0s autopkgtest [21:31:23]: starting date and time: 2024-03-22 21:31:23+0000 0s autopkgtest [21:31:23]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [21:31:23]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.66frey0z/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-kmi --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-3@lcy02-60.secgroup --name adt-noble-i386-r-cran-kmi-20240322-213123-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/ 590s autopkgtest [21:41:13]: testbed dpkg architecture: amd64 590s autopkgtest [21:41:13]: testbed apt version: 2.7.12 590s autopkgtest [21:41:13]: test architecture: i386 590s autopkgtest [21:41:13]: @@@@@@@@@@@@@@@@@@@@ test bed setup 590s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 591s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [498 kB] 591s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [58.8 kB] 591s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4041 kB] 591s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 591s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [463 kB] 591s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [700 kB] 591s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B] 591s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6700 B] 591s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [30.5 kB] 591s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B] 591s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4425 kB] 591s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1312 kB] 591s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B] 591s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [27.6 kB] 591s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [97.3 kB] 591s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B] 594s Fetched 11.8 MB in 2s (7863 kB/s) 594s Reading package lists... 596s Reading package lists... 596s Building dependency tree... 596s Reading state information... 596s Calculating upgrade... 597s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 597s Reading package lists... 597s Building dependency tree... 597s Reading state information... 597s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 598s sh: Attempting to set up Debian/Ubuntu apt sources automatically 598s sh: Distribution appears to be Ubuntu 599s Reading package lists... 599s Building dependency tree... 599s Reading state information... 599s eatmydata is already the newest version (131-1). 599s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 599s Reading package lists... 599s Building dependency tree... 599s Reading state information... 600s dbus is already the newest version (1.14.10-4ubuntu1). 600s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 600s Reading package lists... 600s Building dependency tree... 600s Reading state information... 600s rng-tools-debian is already the newest version (2.4). 600s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 600s Reading package lists... 601s Building dependency tree... 601s Reading state information... 601s The following packages will be REMOVED: 601s cloud-init* python3-configobj* python3-debconf* 601s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 601s After this operation, 3256 kB disk space will be freed. 601s (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.) 601s Removing cloud-init (24.1.2-0ubuntu1) ... 602s Removing python3-configobj (5.0.8-3) ... 602s Removing python3-debconf (1.5.86) ... 602s Processing triggers for man-db (2.12.0-3) ... 603s (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.) 603s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 603s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 603s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 603s invoke-rc.d: policy-rc.d denied execution of try-restart. 603s Reading package lists... 604s Building dependency tree... 604s Reading state information... 604s linux-generic is already the newest version (6.8.0-11.11+1). 604s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 604s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 604s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 604s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 606s Reading package lists... 606s Reading package lists... 606s Building dependency tree... 606s Reading state information... 607s Calculating upgrade... 607s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 607s Reading package lists... 607s Building dependency tree... 607s Reading state information... 607s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 608s autopkgtest [21:41:31]: rebooting testbed after setup commands that affected boot 749s autopkgtest [21:43:52]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024 750s autopkgtest [21:43:53]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-kmi 751s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-kmi 0.5.5-2build1 (dsc) [2047 B] 751s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-kmi 0.5.5-2build1 (tar) [35.7 kB] 751s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-kmi 0.5.5-2build1 (diff) [2556 B] 751s gpgv: Signature made Sat May 30 19:25:09 2020 UTC 751s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 751s gpgv: Can't check signature: No public key 751s dpkg-source: warning: cannot verify inline signature for ./r-cran-kmi_0.5.5-2build1.dsc: no acceptable signature found 751s autopkgtest [21:43:54]: testing package r-cran-kmi version 0.5.5-2build1 751s autopkgtest [21:43:54]: build not needed 753s autopkgtest [21:43:56]: test run-unit-test: preparing testbed 756s Note, using file '/tmp/autopkgtest.trzW8o/1-autopkgtest-satdep.dsc' to get the build dependencies 756s Reading package lists... 756s Building dependency tree... 756s Reading state information... 756s Starting pkgProblemResolver with broken count: 0 756s Starting 2 pkgProblemResolver with broken count: 0 756s Done 757s The following NEW packages will be installed: 757s build-essential cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu 757s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono g++ g++-13 757s g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-13 757s gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu libasan8 libatomic1 libblas3 757s libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libdatrie1 757s libdeflate0 libfontconfig1 libgcc-13-dev libgfortran5 libgomp1 757s libgraphite2-3 libharfbuzz0b libhwasan0 libice6 libisl23 libitm1 libjbig0 757s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 liblsan0 libmpc3 libnsl-dev 757s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 757s libpaper1 libpixman-1-0 libquadmath0 libsharpyuv0 libsm6 libstdc++-13-dev 757s libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 757s libubsan1 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 757s libxt6 linux-libc-dev r-base-core r-cran-dbi r-cran-kmi r-cran-lattice 757s r-cran-matrix r-cran-mitools r-cran-survival rpcsvc-proto unzip x11-common 757s xdg-utils zip 757s 0 upgraded, 83 newly installed, 0 to remove and 0 not upgraded. 757s Need to get 117 MB of archives. 