/site-library’: 319s 319s GPArotation Gradient Projection Factor Rotation 319s 319s Packages in library ‘/usr/lib/R/library’: 319s 319s base The R Base Package 319s compiler The R Compiler Package 319s datasets The R Datasets Package 319s graphics The R Graphics Package 319s grDevices The R Graphics Devices and Support for Colours 319s and Fonts 319s grid The Grid Graphics Package 319s methods Formal Methods and Classes 319s parallel Support for Parallel Computation in R 319s splines Regression Spline Functions and Classes 319s stats The R Stats Package 319s stats4 Statistical Functions using S4 Classes 319s tcltk Tcl/Tk Interface 319s tools Tools for Package Development 319s utils The R Utils Package 319s 319s > require("GPArotation") 319s Warning message: 319s In library() : library ‘/usr/local/lib/R/site-library’ contains no packages 319s Loading required package: GPArotation 319s > search() 319s [1] ".GlobalEnv" "package:GPArotation" "package:stats" 319s [4] "package:graphics" "package:grDevices" "package:utils" 319s [7] "package:datasets" "package:methods" "Autoloads" 319s [10] "package:base" 319s > Sys.info() 319s sysname 319s "Linux" 319s release 319s "6.8.0-11-generic" 319s version 319s "#11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024" 319s nodename 319s "autopkgtest" 319s machine 319s "x86_64" 319s login 319s "ubuntu" 319s user 319s "ubuntu" 319s effective_user 319s "ubuntu" 319s > 319s > require("stats") 319s > require("GPArotation") 319s > 319s > fuzz <- 1e-6 319s > all.ok <- TRUE 319s > 319s > 319s > data(ability.cov) 319s > L <- loadings(factanal(factors = 2, covmat=ability.cov)) 319s > 319s > 319s > if( 0.001 < max(abs(varimax(L, normalize=FALSE)$loadings - 319s + Varimax(L, normalize=FALSE)$loadings))) { 319s + cat("Calculated difference exceeds tolerance\n") 319s + cat("difference:\n") 319s + print(varimax(L, normalize=FALSE)$loadings - 319s + Varimax(L, normalize=FALSE)$loadings, digits=18) 319s + all.ok <- FALSE 319s + } 319s > 319s > if( 0.01 < max(abs(varimax(L, normalize=TRUE)$loadings - 319s + Varimax(L, normalize=TRUE, eps=1e-5)$loadings))) { 319s + cat("Calculated difference exceeds tolerance\n") 319s + cat("difference:\n") 319s + print(varimax(L, normalize=TRUE)$loadings - 319s + Varimax(L, normalize=TRUE, eps=1e-5)$loadings, digits=18) 319s + all.ok <- FALSE 319s + } 319s > 319s > 319s > v <- oblimin(L, eps=1e-8)$loadings 319s > tst <- t(matrix(c( 319s + 0.3863615904740822504, 0.4745127741495974161, 319s + -0.0110059418769087539, 0.6458720769633764514, 319s + -0.0262926272350604423, 0.8961141105684561348, 319s + -0.0180200526810754824, 0.4882928281695405048, 319s + 0.9900944939102318543, -0.0370718282544326011, 319s + 0.7905657274265397438, 0.0526109550054999417 319s + ), 2, 6)) 319s > 319s > if( fuzz < max(abs(v - tst))) { 319s + cat("Calculated value is not the same as test value in test rotations 1. Value:\n") 319s + print(v, digits=18) 319s + cat("difference:\n") 319s + print(v - tst, digits=18) 319s + all.ok <- FALSE 319s + } 319s > 319s > 319s > v <- quartimin(L, eps=1e-8)$loadings 319s > tst <- t(matrix(c( 319s + 0.3863615904740822504, 0.4745127741495974161, 319s + -0.0110059418769087539, 0.6458720769633764514, 319s + -0.0262926272350604423, 0.8961141105684561348, 319s + -0.0180200526810754824, 0.4882928281695405048, 319s + 0.9900944939102318543, -0.0370718282544326011, 319s + 0.7905657274265397438, 0.0526109550054999417 319s + ), 2, 6)) 319s > 319s > if( fuzz < max(abs(v - tst))) { 319s + cat("Calculated value is not the same as test value in test rotations 2. Value:\n") 319s + print(v, digits=18) 319s + cat("difference:\n") 319s + print(v - tst, digits=18) 319s + all.ok <- FALSE 319s + } 319s > 319s > 319s > v <- targetT(L, Target=matrix(c(rep(1,3),rep(0,6),rep(1,3)), 6,2), 319s + eps=1e-5)$loadings 319s > tst <- t(matrix(c( 319s + 0.551529228817982942, 0.4905002767031292898, 319s + 0.217748645523411000, 0.6027046291262584399, 319s + 0.291173432863349457, 0.8348885228488550636, 319s + 0.154994397662456290, 0.4544843569140373241, 319s + 0.969702339393929247, 0.0850652965070581996, 319s + 0.803390575440818822, 0.1448091121037717866 319s + ), 2, 6)) 319s > 319s > if( fuzz < max(abs(v - tst))) { 319s + cat("Calculated value is not the same as test value in test rotations 3. Value:\n") 