757s After this operation, 341 MB of additional disk space will be used. 757s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.39-0ubuntu2 [20.4 kB] 757s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB] 757s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB] 757s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-dev amd64 1.3.4+ds-1build1 [222 kB] 757s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl-dev amd64 1.3.0-3 [71.2 kB] 757s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu6 [68.5 kB] 757s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.39-0ubuntu2 [2126 kB] 757s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libisl23 amd64 0.26-3 [741 kB] 757s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libmpc3 amd64 1.3.1-1 [54.1 kB] 757s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.2 MB] 757s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-17ubuntu2 [1030 B] 757s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] 757s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] 757s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 14-20240303-1ubuntu1 [47.7 kB] 757s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240303-1ubuntu1 [147 kB] 757s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240303-1ubuntu1 [29.1 kB] 757s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240303-1ubuntu1 [10.4 kB] 757s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240303-1ubuntu1 [3026 kB] 757s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240303-1ubuntu1 [1310 kB] 757s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240303-1ubuntu1 [2732 kB] 757s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240303-1ubuntu1 [1172 kB] 757s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240303-1ubuntu1 [1629 kB] 757s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240303-1ubuntu1 [155 kB] 757s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-17ubuntu2 [2687 kB] 757s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [21.9 MB] 757s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-17ubuntu2 [477 kB] 757s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] 757s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] 757s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-17ubuntu2 [2340 kB] 757s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [12.5 MB] 758s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-17ubuntu2 [14.5 kB] 758s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] 758s Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] 758s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 758s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 758s Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 758s Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig-config amd64 2.15.0-1ubuntu1 [36.9 kB] 758s Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 libfontconfig1 amd64 2.15.0-1ubuntu1 [139 kB] 758s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig amd64 2.15.0-1ubuntu1 [180 kB] 758s Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.12.0-3 [238 kB] 758s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libpixman-1-0 amd64 0.42.2-1 [268 kB] 758s Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-render0 amd64 1.15-1 [16.3 kB] 758s Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-shm0 amd64 1.15-1 [5740 B] 758s Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB] 758s Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 libcairo2 amd64 1.18.0-1 [572 kB] 758s Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 libdatrie1 amd64 0.2.13-3 [20.9 kB] 758s Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate0 amd64 1.19-1 [43.7 kB] 758s Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran5 amd64 14-20240303-1ubuntu1 [924 kB] 758s Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 libgraphite2-3 amd64 1.3.14-2 [83.1 kB] 758s Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 libharfbuzz0b amd64 8.3.0-2 [469 kB] 758s Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 758s Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libice6 amd64 2:1.0.10-1build2 [42.6 kB] 758s Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu1 [147 kB] 758s Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 758s Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.12.0-3 [2649 kB] 758s Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu1 [184 kB] 758s Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 libthai-data all 0.1.29-2 [158 kB] 758s Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 libthai0 amd64 0.1.29-2 [18.8 kB] 758s Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 libpango-1.0-0 amd64 1.51.0+ds-4 [228 kB] 758s Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 libpangoft2-1.0-0 amd64 1.51.0+ds-4 [42.1 kB] 758s Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 libpangocairo-1.0-0 amd64 1.51.0+ds-4 [29.0 kB] 758s Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper1 amd64 1.1.29 [13.4 kB] 758s Get:63 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper-utils amd64 1.1.29 [8658 B] 758s Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 libsharpyuv0 amd64 1.3.2-0.4 [15.6 kB] 758s Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 libsm6 amd64 2:1.2.3-1build2 [16.7 kB] 758s Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [984 kB] 758s Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 libjbig0 amd64 2.1-6.1ubuntu1 [29.3 kB] 758s Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 libwebp7 amd64 1.3.2-0.4 [230 kB] 758s Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 libtiff6 amd64 4.5.1+git230720-3ubuntu1 [232 kB] 758s Get:70 http://ftpmaster.internal/ubuntu noble/main amd64 libxft2 amd64 2.3.6-1 [44.5 kB] 758s Get:71 http://ftpmaster.internal/ubuntu noble/main amd64 libxss1 amd64 1:1.2.3-1build2 [8476 B] 758s Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 libtk8.6 amd64 8.6.13-2 [776 kB] 758s Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 libxt6 amd64 1:1.2.1-1.1 [173 kB] 758s Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 zip amd64 3.0-13 [176 kB] 758s Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 unzip amd64 6.0-28ubuntu3 [174 kB] 758s Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 758s Get:77 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-core amd64 4.3.2-1build1 [27.0 MB] 758s Get:78 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-dbi all 1.2.2-1 [823 kB] 758s Get:79 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mitools all 2.4-2build1 [265 kB] 758s Get:80 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lattice amd64 0.22-5-1 [1342 kB] 758s Get:81 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-matrix amd64 1.6-5-1 [3830 kB] 758s Get:82 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-survival amd64 3.5-8-1 [6120 kB] 758s Get:83 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-kmi all 0.5.5-2build1 [78.3 kB] 758s Preconfiguring packages ... 759s Fetched 117 MB in 1s (119 MB/s) 759s Selecting previously unselected package libc-dev-bin. 759s (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.) 759s Preparing to unpack .../00-libc-dev-bin_2.39-0ubuntu2_amd64.deb ... 759s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 759s Selecting previously unselected package linux-libc-dev:amd64. 759s Preparing to unpack .../01-linux-libc-dev_6.8.0-11.11_amd64.deb ... 759s Unpacking linux-libc-dev:amd64 (6.8.0-11.11) ... 759s Selecting previously unselected package libcrypt-dev:amd64. 759s Preparing to unpack .../02-libcrypt-dev_1%3a4.4.36-4_amd64.deb ... 759s Unpacking libcrypt-dev:amd64 (1:4.4.36-4) ... 759s Selecting previously unselected package libtirpc-dev:amd64. 759s Preparing to unpack .../03-libtirpc-dev_1.3.4+ds-1build1_amd64.deb ... 759s Unpacking libtirpc-dev:amd64 (1.3.4+ds-1build1) ... 759s Selecting previously unselected package libnsl-dev:amd64. 759s Preparing to unpack .../04-libnsl-dev_1.3.0-3_amd64.deb ... 759s Unpacking libnsl-dev:amd64 (1.3.0-3) ... 