319s + print(v, digits=18) 319s + cat("difference:\n") 319s + print(v - tst, digits=18) 319s + all.ok <- FALSE 319s + } 319s > 319s > 319s > v <- targetQ(L, Target=matrix(c(rep(1,3),rep(0,6),rep(1,3)), 6,2), 319s + eps=1e-5)$loadings 319s > tst <- t(matrix(c( 319s + 0.735795682866631218, 0.565351705145453853, 319s + 0.433590223819374398, 0.664644550038417159, 319s + 0.589924557708411568, 0.920006940799857786, 319s + 0.317543426981046928, 0.500590650032113116, 319s + 1.021758247914384077, 0.155121528590726393, 319s + 0.872521244896209747, 0.208735706420634437 319s + ), 2, 6)) 319s > 319s > if( fuzz < max(abs(v - tst))) { 319s + cat("Calculated value is not the same as test value in test rotations 4. Value:\n") 319s + print(v, digits=18) 319s + cat("difference:\n") 319s + print(v - tst, digits=18) 319s + all.ok <- FALSE 319s + } 319s > 319s > 319s > # Does not converge even with maxit=10000, but the loadings matrix is not 319s > # changing. Possibly the gradient is extremely large even very close to opt. 319s > v <- pstT(L, W = matrix(c(rep(.4,6),rep(.6,6)), 6,2), 319s + Target= matrix(c(rep(1,3),rep(0,6),rep(1,3)), 6,2), 319s + maxit=1000, eps=1e-5)$loadings 320s Warning message: 320s In GPForth(A, Tmat = Tmat, normalize = normalize, eps = eps, maxit = maxit, : 320s convergence not obtained in GPForth. 1000 iterations used. 320s > tst <- t(matrix(c( 320s + 0.37067889993474656407, 0.638257130653133720, 320s + 0.01855112570739854416, 0.640564749523800270, 320s + 0.01576132191496706567, 0.884065831441111172, 320s + 0.00524531003824213384, 0.480158078874985073, 320s + 0.89458633399812259590, 0.383762977265515448, 320s + 0.71793428958051475064, 0.388556883222951677 320s + ), 2, 6)) 320s > 320s > if( fuzz < max(abs(v - tst))) { 320s + cat("Calculated value is not the same as test value in test rotations 5. Value:\n") 320s + print(v, digits=18) 320s + cat("difference:\n") 320s + print(v - tst, digits=18) 320s + all.ok <- FALSE 320s + } 320s > 320s > 320s > # Does not converge even with maxit=10000, but the loadings matrix is not 320s > # changing. Possibly the gradient is extremely large even very close to opt. 320s > v <- pstQ(L, W = matrix(c(rep(.4,6),rep(.6,6)), 6,2), 320s + Target= matrix(c(rep(1,3),rep(0,6),rep(1,3)), 6,2), 320s + maxit=1000, eps=1e-5)$loadings 321s > tst <- t(matrix(c( 321s + 0.573125161748393785, 0.700868331877288475, 321s + 0.214899397066479453, 0.681727425525818886, 321s + 0.286558275327103040, 0.940272379393286339, 321s + 0.152257795885557295, 0.510481967637567036, 321s + 1.029289798076480578, 0.462598702071116141, 321s + 0.850691132520651205, 0.456859727346562328 321s + ), 2, 6)) 321s > 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 6. Value:\n") 321s Warning message: 321s In GPFoblq(A, Tmat = Tmat, normalize = normalize, eps = eps, maxit = maxit, : 321s convergence not obtained in GPFoblq. 1000 iterations used. 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > # oblimax 321s > # this is test value on one computer 321s > # tst <- t(matrix(c( 321s > # -8111059.94622692652, 8111060.62253121007, 321s > # 1495036.43465861562, -1495035.79614594672, 321s > # 2331634.63904705830, -2331633.75893370388, 321s > # 1356735.91680212389, -1356735.43916810025, 321s > # -23187491.19758165255, 23187491.68068471923, 321s > # -18357040.58573083207, 18357041.05348757654 321s > # ), 2, 6)) 321s > # 321s > # this is test value on another computer 321s > # tst <- t(matrix(c( 321s > # 2694770.06630349346, -2694769.38999920478, 321s > # -496701.45733913727, 496702.09585180727, 321s > # -774647.63529061736, 774648.51540397422, 321s > # -450753.43529273639, 450753.91292676108, 321s > # 7703672.48495316971, -7703672.00185009185, 321s > # 6098832.71036116872, -6098832.24260441773 321s > # ), 2, 6)) 321s > # 321s > # this does not converge on all platforms and has large differences possible a mistake ??? 321s > # v <- oblimax(L, eps=1e-5)$loadings 321s > # if( fuzz < max(abs(v - tst))) { 321s > # cat("Calculated value is not the same as test value in test rotations 7. Value:\n") 321s > # print(v, digits=18) 321s > # cat("difference:\n") 321s > # print(v - tst, digits=18) 321s > # all.ok <- FALSE 321s > # } 321s > 321s > 321s > v <- entropy(L, maxit=3000, eps=1e-5)$loadings 321s > tst <- t(matrix(c( 321s + 0.528292107548243184, 0.515443945340967824, 321s + 0.189686511729033253, 0.612116304198454975, 321s + 0.252311894464850861, 0.847442931117894815, 321s + 0.133843268148035738, 0.461156452364903380, 321s + 0.964740133927989407, 0.129750551769587635, 321s + 0.795847094000000532, 0.181751199795689433 321s + ), 2, 6)) 321s > 321s > if( 0.01 < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 8. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > 321s > v <- quartimax(L, eps=1e-5)$loadings 321s > tst <- t(matrix(c( 321s + 0.534714740804540178, 0.508778102568043678, 321s + 0.197348140750149392, 0.609689309353509956, 321s + 0.262919828098457153, 0.844212045390758559, 321s + 0.139616102327241837, 0.459441658926639795, 321s + 0.966291466215733252, 0.117641548844535412, 321s + 0.798063848020893585, 0.171756193883937508 321s + ), 2, 6)) 321s > 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 9. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > 321s > v <- Varimax(L, eps=1e-8)$loadings 321s > tst <- t(matrix(c( 321s + 0.515866523962843160, 0.527879475961036904, 321s + 0.175054634278874244, 0.616460231981747930, 321s + 0.232057748479543163, 0.853211588623112749, 321s + 0.122822468397975171, 0.464213243286899446, 321s + 0.961376376417989453, 0.152689863976982837, 321s + 0.791292800869773050, 0.200653429940987366 321s + ), 2, 6)) 321s > 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 10. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > 321s > v <- simplimax(L, eps=1e-5)$loadings 321s > tst <- t(matrix(c( 321s + 0.3384175759313114429, 0.508414890494446547464, 321s + -0.0654601124161610648, 0.670992229004664153535, 321s + -0.1016231721735353366, 0.930535379393095940515, 321s + -0.0589933707274080121, 0.506904360351960181497, 321s + 0.9733094402675376289, 0.000234046050254643859, 321s + 0.7702037184085044341, 0.085651123319384916965 321s + ), 2, 6)) 321s > 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 11. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > 321s > v <- bentlerT(L, eps=1e-8)$loadings 321s > tst <- t(matrix(c( 321s + 0.523583611303327312, 0.520226117818945788, 321s + 0.184113022124463677, 0.613815719643687197, 321s + 0.244596116053327067, 0.849702038129718673, 321s + 0.129644684715025493, 0.462354355134084738, 321s + 0.963520501269179652, 0.138517057902201340, 321s + 0.794161628656258278, 0.188979901644201559 321s + ), 2, 6)) 321s > 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 12. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > 321s > v <- bentlerQ(L, eps=1e-8)$loadings 321s > tst <- t(matrix(c( 321s + 0.3801726240258240241, 0.4741208368044214638, 321s + -0.0223632969057368826, 0.6514196922540864687, 321s + -0.0421105927111659756, 0.9039359851665277334, 321s + -0.0266594447192576613, 0.4925968005718689424, 321s + 0.9961524457620027917, -0.0485973498906049697, 321s + 0.7939648477384558811, 0.0440983921679098251 321s + ), 2, 6)) 321s > 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 13. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > 321s > v <- tandemI(L, eps=1e-5)$loadings 321s > tst <- t(matrix(c( 321s + 0.615424480780047745, 0.4074649925368262759, 321s + 0.300894306348887419, 0.5658002819054848143, 321s + 0.406455233467338028, 0.7852483408305571677, 321s + 0.217785179074990981, 0.4279590047675180808, 321s + 0.971977129465111611, -0.0530960591067626969, 321s + 0.815800376450207976, 0.0295946184147908228 321s + ), 2, 6)) 321s > 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 14. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > 321s > 321s > v <- tandemII(L, eps=1e-5)$loadings 321s > tst <- t(matrix(c( 321s + 0.512160139332842212, 0.531476249107136312, 321s + 0.170736763115044710, 0.617670057812827134, 321s + 0.226081850628144149, 0.854814488884392154, 321s + 0.119571200821562001, 0.465061309851099225, 321s + 0.960284416460420398, 0.159413208985883820, 321s + 0.789869387186175276, 0.206185467095899383 321s + ), 2, 6)) 321s > 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 15. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > 321s > v <- geominT(L, eps=1e-5)$loadings 321s > tst <- t(matrix(c( 321s + 0.572197044101002361, 0.4662247895688098054, 321s + 0.243573415560656120, 0.5927388411683653935, 321s + 0.326956608263186954, 0.8215352639437966120, 321s + 0.174476792179181994, 0.4473668997335142894, 321s + 0.972471249855535680, 0.0431091626026945812, 321s + 0.808894688433769660, 0.1099794466209375043 321s + ), 2, 6)) 321s > 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 16. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > 321s > v <- geominQ(L, eps=1e-5)$loadings 321s > tst <- t(matrix(c( 321s + 0.39672053553904490508, 0.4713295988080449250, 321s + 0.00424452688463150020, 0.6389466007374070555, 321s + -0.00510976786312981532, 0.8864521406378518265, 321s + -0.00646959173137159373, 0.4830101828530461994, 321s + 0.98709860078485589518, -0.0318959930081098297, 321s + 0.79011178369962709045, 0.0558689642678330683 321s + ), 2, 6)) 321s > 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 17. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > 321s > v <- cfT(L, eps=1e-8)$loadings 321s > tst <- t(matrix(c( 321s + 0.534721263659975854, 0.508771247100584523, 321s + 0.197355957387199576, 0.609686779159006154, 321s + 0.262930651479430233, 0.844208674501022327, 321s + 0.139621992686633722, 0.459439868910532512, 321s + 0.966292974385164483, 0.117629160286744874, 321s + 0.798066049992627313, 0.171745962120156664 321s + ), 2, 6)) 321s > 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 18. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > 321s > v <- cfQ(L, eps=1e-8)$loadings 321s > tst <- t(matrix(c( 321s + 0.3863615904740822504, 0.4745127741495974161, 321s + -0.0110059418769087539, 0.6458720769633764514, 321s + -0.0262926272350604423, 0.8961141105684561348, 321s + -0.0180200526810754824, 0.4882928281695405048, 321s + 0.9900944939102318543, -0.0370718282544326011, 321s + 0.7905657274265397438, 0.0526109550054999417 321s + ), 2, 6)) 321s > 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 19. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > 321s > v <- infomaxT(L, eps=1e-5)$loadings 321s > tst <- t(matrix(c( 321s + 0.495330443338021176, 0.547195361446864537, 321s + 0.151384273205308784, 0.622695868320644275, 321s + 0.199304253086364791, 0.861451466010626055, 321s + 0.105004533733904976, 0.468565194910632365, 321s + 0.954843809781045660, 0.189293503899924942, 321s + 0.783052579543945471, 0.230726576980168713 321s + ), 2, 6)) 321s > 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 20. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > 321s > v <- infomaxQ(L, eps=1e-5)$loadings 321s > tst <- t(matrix(c( 321s + 0.39327554287862442894, 0.4693137508305071925, 321s + -0.00319802321222481794, 0.6422985517185823001, 321s + -0.01549245038490981718, 0.8912279460026399924, 321s + -0.01214605901641467763, 0.4856544522916727002, 321s + 0.99260028929193111491, -0.0433225495465055510, 321s + 0.79356458059567791530, 0.0471559021503157039 321s + ), 2, 6)) 321s > 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 21. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > 321s > v <- mccammon(L, eps=1e-5)$loadings 321s > tst <- t(matrix(c( 321s + 0.4293472299617892007, 0.600363196582340275, 321s + 0.0790140496845253004, 0.635943490060206229, 321s + 0.0992523811009183854, 0.878618107277518656, 321s + 0.0506062164774049028, 0.477512622702450096, 321s + 0.9268544198491108776, 0.297488850382792269, 321s + 0.7514463663627769519, 0.318958389348199534 321s + ), 2, 6)) 321s > 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 22. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > 321s > ###### ADDED IN NOVEMBER 2022 FOR EQUAMAX, PARSIMAX, VARIMIN, OBLIMAX 321s > 321s > data(Thurstone) 321s > v <- equamax(box26, eps=1e-5)$loadings 321s > tst <- t(matrix(c( 321s + 0.511813618717971597, 0.1252460667724786814, 0.835031881099661200, 321s + 0.211275278125612587, 0.9469860693462274215, 0.024701038786419674, 321s + 0.923671387190205140, 0.1861505968810791833, -0.278366886980007111, 321s + 0.414270797796799317, 0.7243752493532077397, 0.530526346393166759, 321s + 0.927099794400001564, 0.1710560637343615797, 0.314400690653154735, 321s + 0.685509679739711331, 0.6873945075387188908, -0.212674093365320949, 321s + 0.500975325417812756, 0.4985944480056956341, 0.693100497576226382, 321s + 0.350251174602310256, 0.8631423492204841619, 0.303299191676876356, 321s + 0.809196181501955492, 0.1468111894018074293, 0.540855816747015439, 321s + 1.051940508364259674, 0.2023337382785123650, 0.126016765617061266, 