759s Selecting previously unselected package rpcsvc-proto. 759s Preparing to unpack .../05-rpcsvc-proto_1.4.2-0ubuntu6_amd64.deb ... 759s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 759s Selecting previously unselected package libc6-dev:amd64. 759s Preparing to unpack .../06-libc6-dev_2.39-0ubuntu2_amd64.deb ... 759s Unpacking libc6-dev:amd64 (2.39-0ubuntu2) ... 759s Selecting previously unselected package libisl23:amd64. 759s Preparing to unpack .../07-libisl23_0.26-3_amd64.deb ... 759s Unpacking libisl23:amd64 (0.26-3) ... 759s Selecting previously unselected package libmpc3:amd64. 759s Preparing to unpack .../08-libmpc3_1.3.1-1_amd64.deb ... 759s Unpacking libmpc3:amd64 (1.3.1-1) ... 759s Selecting previously unselected package cpp-13-x86-64-linux-gnu. 759s Preparing to unpack .../09-cpp-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 759s Unpacking cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 760s Selecting previously unselected package cpp-13. 760s Preparing to unpack .../10-cpp-13_13.2.0-17ubuntu2_amd64.deb ... 760s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 760s Selecting previously unselected package cpp-x86-64-linux-gnu. 760s Preparing to unpack .../11-cpp-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 760s Unpacking cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 760s Selecting previously unselected package cpp. 760s Preparing to unpack .../12-cpp_4%3a13.2.0-7ubuntu1_amd64.deb ... 760s Unpacking cpp (4:13.2.0-7ubuntu1) ... 760s Selecting previously unselected package libcc1-0:amd64. 760s Preparing to unpack .../13-libcc1-0_14-20240303-1ubuntu1_amd64.deb ... 760s Unpacking libcc1-0:amd64 (14-20240303-1ubuntu1) ... 760s Selecting previously unselected package libgomp1:amd64. 760s Preparing to unpack .../14-libgomp1_14-20240303-1ubuntu1_amd64.deb ... 760s Unpacking libgomp1:amd64 (14-20240303-1ubuntu1) ... 760s Selecting previously unselected package libitm1:amd64. 760s Preparing to unpack .../15-libitm1_14-20240303-1ubuntu1_amd64.deb ... 760s Unpacking libitm1:amd64 (14-20240303-1ubuntu1) ... 760s Selecting previously unselected package libatomic1:amd64. 760s Preparing to unpack .../16-libatomic1_14-20240303-1ubuntu1_amd64.deb ... 760s Unpacking libatomic1:amd64 (14-20240303-1ubuntu1) ... 760s Selecting previously unselected package libasan8:amd64. 760s Preparing to unpack .../17-libasan8_14-20240303-1ubuntu1_amd64.deb ... 760s Unpacking libasan8:amd64 (14-20240303-1ubuntu1) ... 760s Selecting previously unselected package liblsan0:amd64. 760s Preparing to unpack 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.../28-libstdc++-13-dev_13.2.0-17ubuntu2_amd64.deb ... 761s Unpacking libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ... 761s Selecting previously unselected package g++-13-x86-64-linux-gnu. 761s Preparing to unpack .../29-g++-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 761s Unpacking g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 761s Selecting previously unselected package g++-13. 761s Preparing to unpack .../30-g++-13_13.2.0-17ubuntu2_amd64.deb ... 761s Unpacking g++-13 (13.2.0-17ubuntu2) ... 761s Selecting previously unselected package g++-x86-64-linux-gnu. 761s Preparing to unpack .../31-g++-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 761s Unpacking g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 761s Selecting previously unselected package g++. 761s Preparing to unpack .../32-g++_4%3a13.2.0-7ubuntu1_amd64.deb ... 761s Unpacking g++ (4:13.2.0-7ubuntu1) ... 761s Selecting previously unselected package build-essential. 761s Preparing to unpack .../33-build-essential_12.10ubuntu1_amd64.deb ... 761s Unpacking build-essential (12.10ubuntu1) ... 761s Selecting previously unselected package fonts-dejavu-mono. 761s Preparing to unpack .../34-fonts-dejavu-mono_2.37-8_all.deb ... 761s Unpacking fonts-dejavu-mono (2.37-8) ... 761s Selecting previously unselected package fonts-dejavu-core. 761s Preparing to unpack .../35-fonts-dejavu-core_2.37-8_all.deb ... 761s Unpacking fonts-dejavu-core (2.37-8) ... 761s Selecting previously unselected package fontconfig-config. 761s Preparing to unpack .../36-fontconfig-config_2.15.0-1ubuntu1_amd64.deb ... 762s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 762s Selecting previously unselected package libfontconfig1:amd64. 762s Preparing to unpack .../37-libfontconfig1_2.15.0-1ubuntu1_amd64.deb ... 762s Unpacking libfontconfig1:amd64 (2.15.0-1ubuntu1) ... 762s Selecting previously unselected package fontconfig. 762s Preparing to unpack .../38-fontconfig_2.15.0-1ubuntu1_amd64.deb ... 762s Unpacking fontconfig (2.15.0-1ubuntu1) ... 762s Selecting previously unselected package libblas3:amd64. 762s Preparing to unpack .../39-libblas3_3.12.0-3_amd64.deb ... 762s Unpacking libblas3:amd64 (3.12.0-3) ... 762s Selecting previously unselected package libpixman-1-0:amd64. 762s Preparing to unpack .../40-libpixman-1-0_0.42.2-1_amd64.deb ... 762s Unpacking libpixman-1-0:amd64 (0.42.2-1) ... 762s Selecting previously unselected package libxcb-render0:amd64. 762s Preparing to unpack .../41-libxcb-render0_1.15-1_amd64.deb ... 762s Unpacking libxcb-render0:amd64 (1.15-1) ... 762s Selecting previously unselected package libxcb-shm0:amd64. 762s Preparing to unpack .../42-libxcb-shm0_1.15-1_amd64.deb ... 762s Unpacking libxcb-shm0:amd64 (1.15-1) ... 762s Selecting previously unselected package libxrender1:amd64. 762s Preparing to unpack .../43-libxrender1_1%3a0.9.10-1.1_amd64.deb ... 762s Unpacking libxrender1:amd64 (1:0.9.10-1.1) ... 762s Selecting previously unselected package libcairo2:amd64. 762s Preparing to unpack .../44-libcairo2_1.18.0-1_amd64.deb ... 762s Unpacking libcairo2:amd64 (1.18.0-1) ... 762s Selecting previously unselected package libdatrie1:amd64. 762s Preparing to unpack .../45-libdatrie1_0.2.13-3_amd64.deb ... 762s Unpacking libdatrie1:amd64 (0.2.13-3) ... 762s Selecting previously unselected package libdeflate0:amd64. 762s Preparing to unpack .../46-libdeflate0_1.19-1_amd64.deb ... 762s Unpacking libdeflate0:amd64 (1.19-1) ... 762s Selecting previously unselected package libgfortran5:amd64. 762s Preparing to unpack .../47-libgfortran5_14-20240303-1ubuntu1_amd64.deb ... 762s Unpacking libgfortran5:amd64 (14-20240303-1ubuntu1) ... 762s Selecting previously unselected package libgraphite2-3:amd64. 762s Preparing to unpack .../48-libgraphite2-3_1.3.14-2_amd64.deb ... 762s Unpacking libgraphite2-3:amd64 (1.3.14-2) ... 762s Selecting previously unselected package libharfbuzz0b:amd64. 762s Preparing to unpack .../49-libharfbuzz0b_8.3.0-2_amd64.deb ... 762s Unpacking libharfbuzz0b:amd64 (8.3.0-2) ... 762s Selecting previously unselected package x11-common. 762s Preparing to unpack .../50-x11-common_1%3a7.7+23ubuntu2_all.deb ... 762s Unpacking x11-common (1:7.7+23ubuntu2) ... 762s Selecting previously unselected package libice6:amd64. 762s Preparing to unpack .../51-libice6_2%3a1.0.10-1build2_amd64.deb ... 762s Unpacking libice6:amd64 (2:1.0.10-1build2) ... 762s Selecting previously unselected package libjpeg-turbo8:amd64. 762s Preparing to unpack .../52-libjpeg-turbo8_2.1.5-2ubuntu1_amd64.deb ... 762s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ... 762s Selecting previously unselected package libjpeg8:amd64. 762s Preparing to unpack .../53-libjpeg8_8c-2ubuntu11_amd64.deb ... 762s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 762s Selecting previously unselected package liblapack3:amd64. 762s Preparing to unpack .../54-liblapack3_3.12.0-3_amd64.deb ... 