321s + 0.528246625368315792, 0.8145581663496035407, -0.154555803579673606, 321s + 0.791784749686200273, 0.5353191515116044741, -0.254010464723911089, 321s + 0.283760830721282831, -0.7132278971933163625, 0.633221728633476699, 321s + -0.283760830721282831, 0.7132278971933163625, -0.633221728633476699, 321s + -0.351981708826951678, 0.0145585781278812498, 0.920862598031950474, 321s + 0.351981708826951678, -0.0145585781278812498, -0.920862598031950474, 321s + -0.641238077659381234, 0.7340358583767647715, 0.211813801195267382, 321s + 0.641238077659381234, -0.7340358583767647715, -0.211813801195267382, 321s + 0.370916272566192251, 0.7781992933002486179, 0.457012011497068604, 321s + 0.943267697340363864, 0.1458935486092693412, 0.269085717994103968, 321s + 0.683769139477491628, 0.6932804480935084168, -0.193612975261152009, 321s + 0.375506314902942506, 0.7683789003013250518, 0.444462454027040654, 321s + 0.921697465732450816, 0.1542330203892136042, 0.244709944799956780, 321s + 0.664806997738585315, 0.6918110118942031317, -0.165931249557543792, 321s + 0.748952844572093657, 0.5985308972371030656, 0.239842451746804020, 321s + 0.716556890444816297, 0.6343221919993241587, 0.139425892477791219 321s + ), 3, 26)) 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 22. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > ### SAME FOR CRAWFORD FERGUSON WITH KAPPA = m / (2 * p) = 3 / (2 * 26) 321s > v <- cfT(box26, kappa = (3 / (2 * 26)), eps=1e-5)$loadings 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 22. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > 321s > v <- parsimax(box26, eps=1e-5)$loadings 321s > tst <- t(matrix(c( 321s + 0.7201835790622810318, -0.2820790149262949464, 0.6137467244615277817, 321s + -0.0679423851913938670, 0.6010788795762025405, 0.7590243822315081434, 321s + 0.6707172136894012926, 0.7174085874409354968, -0.0277909684381195121, 321s + 0.3564975652920873705, 0.2169149780725644350, 0.8964682806594965747, 321s + 0.8905375652375422391, 0.2961288407436278303, 0.3269136806262873951, 321s + 0.3419238671745732927, 0.8395902605853544642, 0.4072361273101923196, 321s + 0.5551801796495600128, 0.0181442676741417341, 0.8193941381745735164, 321s + 0.1791815177720131602, 0.4232257028261393605, 0.8651329309165379788, 321s + 0.8735154515073240145, 0.0707778916688399651, 0.4481498031114935499, 321s + 0.9254209439635597834, 0.5018907196720771013, 0.2347334274887991901, 321s + 0.1871266535649374341, 0.7975561080494565358, 0.5434380093797205324, 321s + 0.4642991413806251688, 0.8329607560592182658, 0.2619421428072832847, 321s + 0.6793187635833454197, -0.7070938474525871875, -0.1694942722875707464, 321s + -0.6793187635833454197, 0.7070938474525871875, 0.1694942722875707464, 321s + 0.0126413340577520572, -0.7959999181796318934, 0.5816488003350992475, 321s + -0.0126413340577520572, 0.7959999181796318934, -0.5816488003350992475, 321s + -0.7005089039174136056, -0.0349340740508546910, 0.7091733821870598309, 321s + 0.7005089039174136056, 0.0349340740508546910, -0.7091733821870598309, 321s + 0.2764675266718980007, 0.2782887989292237019, 0.8933946782281918519, 321s + 0.8957285854821546156, 0.3212930506383097073, 0.2790825626255922787, 321s + 0.3455615085575033385, 0.8287155760723180498, 0.4236528505493507568, 321s + 0.2788032457489866833, 0.2837361452757249936, 0.8779069142135194070, 321s + 0.8654448252950356357, 0.3331277242202841382, 0.2706070467039994321, 321s + 0.3390107603224090660, 0.7999236919074760310, 0.4396564471388281214, 321s + 0.5855440811683275681, 0.5029973433114328651, 0.6171108503586539840, 321s + 0.5106729412991620753, 0.5782224406112924653, 0.5832066153589001711 321s + ), 3, 26)) 321s > 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 22. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > ### SAME FOR CRAWFORD FERGUSON WITH KAPPA = (m - 1) / (p + m - 2) = (3 -1) / (26 + 3 - 2) 321s > v <- cfT(box26, kappa=( (3-1)/(26+3-2) ), eps=1e-5)$loadings 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 22. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > data(Harman, package= "GPArotation") 321s > v <- varimin(Harman8, eps=1e-5)$loadings 321s > tst <- t(matrix(c( 321s + 321s + 0.800626657046876855, -0.452452158825595752, 321s + 0.783606930490612252, -0.524447498313301397, 321s + 0.742635936060292656, -0.522609669324872517, 321s + 0.768357486963803682, -0.455227165519225097, 321s + 0.818696625686402668, 0.444445536696790211, 321s + 0.702064973637186673, 0.410429985249392060, 321s + 0.623283524595303340, 0.401857745935120247, 321s + 0.668480210595655877, 0.287458184858228272 321s + ), 2, 8)) 321s > 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 22. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > 321s > 321s > 321s > v <- oblimax(Harman8, eps=1e-5)$loadings 321s > tst <- t(matrix(c( 321s + 0.93395421734409445058, -0.0302013026726007383, 321s + 0.99243032312927881300, -0.1121899246869615951, 321s + 0.96509469978483286567, -0.1322258547171115683, 321s + 0.91647702431117861188, -0.0502569243958834178, 321s + 0.08441855308346873921, 0.8875309317276611765, 321s + 0.04427084251510177149, 0.7907585046311147448, 321s + 0.00332736511424391868, 0.7399752420126202157, 321s + 0.14133359391312094733, 0.6483050831171799366 321s + ), 2, 8)) 321s > 321s > if( fuzz < max(abs(v - tst))) { 321s + cat("Calculated value is not the same as test value in test rotations 22. Value:\n") 321s + print(v, digits=18) 321s + cat("difference:\n") 321s + print(v - tst, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > 321s > cat("tests completed.\n") 321s tests completed. 321s > 321s > 321s > if (! all.ok) stop("some tests FAILED") 321s > 321s BEGIN TEST varimaxVarimax.R 321s 321s R version 4.3.2 (2023-10-31) -- "Eye Holes" 321s Copyright (C) 2023 The R Foundation for Statistical Computing 321s Platform: x86_64-pc-linux-gnu (64-bit) 321s 321s R is free software and comes with ABSOLUTELY NO WARRANTY. 321s You are welcome to redistribute it under certain conditions. 321s Type 'license()' or 'licence()' for distribution details. 321s 321s R is a collaborative project with many contributors. 321s Type 'contributors()' for more information and 321s 'citation()' on how to cite R or R packages in publications. 321s 321s Type 'demo()' for some demos, 'help()' for on-line help, or 321s 'help.start()' for an HTML browser interface to help. 321s Type 'q()' to quit R. 321s 321s > # Also see the first test in rotations.R 321s > # compares varimax to Varimax to 0.001 discrepancy 321s > 321s > Sys.getenv("R_LIBS") 321s [1] "" 321s > library() 321s Packages in library ‘/usr/lib/R/site-library’: 321s 321s GPArotation Gradient Projection Factor Rotation 321s 321s Packages in library ‘/usr/lib/R/library’: 321s 321s base The R Base Package 321s compiler The R Compiler Package 321s datasets The R Datasets Package 321s graphics The R Graphics Package 321s grDevices The R Graphics Devices and Support for Colours 321s and Fonts 321s grid The Grid Graphics Package 321s methods Formal Methods and Classes 321s parallel Support for Parallel Computation in R 321s splines Regression Spline Functions and Classes 321s stats The R Stats Package 321s stats4 Statistical Functions using S4 Classes 321s tcltk Tcl/Tk Interface 321s tools Tools for Package Development 321s utils The R Utils Package 321s 321s Warning message: 321s In library() : library ‘/usr/local/lib/R/site-library’ contains no packages 321s > require("GPArotation") 321s Loading required package: GPArotation 321s > search() 321s [1] ".GlobalEnv" "package:GPArotation" "package:stats" 321s [4] "package:graphics" "package:grDevices" "package:utils" 321s [7] "package:datasets" "package:methods" "Autoloads" 321s [10] "package:base" 321s > Sys.info() 321s sysname 321s "Linux" 321s release 321s "6.8.0-11-generic" 321s version 321s "#11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024" 321s nodename 321s "autopkgtest" 321s machine 321s "x86_64" 321s login 321s "ubuntu" 321s user 321s "ubuntu" 321s effective_user 321s "ubuntu" 321s > 321s > ### note that this is a slightly lower bar than other tests 321s > ### to correct for the built-in varimax function working differently 321s > ### than GPA, and to ensure Varimax convergence 321s > ### these are differences in the 4th decimal or better 321s > fuzz <- 1e-4 321s > ### 321s > all.ok <- TRUE 321s > 321s > sortFac <- function(x){ # Based on Fungible faSort 321s + vx <- order(colSums(x$loadings^2), decreasing = TRUE) 321s + Dsgn <- diag(sign(colSums(x$loadings^3))) [ , vx] 321s + x$Th <- x$Th %*% Dsgn 321s + x$loadings <- x$loadings %*% Dsgn 321s + if ("Phi" %in% names(x)) { 