762s Unpacking liblapack3:amd64 (3.12.0-3) ... 762s Selecting previously unselected package liblerc4:amd64. 762s Preparing to unpack .../55-liblerc4_4.0.0+ds-4ubuntu1_amd64.deb ... 762s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu1) ... 762s Selecting previously unselected package libthai-data. 762s Preparing to unpack .../56-libthai-data_0.1.29-2_all.deb ... 762s Unpacking libthai-data (0.1.29-2) ... 762s Selecting previously unselected package libthai0:amd64. 762s Preparing to unpack .../57-libthai0_0.1.29-2_amd64.deb ... 762s Unpacking libthai0:amd64 (0.1.29-2) ... 762s Selecting previously unselected package libpango-1.0-0:amd64. 762s Preparing to unpack .../58-libpango-1.0-0_1.51.0+ds-4_amd64.deb ... 762s Unpacking libpango-1.0-0:amd64 (1.51.0+ds-4) ... 762s Selecting previously unselected package libpangoft2-1.0-0:amd64. 762s Preparing to unpack .../59-libpangoft2-1.0-0_1.51.0+ds-4_amd64.deb ... 762s Unpacking libpangoft2-1.0-0:amd64 (1.51.0+ds-4) ... 762s Selecting previously unselected package libpangocairo-1.0-0:amd64. 762s Preparing to unpack .../60-libpangocairo-1.0-0_1.51.0+ds-4_amd64.deb ... 762s Unpacking libpangocairo-1.0-0:amd64 (1.51.0+ds-4) ... 762s Selecting previously unselected package libpaper1:amd64. 762s Preparing to unpack .../61-libpaper1_1.1.29_amd64.deb ... 762s Unpacking libpaper1:amd64 (1.1.29) ... 762s Selecting previously unselected package libpaper-utils. 762s Preparing to unpack .../62-libpaper-utils_1.1.29_amd64.deb ... 762s Unpacking libpaper-utils (1.1.29) ... 763s Selecting previously unselected package libsharpyuv0:amd64. 763s Preparing to unpack .../63-libsharpyuv0_1.3.2-0.4_amd64.deb ... 763s Unpacking libsharpyuv0:amd64 (1.3.2-0.4) ... 763s Selecting previously unselected package libsm6:amd64. 763s Preparing to unpack .../64-libsm6_2%3a1.2.3-1build2_amd64.deb ... 763s Unpacking libsm6:amd64 (2:1.2.3-1build2) ... 763s Selecting previously unselected package libtcl8.6:amd64. 763s Preparing to unpack .../65-libtcl8.6_8.6.13+dfsg-2_amd64.deb ... 763s Unpacking libtcl8.6:amd64 (8.6.13+dfsg-2) ... 763s Selecting previously unselected package libjbig0:amd64. 763s Preparing to unpack .../66-libjbig0_2.1-6.1ubuntu1_amd64.deb ... 763s Unpacking libjbig0:amd64 (2.1-6.1ubuntu1) ... 763s Selecting previously unselected package libwebp7:amd64. 763s Preparing to unpack .../67-libwebp7_1.3.2-0.4_amd64.deb ... 763s Unpacking libwebp7:amd64 (1.3.2-0.4) ... 763s Selecting previously unselected package libtiff6:amd64. 763s Preparing to unpack .../68-libtiff6_4.5.1+git230720-3ubuntu1_amd64.deb ... 763s Unpacking libtiff6:amd64 (4.5.1+git230720-3ubuntu1) ... 763s Selecting previously unselected package libxft2:amd64. 763s Preparing to unpack .../69-libxft2_2.3.6-1_amd64.deb ... 763s Unpacking libxft2:amd64 (2.3.6-1) ... 763s Selecting previously unselected package libxss1:amd64. 763s Preparing to unpack .../70-libxss1_1%3a1.2.3-1build2_amd64.deb ... 763s Unpacking libxss1:amd64 (1:1.2.3-1build2) ... 763s Selecting previously unselected package libtk8.6:amd64. 763s Preparing to unpack .../71-libtk8.6_8.6.13-2_amd64.deb ... 763s Unpacking libtk8.6:amd64 (8.6.13-2) ... 763s Selecting previously unselected package libxt6:amd64. 763s Preparing to unpack .../72-libxt6_1%3a1.2.1-1.1_amd64.deb ... 763s Unpacking libxt6:amd64 (1:1.2.1-1.1) ... 763s Selecting previously unselected package zip. 763s Preparing to unpack .../73-zip_3.0-13_amd64.deb ... 763s Unpacking zip (3.0-13) ... 763s Selecting previously unselected package unzip. 763s Preparing to unpack .../74-unzip_6.0-28ubuntu3_amd64.deb ... 763s Unpacking unzip (6.0-28ubuntu3) ... 763s Selecting previously unselected package xdg-utils. 763s Preparing to unpack .../75-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 763s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 763s Selecting previously unselected package r-base-core. 763s Preparing to unpack .../76-r-base-core_4.3.2-1build1_amd64.deb ... 763s Unpacking r-base-core (4.3.2-1build1) ... 763s Selecting previously unselected package 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Setting up libgraphite2-3:amd64 (1.3.14-2) ... 764s Setting up libpixman-1-0:amd64 (0.42.2-1) ... 764s Setting up libsharpyuv0:amd64 (1.3.2-0.4) ... 764s Setting up libpaper1:amd64 (1.1.29) ... 764s 764s Creating config file /etc/papersize with new version 764s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu1) ... 764s Setting up libxrender1:amd64 (1:0.9.10-1.1) ... 764s Setting up libdatrie1:amd64 (0.2.13-3) ... 764s Setting up libxcb-render0:amd64 (1.15-1) ... 764s Setting up unzip (6.0-28ubuntu3) ... 764s Setting up x11-common (1:7.7+23ubuntu2) ... 764s Setting up libdeflate0:amd64 (1.19-1) ... 764s Setting up linux-libc-dev:amd64 (6.8.0-11.11) ... 764s Setting up libxcb-shm0:amd64 (1.15-1) ... 764s Setting up libpaper-utils (1.1.29) ... 764s Setting up libgomp1:amd64 (14-20240303-1ubuntu1) ... 764s Setting up libjbig0:amd64 (2.1-6.1ubuntu1) ... 764s Setting up zip (3.0-13) ... 764s Setting up libblas3:amd64 (3.12.0-3) ... 764s 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 764s Setting up libtirpc-dev:amd64 (1.3.4+ds-1build1) ... 764s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 764s Setting up libquadmath0:amd64 (14-20240303-1ubuntu1) ... 764s Setting up fonts-dejavu-mono (2.37-8) ... 764s Setting up libmpc3:amd64 (1.3.1-1) ... 764s Setting up libatomic1:amd64 (14-20240303-1ubuntu1) ... 764s Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ... 764s Setting up fonts-dejavu-core (2.37-8) ... 764s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ... 764s Setting up libgfortran5:amd64 (14-20240303-1ubuntu1) ... 764s Setting up libwebp7:amd64 (1.3.2-0.4) ... 764s Setting up libubsan1:amd64 (14-20240303-1ubuntu1) ... 764s Setting up libnsl-dev:amd64 (1.3.0-3) ... 764s Setting up libhwasan0:amd64 (14-20240303-1ubuntu1) ... 764s Setting up libcrypt-dev:amd64 (1:4.4.36-4) ... 764s Setting up libasan8:amd64 (14-20240303-1ubuntu1) ... 764s Setting up libharfbuzz0b:amd64 (8.3.0-2) ... 764s Setting up libthai-data (0.1.29-2) ... 764s Setting up libxss1:amd64 (1:1.2.3-1build2) ... 764s Setting up libtsan2:amd64 (14-20240303-1ubuntu1) ... 764s Setting up libisl23:amd64 (0.26-3) ... 764s Setting up libc-dev-bin (2.39-0ubuntu2) ... 764s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 764s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 764s Setting up libcc1-0:amd64 (14-20240303-1ubuntu1) ... 764s Setting up liblsan0:amd64 (14-20240303-1ubuntu1) ... 764s Setting up libitm1:amd64 (14-20240303-1ubuntu1) ... 764s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 764s Setting up libice6:amd64 (2:1.0.10-1build2) ... 764s Setting up liblapack3:amd64 (3.12.0-3) ... 764s 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 764s Setting up cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 764s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 765s Setting up libthai0:amd64 (0.1.29-2) ... 765s Setting up libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ... 765s Setting up libtiff6:amd64 (4.5.1+git230720-3ubuntu1) ... 765s Setting up libc6-dev:amd64 (2.39-0ubuntu2) ... 765s Setting up libfontconfig1:amd64 (2.15.0-1ubuntu1) ... 765s Setting up libsm6:amd64 (2:1.2.3-1build2) ... 765s Setting up libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ... 765s Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 765s Setting up fontconfig (2.15.0-1ubuntu1) ... 767s Regenerating fonts cache... done. 767s Setting up libxft2:amd64 (2.3.6-1) ... 767s Setting up cpp-13 (13.2.0-17ubuntu2) ... 767s Setting up gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 767s Setting up libtk8.6:amd64 (8.6.13-2) ... 767s Setting up libpango-1.0-0:amd64 (1.51.0+ds-4) ... 767s Setting up libcairo2:amd64 (1.18.0-1) ... 767s Setting up gcc-13 (13.2.0-17ubuntu2) ... 767s Setting up libxt6:amd64 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r-cran-kmi (0.5.5-2build1) ... 767s Processing triggers for libc-bin (2.39-0ubuntu2) ... 767s Processing triggers for man-db (2.12.0-3) ... 769s Processing triggers for install-info (7.1-3) ... 769s Reading package lists... 770s Building dependency tree... 770s Reading state information... 770s Starting pkgProblemResolver with broken count: 0 770s Starting 2 pkgProblemResolver with broken count: 0 770s Done 771s The following NEW packages will be installed: 771s autopkgtest-satdep 771s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 771s Need to get 0 B/696 B of archives. 771s After this operation, 0 B of additional disk space will be used. 771s Get:1 /tmp/autopkgtest.trzW8o/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B] 771s Selecting previously unselected package autopkgtest-satdep. 771s (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 ... 76855 files and directories currently installed.) 771s Preparing to unpack .../2-autopkgtest-satdep.deb ... 771s Unpacking autopkgtest-satdep (0) ... 771s Setting up autopkgtest-satdep (0) ... 773s (Reading database ... 76855 files and directories currently installed.) 773s Removing autopkgtest-satdep (0) ... 773s autopkgtest [21:44:16]: test run-unit-test: [----------------------- 773s BEGIN TEST test.kmi.R 773s 773s R version 4.3.2 (2023-10-31) -- "Eye Holes" 773s Copyright (C) 2023 The R Foundation for Statistical Computing 773s Platform: x86_64-pc-linux-gnu (64-bit) 773s 773s R is free software and comes with ABSOLUTELY NO WARRANTY. 773s You are welcome to redistribute it under certain conditions. 773s Type 'license()' or 'licence()' for distribution details. 773s 773s R is a collaborative project with many contributors. 773s Type 'contributors()' for more information and 773s 'citation()' on how to cite R or R packages in publications. 773s 773s Type 'demo()' for some demos, 'help()' for on-line help, or 773s 'help.start()' for an HTML browser interface to help. 773s Type 'q()' to quit R. 773s 773s > require(survival) 773s Loading required package: survival 774s > require(kmi) 774s Loading required package: kmi 774s > 774s > ### test 1 774s > 774s > id <- 1:10 774s > time <- 1:10 774s > ev <- c(0, 0, 0, rep(1, 3), rep(2, 4)) 774s > data <- data.frame(id, time, ev) 774s > 774s > aa <- kmi(Surv(time, ev != 0) ~ 1, data, etype = ev) 774s > 774s > bb <- aa$imputed.data 774s > test1 <- lapply(bb, function(x) { 774s + x[aa$original.data$id %in% 7:10, ] 774s + }) 774s > test1 <- do.call(rbind, test1) 774s > 774s > all(test1[, 1] == 11) 774s [1] TRUE 774s > all(test1[, 2] == 0) 774s [1] TRUE 774s > 774s > aa <- kmi(Surv(time, ev != 0) ~ 1, data, etype = ev, failcode = 2) 774s > 774s > bb <- aa$imputed.data 774s > test1 <- lapply(bb, function(x) { 774s + x[aa$original.data$id %in% 4:6, ] 774s + }) 774s > test1 <- do.call(rbind, test1) 774s > 774s > all(test1[, 1] == 11) 774s [1] TRUE 774s > all(test1[, 2] == 0) 774s [1] TRUE 774s > 774s > aa <- kmi(Surv(time, ev != 0) ~ 1, data, etype = ev, epsilon = 2) 774s > 774s > bb <- aa$imputed.data 774s > test1 <- lapply(bb, function(x) { 774s + x[aa$original.data$id %in% 7:10, ] 774s + }) 774s > test1 <- do.call(rbind, test1) 774s > 774s > all(test1[, 1] == 12) 774s [1] TRUE 774s > all(test1[, 2] == 0) 774s [1] TRUE 774s > 774s > aa <- kmi(Surv(time, ev != 0) ~ 1, data, etype = ev, nimp = 13) 774s > length(aa$imputed.data) == 13 774s [1] TRUE 774s > 774s > 774s > ### test 2 774s > 774s > set.seed(198740) 774s > time <- rexp(100) 774s > ev <- sample(c(0, 1, 2), 100, replace = TRUE) 774s > cov <- rbinom(100, 1, 0.5) 774s > dd <- data.frame(time, ev, cov) 774s > 774s > ## add a test when etype is a factor 774s > dd$status <- factor(ifelse(dd$ev == 0, "cens", ifelse(dd$ev == 1, "rel", "dc"))) 774s > 774s > set.seed(1440293) 774s > dat.kmi <- kmi(Surv(time, ev != 0) ~ 1, dd, etype = ev, nimp = 5) 774s > set.seed(1440293) 774s > dat.kmi.fact <- kmi(Surv(time, status != "cens") ~ 1, dd, etype = status, 774s + nimp = 5, failcode = "rel") 774s > set.seed(1440293) 774s > dat.kmi.mixed1 <- kmi(Surv(time, ev != 0) ~ 1, dd, etype = status, 774s + nimp = 5, failcode = "rel") 774s > set.seed(1440293) 774s > dat.kmi.mixed2 <- kmi(Surv(time, status != "cens") ~ 1, dd, etype = ev, 774s + nimp = 5, failcode = 1) 774s > 774s > 774s > fit.kmi <- cox.kmi(Surv(time, ev == 1) ~ cov, dat.kmi) 774s > fit.kmi.fact <- cox.kmi(Surv(time, status == "rel") ~ cov, dat.kmi) 774s > fit.kmi.mixed1 <- cox.kmi(Surv(time, status == "rel") ~ cov, dat.kmi.mixed1) 774s > fit.kmi.mixed2 <- cox.kmi(Surv(time, ev == 1) ~ cov, dat.kmi.mixed2) 774s > 774s > all.equal(coef(fit.kmi), coef(fit.kmi.fact)) 774s [1] TRUE 774s > all.equal(coef(fit.kmi), coef(fit.kmi.mixed1)) 774s [1] TRUE 774s > all.equal(coef(fit.kmi), coef(fit.kmi.mixed2)) 774s [1] TRUE 774s > all.equal(fit.kmi$variance, fit.kmi.fact$variance) 774s [1] TRUE 774s > all.equal(fit.kmi$variance, fit.kmi.mixed1$variance) 774s [1] TRUE 774s > all.equal(fit.kmi$variance, fit.kmi.mixed2$variance) 774s [1] TRUE 774s > 774s > ## fit.kmi 774s > 774s > ## summary(fit.kmi) 774s > 774s > ## fit.kmi.fact 774s > 774s > ## summary(fit.kmi.fact) 774s > 774s > ## avec bootstrap 774s > 774s > set.seed(867988) 774s > dat.kmib <- kmi(Surv(time, ev != 0) ~ 1, dd, etype = ev, nimp = 5, 774s + boot = TRUE, nboot = 5) 774s > set.seed(867988) 774s > dat.kmib.fact <- kmi(Surv(time, ev != 0) ~ 1, dd, etype = status, nimp = 5, 774s + boot = TRUE, nboot = 5, failcode = "rel") 774s > 774s > fit.kmib <- cox.kmi(Surv(time, ev == 1) ~ cov, dat.kmib) 774s > fit.kmib.fact <- cox.kmi(Surv(time, status == "rel") ~ cov, dat.kmib.fact) 774s > 774s > all.equal(coef(fit.kmib), coef(fit.kmib.fact)) 774s [1] TRUE 774s > 774s > fit.kmib 774s Call: 774s cox.kmi(formula = Surv(time, ev == 1) ~ cov, imp.data = dat.kmib) 774s 774s ***************** 774s Pooled estimates: 774s ***************** 774s coef exp(coef) se(coef) t p 774s cov -0.07328941 0.9293318 0.3126316 -0.2344274 0.8146571 774s 774s > fit.kmib.fact 774s Call: 774s cox.kmi(formula = Surv(time, status == "rel") ~ cov, imp.data = dat.kmib.fact) 774s 774s ***************** 774s Pooled estimates: 774s ***************** 774s coef exp(coef) se(coef) t p 774s cov -0.07328941 0.9293318 0.3126316 -0.2344274 0.8146571 774s 774s > 774s > summary(fit.kmib) 774s Call: 774s cox.kmi(formula = Surv(time, ev == 1) ~ cov, imp.data = dat.kmib) 774s 774s 774s ***************** 774s Pooled estimates: 774s ***************** 774s coef exp(coef) se(coef) t Pr(>|t|) 774s cov -0.07329 0.92933 0.31263 -0.234 0.815 774s 774s exp(coef) exp(-coef) lower .95 upper .95 774s cov 0.9293 1.076 0.5035 1.715 774s 774s > 774s > 774s > ### test 4 774s > 774s > data(icu.pneu) 774s > 774s > set.seed(1313) 774s > dat <- kmi(Surv(start, stop, status) ~ 1, data = icu.pneu, 774s + etype = event, id= id, failcode = 2, nimp = 5) 775s > 775s > ### add a factor for testing purposes 775s > icu.pneu$ev.fact <- factor(ifelse(icu.pneu$event == 3, "disch", "death")) 775s > 775s > icu.pneu$ev <- icu.pneu$event 775s > icu.pneu$ev[icu.pneu$status == 0] <- 0 775s > 775s > set.seed(1313) 775s > dat2 <- kmi(Surv(start, stop, ev != 0) ~ 1, data = icu.pneu, 775s + etype = ev, id= id, failcode = 2, nimp = 5) 775s > 775s > set.seed(1313) 775s > dat3 <- kmi(Surv(start, stop, status) ~ 1, data = icu.pneu, 775s + etype = ev.fact, id = id, failcode = "death", nimp = 5) 775s > 775s > a <- logical(5) 775s > for (i in 1:5) a[i] <- all.equal(dat$imputed.data[[i]][, 1], dat2$imputed.data[[i]][, 1]) 775s > a 775s [1] TRUE TRUE TRUE TRUE TRUE 775s > 775s > fit.kmi <- cox.kmi(Surv(start, stop, event == 2) ~ pneu, dat) 775s > 775s > fit.kmi2 <- cox.kmi(Surv(start, stop, ev == 2) ~ pneu, dat2) 775s > 775s > fit.kmi3 <- cox.kmi(Surv(start, stop, ev.fact == "death") ~ pneu, dat3) 775s > 775s > all.equal(fit.kmi$coefficients, fit.kmi2$coefficients) 775s [1] TRUE 775s > all.equal(coef(fit.kmi), coef(fit.kmi3)) 775s [1] TRUE 775s > all.equal(fit.kmi$variance, fit.kmi2$variance) 775s [1] TRUE 775s > 775s > fit.kmi 775s Call: 775s cox.kmi(formula = Surv(start, stop, event == 2) ~ pneu, imp.data = dat) 775s 775s ***************** 775s Pooled estimates: 775s ***************** 775s coef exp(coef) se(coef) t p 775s pneu1 1.10382 3.015664 0.2398608 4.60192 4.186147e-06 775s 775s > 775s > fit.kmi2 775s Call: 775s cox.kmi(formula = Surv(start, stop, ev == 2) ~ pneu, imp.data = dat2) 775s 775s ***************** 775s Pooled estimates: 775s ***************** 775s coef exp(coef) se(coef) t p 775s pneu1 1.10382 3.015664 0.2398608 4.60192 4.186147e-06 775s 775s > 775s > fit.kmi3 775s Call: 775s cox.kmi(formula = Surv(start, stop, ev.fact == "death") ~ pneu, 775s imp.data = dat3) 775s 775s ***************** 775s Pooled estimates: 775s ***************** 775s coef exp(coef) se(coef) t p 775s pneu1 1.10382 3.015664 0.2398608 4.60192 4.186147e-06 775s 775s > 775s > ## avec bootstrap 775s > 775s > set.seed(598085) 775s > dat <- kmi(Surv(start, stop, status) ~ 1, data = icu.pneu, 775s + etype = event, id= id, failcode = 2, nimp = 5, 775s + boot = TRUE, nboot = 5) 775s > 775s > set.seed(598085) 775s > dat2 <- kmi(Surv(start, stop, ev != 0) ~ 1, data = icu.pneu, 775s + etype = ev, id= id, failcode = 2, nimp = 5, 775s + boot = TRUE, nboot = 5) 775s > 775s > set.seed(598085) 775s > dat3 <- kmi(Surv(start, stop, status) ~ 1, data = icu.pneu, 775s + etype = ev.fact, id = id, failcode = "death", nimp = 5, 775s + boot = TRUE, nboot = 5) 775s > 775s > 775s > a <- logical(5) 775s > for (i in 1:5) a[i] <- all.equal(dat$imputed.data[[i]][, 1], dat2$imputed.data[[i]][, 1]) 775s > a 775s [1] TRUE TRUE TRUE TRUE TRUE 775s > 775s > fit.kmi <- cox.kmi(Surv(start, stop, event == 2) ~ pneu, dat) 775s > 775s > fit.kmi2 <- cox.kmi(Surv(start, stop, ev == 2) ~ pneu, dat2) 775s > 775s > fit.kmi3 <- cox.kmi(Surv(start, stop, ev.fact == "death") ~ pneu, dat3) 775s > 775s > all.equal(fit.kmi$coefficients, fit.kmi2$coefficients) 775s [1] TRUE 775s > all.equal(coef(fit.kmi), coef(fit.kmi3)) 775s [1] TRUE 775s > all.equal(fit.kmi$variance, fit.kmi2$variance) 775s [1] TRUE 775s > 775s > fit.kmi 775s Call: 775s cox.kmi(formula = Surv(start, stop, event == 2) ~ pneu, imp.data = dat) 775s 775s ***************** 775s Pooled estimates: 775s ***************** 775s coef exp(coef) se(coef) t p 775s pneu1 1.104148 3.016652 0.2399367 4.601829 4.188064e-06 775s 775s > 775s > fit.kmi2 775s Call: 775s cox.kmi(formula = Surv(start, stop, ev == 2) ~ pneu, imp.data = dat2) 775s 775s ***************** 775s Pooled estimates: 775s ***************** 775s coef exp(coef) se(coef) t p 775s pneu1 1.104148 3.016652 0.2399367 4.601829 4.188064e-06 775s 775s > 775s > fit.kmi3 775s Call: 775s cox.kmi(formula = Surv(start, stop, ev.fact == "death") ~ pneu, 775s imp.data = dat3) 775s 775s ***************** 775s Pooled estimates: 775s ***************** 775s coef exp(coef) se(coef) t p 775s pneu1 1.104148 3.016652 0.2399367 4.601829 4.188064e-06 775s 775s > 775s > ### with covariates 775s > ## classic 775s > set.seed(1) 775s > dd$juhu <- rnorm(nrow(dd)) 775s > 775s > set.seed(78223) 775s > imp.dd <- kmi(Surv(time, ev != 0) ~ juhu, dd, 775s + etype = ev, nimp = 5) 775s > set.seed(44889) 775s > imp.ddb <- kmi(Surv(time, ev != 0) ~ juhu, dd, nimp = 5, 775s + etype = ev, boot = TRUE, nboot = 5) 775s > 775s > summary(cox.kmi(Surv(time, ev == 1) ~ cov, imp.dd)) 775s Call: 775s cox.kmi(formula = Surv(time, ev == 1) ~ cov, imp.data = imp.dd) 775s 775s 775s ***************** 775s Pooled estimates: 775s ***************** 775s coef exp(coef) se(coef) t Pr(>|t|) 775s cov -0.0485 0.9527 0.3155 -0.154 0.878 775s 775s exp(coef) exp(-coef) lower .95 upper .95 775s cov 0.9527 1.05 0.5132 1.768 775s 775s > summary(cox.kmi(Surv(time, ev == 1) ~ cov, imp.ddb)) 775s Call: 775s cox.kmi(formula = Surv(time, ev == 1) ~ cov, imp.data = imp.ddb) 775s 775s 775s ***************** 775s Pooled estimates: 775s ***************** 775s coef exp(coef) se(coef) t Pr(>|t|) 775s cov -0.08706 0.91662 0.31606 -0.275 0.783 775s 775s exp(coef) exp(-coef) lower .95 upper .95 775s cov 0.9166 1.091 0.4932 1.704 775s 775s > 775s > ## time-dependent covariates 775s > set.seed(9763) 775s > imp.dat.c <- kmi(Surv(start, stop, status) ~ age + sex, 775s + data = icu.pneu, etype = event, id = id, 775s + failcode = 2, nimp = 5) 776s > 776s > set.seed(19832) 776s > imp.dat.cb <- kmi(Surv(start, stop, status) ~ age + sex, 776s + data = icu.pneu, etype = event, id = id, 776s + failcode = 2, nimp = 5, boot = TRUE, 776s + nboot = 5) 777s > 777s > summary(cox.kmi(Surv(start, stop, event == 2) ~ pneu, 777s + imp.dat.c)) 777s Call: 777s cox.kmi(formula = Surv(start, stop, event == 2) ~ pneu, imp.data = imp.dat.c) 777s 777s 777s ***************** 777s Pooled estimates: 777s ***************** 777s coef exp(coef) se(coef) t Pr(>|t|) 777s pneu1 1.117 3.055 0.240 4.654 3.25e-06 *** 777s --- 777s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 777s 777s exp(coef) exp(-coef) lower .95 upper .95 777s pneu1 3.055 0.3273 1.909 4.89 777s 777s > summary(cox.kmi(Surv(start, stop, event == 2) ~ pneu, 777s + imp.dat.cb)) 777s Call: 777s cox.kmi(formula = Surv(start, stop, event == 2) ~ pneu, imp.data = imp.dat.cb) 777s 777s 777s ***************** 777s Pooled estimates: 777s ***************** 777s coef exp(coef) se(coef) t Pr(>|t|) 777s pneu1 1.1077 3.0274 0.2403 4.609 4.04e-06 *** 777s --- 777s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 777s 777s exp(coef) exp(-coef) lower .95 upper .95 777s pneu1 3.027 0.3303 1.89 4.849 777s 777s > 777s > 777s > ## Test ordering of the data set 777s > 777s > data(icu.pneu) 777s > icu.pneu$outcome <- with(icu.pneu, status * event) 777s > 777s > mydata1 <- icu.pneu[1:2, ] 777s > mydata2 <- icu.pneu[3:1421, ] 777s > 777s > ## page 221 777s > set.seed(453) 777s > imp.dat <- kmi(Surv(start, stop, outcome != 0) ~ 1, 777s + data = icu.pneu, etype = outcome, 777s + id = id, failcode = 2, nimp = 10) 777s > 777s > ## page 222 777s > kmi.sh.hap <- cox.kmi(Surv(start, stop, outcome == 2) ~ pneu, imp.dat) 777s > summary(kmi.sh.hap) 777s Call: 777s cox.kmi(formula = Surv(start, stop, outcome == 2) ~ pneu, imp.data = imp.dat) 777s 777s 777s ***************** 777s Pooled estimates: 777s ***************** 777s coef exp(coef) se(coef) t Pr(>|t|) 777s pneu1 1.1057 3.0213 0.2399 4.608 4.06e-06 *** 777s --- 777s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 777s 777s exp(coef) exp(-coef) lower .95 upper .95 777s pneu1 3.021 0.331 1.888 4.835 777s 777s > 777s > newicu.pneu <- as.data.frame(rbind( mydata2, mydata1)) 777s > tail(newicu.pneu) 777s id start stop status event pneu adm.cens.exit age sex outcome 777s 1418 2020485 0 21 1 3 0 445 69.85106 M 3 777s 1419 2020508 0 49 1 3 0 537 60.23257 M 3 777s 1420 2020634 0 35 