321s + x$Phi <- diag(1/diag(Dsgn)) %*% x$Phi %*% Dsgn 321s + } 321s + x 321s + } 321s > data(Thurstone, package="GPArotation") 321s > yv1 <- varimax(box20, normalize = FALSE, eps = 1e-7) #built-in R 321s > names(yv1) <- c("loadings","Th") 321s > yv1 <- sortFac(yv1) 321s > yv2 <- sortFac(Varimax(box20, normalize = FALSE, maxit = 10000, eps = 1e-7)) #GPArotation version 321s > # yv.diff <- unclass(yv1$loadings) - unclass(yv2$loadings) 321s > # max(abs(yv.diff)) 321s > 321s > 321s > if( fuzz < max(abs(yv1$loadings - yv2$loadings))) { 321s + cat("Calculated varimax is not the same as Varimax:\n") 321s + # print(yv2$loadings, digits=18) 321s + cat("difference:\n") 321s + print(yv1$loadings - yv2$loadings, digits=18) 321s + all.ok <- FALSE 321s + } 321s > 321s > 321s autopkgtest [17:48:10]: test run-unit-test: -----------------------] 321s run-unit-test PASS 321s autopkgtest [17:48:10]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 322s autopkgtest [17:48:11]: test pkg-r-autopkgtest: preparing testbed 324s Note, using file '/tmp/autopkgtest.lANRY3/3-autopkgtest-satdep.dsc' to get the build dependencies 324s Reading package lists... 324s Building dependency tree... 324s Reading state information... 325s Starting pkgProblemResolver with broken count: 0 325s Starting 2 pkgProblemResolver with broken count: 0 325s Done 325s The following NEW packages will be installed: 325s dctrl-tools gfortran gfortran-13 gfortran-13-x86-64-linux-gnu 325s gfortran-x86-64-linux-gnu icu-devtools libblas-dev libbz2-dev 325s libgfortran-13-dev libicu-dev libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev 325s liblapack-dev liblzma-dev libncurses-dev libpcre2-16-0 libpcre2-32-0 325s libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev 325s pkg-config pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev zlib1g-dev 325s 0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded. 325s Need to get 33.6 MB of archives. 325s After this operation, 130 MB of additional disk space will be used. 325s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 dctrl-tools amd64 2.24-3build2 [66.9 kB] 325s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran-13-dev amd64 13.2.0-17ubuntu2 [942 kB] 325s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.6 MB] 326s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-13 amd64 13.2.0-17ubuntu2 [10.3 kB] 326s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1024 B] 326s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran amd64 4:13.2.0-7ubuntu1 [1176 B] 326s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 icu-devtools amd64 74.2-1ubuntu1 [212 kB] 326s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libblas-dev amd64 3.12.0-3 [170 kB] 326s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libbz2-dev amd64 1.0.8-5ubuntu1 [33.6 kB] 326s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 libicu-dev amd64 74.2-1ubuntu1 [11.9 MB] 326s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8-dev amd64 2.1.5-2ubuntu1 [294 kB] 326s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B] 326s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B] 326s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack-dev amd64 3.12.0-3 [5196 kB] 326s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libncurses-dev amd64 6.4+20240113-1ubuntu1 [384 kB] 326s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-16-0 amd64 10.42-4ubuntu1 [211 kB] 326s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-32-0 amd64 10.42-4ubuntu1 [198 kB] 326s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-posix3 amd64 10.42-4ubuntu1 [6808 B] 326s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-dev amd64 10.42-4ubuntu1 [743 kB] 326s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libpkgconf3 amd64 1.8.1-2 [31.1 kB] 326s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3ubuntu1 [896 kB] 326s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libpng-dev amd64 1.6.43-1 [264 kB] 326s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libreadline-dev amd64 8.2-3 [167 kB] 326s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf-bin amd64 1.8.1-2 [20.7 kB] 326s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf amd64 1.8.1-2 [16.8 kB] 326s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 pkg-config amd64 1.8.1-2 [7170 B] 326s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 liblzma-dev amd64 5.4.5-0.3 [205 kB] 326s Get:28 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-dev all 4.3.2-1build1 [4336 B] 326s Get:29 http://ftpmaster.internal/ubuntu noble/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 326s Fetched 33.6 MB in 0s (117 MB/s) 326s Selecting previously unselected package dctrl-tools. 