1 3 0 555 59.52186 M 3 777s 1421 2020811 0 3 1 3 0 465 73.95806 F 3 777s 1 12 0 3 1 3 0 421 62.53307 F 3 777s 2 41 0 5 1 3 0 545 75.34153 F 3 777s > 777s > set.seed(453) 777s > imp.datnew <- kmi(Surv(start, stop, outcome != 0) ~ 1, 777s + data = newicu.pneu, etype = outcome, 777s + id = id, failcode = 2, nimp = 10) 777s > 777s > # page 222 777s > kmi.sh.hap <- cox.kmi(Surv(start, stop, outcome == 2) ~ pneu, imp.datnew) 777s > summary(kmi.sh.hap) 777s Call: 777s cox.kmi(formula = Surv(start, stop, outcome == 2) ~ pneu, imp.data = imp.datnew) 777s 777s 777s ***************** 777s Pooled estimates: 777s ***************** 777s coef exp(coef) se(coef) t Pr(>|t|) 777s pneu1 1.1057 3.0213 0.2399 4.608 4.06e-06 *** 777s --- 777s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 777s 777s exp(coef) exp(-coef) lower .95 upper .95 777s pneu1 3.021 0.331 1.888 4.835 777s 777s > 778s autopkgtest [21:44:21]: test run-unit-test: -----------------------] 778s autopkgtest [21:44:21]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 778s run-unit-test PASS 778s autopkgtest [21:44:21]: test pkg-r-autopkgtest: preparing testbed 780s Note, using file '/tmp/autopkgtest.trzW8o/3-autopkgtest-satdep.dsc' to get the build dependencies 780s Reading package lists... 780s Building dependency tree... 780s Reading state information... 780s Starting pkgProblemResolver with broken count: 0 781s Starting 2 pkgProblemResolver with broken count: 0 781s Done 781s The following NEW packages will be installed: 781s dctrl-tools gfortran gfortran-13 gfortran-13-x86-64-linux-gnu 781s gfortran-x86-64-linux-gnu icu-devtools libblas-dev libbz2-dev 781s libgfortran-13-dev libicu-dev libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev 781s liblapack-dev liblzma-dev libncurses-dev libpcre2-16-0 libpcre2-32-0 781s libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev 781s pkg-config pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev zlib1g-dev 781s 0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded. 781s Need to get 33.6 MB of archives. 781s After this operation, 130 MB of additional disk space will be used. 781s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 dctrl-tools amd64 2.24-3build2 [66.9 kB] 781s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran-13-dev amd64 13.2.0-17ubuntu2 [942 kB] 781s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.6 MB] 781s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-13 amd64 13.2.0-17ubuntu2 [10.3 kB] 781s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1024 B] 781s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran amd64 4:13.2.0-7ubuntu1 [1176 B] 781s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 icu-devtools amd64 74.2-1ubuntu1 [212 kB] 781s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libblas-dev amd64 3.12.0-3 [170 kB] 781s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libbz2-dev amd64 1.0.8-5ubuntu1 [33.6 kB] 781s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 libicu-dev amd64 74.2-1ubuntu1 [11.9 MB] 781s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8-dev amd64 2.1.5-2ubuntu1 [294 kB] 781s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B] 781s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B] 781s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack-dev amd64 3.12.0-3 [5196 kB] 781s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libncurses-dev amd64 6.4+20240113-1ubuntu1 [384 kB] 781s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-16-0 amd64 10.42-4ubuntu1 [211 kB] 781s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-32-0 amd64 10.42-4ubuntu1 [198 kB] 781s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-posix3 amd64 10.42-4ubuntu1 [6808 B] 781s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-dev amd64 10.42-4ubuntu1 [743 kB] 781s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libpkgconf3 amd64 1.8.1-2 [31.1 kB] 781s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3ubuntu1 [896 kB] 781s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libpng-dev amd64 1.6.43-1 [264 kB] 781s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libreadline-dev amd64 8.2-3 [167 kB] 781s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf-bin amd64 1.8.1-2 [20.7 kB] 781s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf amd64 1.8.1-2 [16.8 kB] 781s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 pkg-config amd64 1.8.1-2 [7170 B] 781s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 liblzma-dev amd64 5.4.5-0.3 [205 kB] 781s Get:28 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-dev all 4.3.2-1build1 [4336 B] 781s Get:29 http://ftpmaster.internal/ubuntu noble/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 782s Fetched 33.6 MB in 0s (80.5 MB/s) 782s Selecting previously unselected package dctrl-tools. 782s (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 ... 76855 files and directories currently installed.) 782s Preparing to unpack .../00-dctrl-tools_2.24-3build2_amd64.deb ... 782s Unpacking dctrl-tools (2.24-3build2) ... 782s Selecting previously unselected package libgfortran-13-dev:amd64. 782s Preparing to unpack .../01-libgfortran-13-dev_13.2.0-17ubuntu2_amd64.deb ... 782s Unpacking libgfortran-13-dev:amd64 (13.2.0-17ubuntu2) ... 782s Selecting previously unselected package gfortran-13-x86-64-linux-gnu. 782s Preparing to unpack .../02-gfortran-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 782s Unpacking gfortran-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 782s Selecting previously unselected package gfortran-13. 782s Preparing to unpack .../03-gfortran-13_13.2.0-17ubuntu2_amd64.deb ... 782s Unpacking gfortran-13 (13.2.0-17ubuntu2) ... 782s Selecting previously unselected package gfortran-x86-64-linux-gnu. 782s Preparing to unpack .../04-gfortran-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 782s Unpacking gfortran-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 782s Selecting previously unselected package gfortran. 782s Preparing to unpack .../05-gfortran_4%3a13.2.0-7ubuntu1_amd64.deb ... 782s Unpacking gfortran (4:13.2.0-7ubuntu1) ... 782s Selecting previously unselected package icu-devtools. 782s Preparing to unpack .../06-icu-devtools_74.2-1ubuntu1_amd64.deb ... 782s Unpacking icu-devtools (74.2-1ubuntu1) ... 782s Selecting previously unselected package libblas-dev:amd64. 782s Preparing to unpack .../07-libblas-dev_3.12.0-3_amd64.deb ... 782s Unpacking libblas-dev:amd64 (3.12.0-3) ... 782s Selecting previously unselected package libbz2-dev:amd64. 782s Preparing to unpack .../08-libbz2-dev_1.0.8-5ubuntu1_amd64.deb ... 782s Unpacking libbz2-dev:amd64 (1.0.8-5ubuntu1) ... 782s Selecting previously unselected package libicu-dev:amd64. 782s Preparing to unpack .../09-libicu-dev_74.2-1ubuntu1_amd64.deb ... 782s Unpacking libicu-dev:amd64 (74.2-1ubuntu1) ... 782s Selecting previously unselected package libjpeg-turbo8-dev:amd64. 782s Preparing to unpack .../10-libjpeg-turbo8-dev_2.1.5-2ubuntu1_amd64.deb ... 782s Unpacking libjpeg-turbo8-dev:amd64 (2.1.5-2ubuntu1) ... 782s Selecting previously unselected package libjpeg8-dev:amd64. 782s Preparing to unpack .../11-libjpeg8-dev_8c-2ubuntu11_amd64.deb ... 782s Unpacking libjpeg8-dev:amd64 (8c-2ubuntu11) ... 782s Selecting previously unselected package libjpeg-dev:amd64. 782s Preparing to unpack .../12-libjpeg-dev_8c-2ubuntu11_amd64.deb ... 782s Unpacking libjpeg-dev:amd64 (8c-2ubuntu11) ... 782s Selecting previously unselected package liblapack-dev:amd64. 782s Preparing to unpack .../13-liblapack-dev_3.12.0-3_amd64.deb ... 782s Unpacking liblapack-dev:amd64 (3.12.0-3) ... 783s Selecting previously unselected package libncurses-dev:amd64. 783s Preparing to unpack .../14-libncurses-dev_6.4+20240113-1ubuntu1_amd64.deb ... 783s Unpacking libncurses-dev:amd64 (6.4+20240113-1ubuntu1) ... 783s Selecting previously unselected package libpcre2-16-0:amd64. 783s Preparing to unpack .../15-libpcre2-16-0_10.42-4ubuntu1_amd64.deb ... 783s Unpacking libpcre2-16-0:amd64 (10.42-4ubuntu1) ... 783s Selecting previously unselected package libpcre2-32-0:amd64. 783s Preparing to unpack .../16-libpcre2-32-0_10.42-4ubuntu1_amd64.deb ... 783s Unpacking libpcre2-32-0:amd64 (10.42-4ubuntu1) ... 783s Selecting previously unselected package libpcre2-posix3:amd64. 783s Preparing to unpack .../17-libpcre2-posix3_10.42-4ubuntu1_amd64.deb ... 783s Unpacking libpcre2-posix3:amd64 (10.42-4ubuntu1) ... 783s Selecting previously unselected package libpcre2-dev:amd64. 783s Preparing to unpack .../18-libpcre2-dev_10.42-4ubuntu1_amd64.deb ... 783s Unpacking libpcre2-dev:amd64 (10.42-4ubuntu1) ... 783s Selecting previously unselected package libpkgconf3:amd64. 783s Preparing to unpack .../19-libpkgconf3_1.8.1-2_amd64.deb ... 783s Unpacking libpkgconf3:amd64 (1.8.1-2) ... 783s Selecting previously unselected package zlib1g-dev:amd64. 783s Preparing to unpack .../20-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_amd64.deb ... 783s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg-3ubuntu1) ... 783s Selecting previously unselected package libpng-dev:amd64. 783s Preparing to unpack .../21-libpng-dev_1.6.43-1_amd64.deb ... 783s Unpacking libpng-dev:amd64 (1.6.43-1) ... 783s Selecting previously unselected package libreadline-dev:amd64. 783s Preparing to unpack .../22-libreadline-dev_8.2-3_amd64.deb ... 783s Unpacking libreadline-dev:amd64 (8.2-3) ... 783s Selecting previously unselected package pkgconf-bin. 783s Preparing to unpack .../23-pkgconf-bin_1.8.1-2_amd64.deb ... 783s Unpacking pkgconf-bin (1.8.1-2) ... 783s Selecting previously unselected package pkgconf:amd64. 783s Preparing to unpack .../24-pkgconf_1.8.1-2_amd64.deb ... 783s Unpacking pkgconf:amd64 (1.8.1-2) ... 783s Selecting previously unselected package pkg-config:amd64. 783s Preparing to unpack .../25-pkg-config_1.8.1-2_amd64.deb ... 783s Unpacking pkg-config:amd64 (1.8.1-2) ... 783s Selecting previously unselected package liblzma-dev:amd64. 783s Preparing to unpack .../26-liblzma-dev_5.4.5-0.3_amd64.deb ... 783s Unpacking liblzma-dev:amd64 (5.4.5-0.3) ... 783s Selecting previously unselected package r-base-dev. 783s Preparing to unpack .../27-r-base-dev_4.3.2-1build1_all.deb ... 783s Unpacking r-base-dev (4.3.2-1build1) ... 783s Selecting previously unselected package pkg-r-autopkgtest. 783s Preparing to unpack .../28-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 783s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 783s Setting up libjpeg-turbo8-dev:amd64 (2.1.5-2ubuntu1) ... 783s Setting up libncurses-dev:amd64 (6.4+20240113-1ubuntu1) ... 783s Setting up libreadline-dev:amd64 (8.2-3) ... 783s Setting up libpcre2-16-0:amd64 (10.42-4ubuntu1) ... 783s Setting up libpcre2-32-0:amd64 (10.42-4ubuntu1) ... 783s Setting up libpkgconf3:amd64 (1.8.1-2) ... 783s Setting up icu-devtools (74.2-1ubuntu1) ... 783s Setting up pkgconf-bin (1.8.1-2) ... 783s Setting up liblzma-dev:amd64 (5.4.5-0.3) ... 783s Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3ubuntu1) ... 783s Setting up libpcre2-posix3:amd64 (10.42-4ubuntu1) ... 783s Setting up libjpeg8-dev:amd64 (8c-2ubuntu11) ... 783s Setting up libgfortran-13-dev:amd64 (13.2.0-17ubuntu2) ... 783s Setting up libicu-dev:amd64 (74.2-1ubuntu1) ... 783s Setting up libblas-dev:amd64 (3.12.0-3) ... 783s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode 783s Setting up dctrl-tools (2.24-3build2) ... 783s Setting up libbz2-dev:amd64 (1.0.8-5ubuntu1) ... 783s Setting up libpcre2-dev:amd64 (10.42-4ubuntu1) ... 783s Setting up libpng-dev:amd64 (1.6.43-1) ... 783s Setting up libjpeg-dev:amd64 (8c-2ubuntu11) ... 783s Setting up gfortran-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 783s Setting up pkgconf:amd64 (1.8.1-2) ... 783s Setting up gfortran-13 (13.2.0-17ubuntu2) ... 783s Setting up liblapack-dev:amd64 (3.12.0-3) ... 783s 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 783s Setting up pkg-config:amd64 (1.8.1-2) ... 783s Setting up gfortran-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 783s Setting up gfortran (4:13.2.0-7ubuntu1) ... 783s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 783s 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 783s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 783s 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 783s Setting up r-base-dev (4.3.2-1build1) ... 783s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 783s Processing triggers for libc-bin (2.39-0ubuntu2) ... 783s Processing triggers for man-db (2.12.0-3) ... 784s Processing triggers for install-info (7.1-3) ... 785s Reading package lists... 786s Building dependency tree... 786s Reading state information... 786s Starting pkgProblemResolver with broken count: 0 786s Starting 2 pkgProblemResolver with broken count: 0 786s Done 786s The following NEW packages will be installed: 786s autopkgtest-satdep 786s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 786s Need to get 0 B/700 B of archives. 786s After this operation, 0 B of additional disk space will be used. 786s Get:1 /tmp/autopkgtest.trzW8o/4-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [700 B] 787s Selecting previously unselected package autopkgtest-satdep. 787s (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 ... 77584 files and directories currently installed.) 787s Preparing to unpack .../4-autopkgtest-satdep.deb ... 787s Unpacking autopkgtest-satdep (0) ... 787s Setting up autopkgtest-satdep (0) ... 788s (Reading database ... 77584 files and directories currently installed.) 788s Removing autopkgtest-satdep (0) ... 789s autopkgtest [21:44:32]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 789s autopkgtest [21:44:32]: test pkg-r-autopkgtest: [----------------------- 789s Test: Try to load the R library kmi 789s 789s R version 4.3.2 (2023-10-31) -- "Eye Holes" 789s Copyright (C) 2023 The R Foundation for Statistical Computing 789s Platform: x86_64-pc-linux-gnu (64-bit) 789s 789s R is free software and comes with ABSOLUTELY NO WARRANTY. 789s You are welcome to redistribute it under certain conditions. 789s Type 'license()' or 'licence()' for distribution details. 789s 789s R is a collaborative project with many contributors. 789s Type 'contributors()' for more information and 789s 'citation()' on how to cite R or R packages in publications. 789s 789s Type 'demo()' for some demos, 'help()' for on-line help, or 789s 'help.start()' for an HTML browser interface to help. 789s Type 'q()' to quit R. 789s 789s > library('kmi') 790s > 790s > 790s Other tests are currently unsupported! 790s They will be progressively added. 790s autopkgtest [21:44:33]: test pkg-r-autopkgtest: -----------------------] 791s autopkgtest [21:44:34]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 791s pkg-r-autopkgtest PASS 791s autopkgtest [21:44:34]: @@@@@@@@@@@@@@@@@@@@ summary 791s run-unit-test PASS 791s pkg-r-autopkgtest PASS 801s Creating nova instance adt-noble-i386-r-cran-kmi-20240322-213123-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-amd64-server-20240322.img (UUID 485815e0-0f91-4788-a5b5-e5301593a332)...