326s (Reading database ... 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to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode 328s Setting up dctrl-tools (2.24-3build2) ... 328s Setting up libbz2-dev:amd64 (1.0.8-5ubuntu1) ... 328s Setting up libpcre2-dev:amd64 (10.42-4ubuntu1) ... 328s Setting up libpng-dev:amd64 (1.6.43-1) ... 328s Setting up libjpeg-dev:amd64 (8c-2ubuntu11) ... 328s Setting up gfortran-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 328s Setting up pkgconf:amd64 (1.8.1-2) ... 328s Setting up gfortran-13 (13.2.0-17ubuntu2) ... 328s Setting up liblapack-dev:amd64 (3.12.0-3) ... 328s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode 328s Setting up pkg-config:amd64 (1.8.1-2) ... 328s Setting up gfortran-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 328s Setting up gfortran (4:13.2.0-7ubuntu1) ... 328s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 328s 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 328s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 328s 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 328s Setting up r-base-dev (4.3.2-1build1) ... 328s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 328s Processing triggers for libc-bin (2.39-0ubuntu2) ... 328s Processing triggers for man-db (2.12.0-3) ... 328s Processing triggers for install-info (7.1-3) ... 331s Reading package lists... 331s Building dependency tree... 331s Reading state information... 331s Starting pkgProblemResolver with broken count: 0 331s Starting 2 pkgProblemResolver with broken count: 0 331s Done 332s The following NEW packages will be installed: 332s autopkgtest-satdep 332s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 332s Need to get 0 B/696 B of archives. 332s After this operation, 0 B of additional disk space will be used. 332s Get:1 /tmp/autopkgtest.lANRY3/4-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B] 333s Selecting previously unselected package autopkgtest-satdep. 333s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 77214 files and directories currently installed.) 333s Preparing to unpack .../4-autopkgtest-satdep.deb ... 333s Unpacking autopkgtest-satdep (0) ... 333s Setting up autopkgtest-satdep (0) ... 335s (Reading database ... 77214 files and directories currently installed.) 335s Removing autopkgtest-satdep (0) ... 335s autopkgtest [17:48:24]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 335s autopkgtest [17:48:24]: test pkg-r-autopkgtest: [----------------------- 335s Test: Try to load the R library GPArotation 335s 335s R version 4.3.2 (2023-10-31) -- "Eye Holes" 335s Copyright (C) 2023 The R Foundation for Statistical Computing 335s Platform: x86_64-pc-linux-gnu (64-bit) 335s 335s R is free software and comes with ABSOLUTELY NO WARRANTY. 335s You are welcome to redistribute it under certain conditions. 335s Type 'license()' or 'licence()' for distribution details. 335s 335s R is a collaborative project with many contributors. 335s Type 'contributors()' for more information and 335s 'citation()' on how to cite R or R packages in publications. 335s 335s Type 'demo()' for some demos, 'help()' for on-line help, or 335s 'help.start()' for an HTML browser interface to help. 335s Type 'q()' to quit R. 335s 335s > library('GPArotation') 335s > 335s > 335s Other tests are currently unsupported! 335s They will be progressively added. 335s autopkgtest [17:48:24]: test pkg-r-autopkgtest: -----------------------] 336s pkg-r-autopkgtest PASS 336s autopkgtest [17:48:25]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 336s autopkgtest [17:48:25]: @@@@@@@@@@@@@@@@@@@@ summary 336s run-unit-test PASS 336s pkg-r-autopkgtest PASS 345s Creating nova instance adt-noble-i386-r-cran-gparotation-20240322-174249-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-amd64-server-20240321.img (UUID 6f9effbc-61d8-4d0a-a7e9-883547f42ac1)...