0s autopkgtest [23:55:52]: starting date and time: 2024-03-22 23:55:52+0000
  0s autopkgtest [23:55:52]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [23:55:52]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.495yyn64/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-learnbayes --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@lcy02-56.secgroup --name adt-noble-i386-r-cran-learnbayes-20240322-235552-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/
 98s autopkgtest [23:57:30]: testbed dpkg architecture: amd64
 98s autopkgtest [23:57:30]: testbed apt version: 2.7.12
 98s autopkgtest [23:57:30]: test architecture: i386
 98s autopkgtest [23:57:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 98s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
 98s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
 99s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.7 kB]
 99s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [498 kB]
 99s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3979 kB]
 99s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [463 kB]
 99s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [699 kB]
 99s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B]
 99s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6700 B]
 99s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [30.5 kB]
 99s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B]
 99s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1309 kB]
 99s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4449 kB]
 99s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B]
 99s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [27.6 kB]
 99s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [96.8 kB]
 99s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B]
102s Fetched 11.8 MB in 2s (7491 kB/s)
102s Reading package lists...
104s Reading package lists...
104s Building dependency tree...
104s Reading state information...
104s Calculating upgrade...
105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
105s Reading package lists...
105s Building dependency tree...
105s Reading state information...
105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
106s sh: Attempting to set up Debian/Ubuntu apt sources automatically
106s sh: Distribution appears to be Ubuntu
107s Reading package lists...
107s Building dependency tree...
107s Reading state information...
107s eatmydata is already the newest version (131-1).
107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
108s Reading package lists...
108s Building dependency tree...
108s Reading state information...
108s dbus is already the newest version (1.14.10-4ubuntu1).
108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
108s Reading package lists...
109s Building dependency tree...
109s Reading state information...
109s rng-tools-debian is already the newest version (2.4).
109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
109s Reading package lists...
110s Building dependency tree...
110s Reading state information...
110s The following packages will be REMOVED:
110s   cloud-init* python3-configobj* python3-debconf*
111s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
111s After this operation, 3256 kB disk space will be freed.
111s (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.)
111s Removing cloud-init (24.1.2-0ubuntu1) ...
111s Removing python3-configobj (5.0.8-3) ...
112s Removing python3-debconf (1.5.86) ...
112s Processing triggers for man-db (2.12.0-3) ...
112s (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.)
112s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ...
113s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
113s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
113s invoke-rc.d: policy-rc.d denied execution of try-restart.
113s Reading package lists...
113s Building dependency tree...
113s Reading state information...
114s linux-generic is already the newest version (6.8.0-11.11+1).
114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
114s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
114s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
114s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
116s Reading package lists...
116s Reading package lists...
117s Building dependency tree...
117s Reading state information...
117s Calculating upgrade...
117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
117s Reading package lists...
118s Building dependency tree...
118s Reading state information...
118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
118s autopkgtest [23:57:50]: rebooting testbed after setup commands that affected boot
144s autopkgtest [23:58:16]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024
144s autopkgtest [23:58:16]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-learnbayes
145s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-learnbayes 2.15.1-4build1 (dsc) [2089 B]
145s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-learnbayes 2.15.1-4build1 (tar) [795 kB]
145s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-learnbayes 2.15.1-4build1 (diff) [2856 B]
145s gpgv: Signature made Sat May 30 10:10:34 2020 UTC
145s gpgv:                using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2
145s gpgv: Can't check signature: No public key
145s dpkg-source: warning: cannot verify inline signature for ./r-cran-learnbayes_2.15.1-4build1.dsc: no acceptable signature found
145s autopkgtest [23:58:17]: testing package r-cran-learnbayes version 2.15.1-4build1
145s autopkgtest [23:58:17]: build not needed
145s autopkgtest [23:58:17]: test run-unit-test: preparing testbed
148s Note, using file '/tmp/autopkgtest.kZjTh8/1-autopkgtest-satdep.dsc' to get the build dependencies
148s Reading package lists...
148s Building dependency tree...
148s Reading state information...
148s Starting pkgProblemResolver with broken count: 0
148s Starting 2 pkgProblemResolver with broken count: 0
148s Done
149s The following NEW packages will be installed:
149s   build-essential cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu
149s   fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono g++ g++-13
149s   g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-13
149s   gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu libasan8 libatomic1 libblas3
149s   libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libdatrie1
149s   libdeflate0 libfontconfig1 libgcc-13-dev libgfortran5 libgomp1
149s   libgraphite2-3 libharfbuzz0b libhwasan0 libice6 libisl23 libitm1 libjbig0
149s   libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 liblsan0 libmpc3 libnsl-dev
149s   libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
149s   libpaper1 libpixman-1-0 libquadmath0 libsharpyuv0 libsm6 libstdc++-13-dev
149s   libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2
149s   libubsan1 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1
149s   libxt6 linux-libc-dev r-base-core r-cran-learnbayes rpcsvc-proto unzip
149s   x11-common xdg-utils zip
149s 0 upgraded, 78 newly installed, 0 to remove and 0 not upgraded.
149s Need to get 105 MB of archives.
149s After this operation, 323 MB of additional disk space will be used.
149s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.39-0ubuntu2 [20.4 kB]
149s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB]
149s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB]
149s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-dev amd64 1.3.4+ds-1build1 [222 kB]
149s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl-dev amd64 1.3.0-3 [71.2 kB]
149s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu6 [68.5 kB]
149s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.39-0ubuntu2 [2126 kB]
149s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libisl23 amd64 0.26-3 [741 kB]
149s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libmpc3 amd64 1.3.1-1 [54.1 kB]
149s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.2 MB]
149s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-17ubuntu2 [1030 B]
149s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B]
149s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB]
149s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 14-20240303-1ubuntu1 [47.7 kB]
149s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240303-1ubuntu1 [147 kB]
149s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240303-1ubuntu1 [29.1 kB]
149s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240303-1ubuntu1 [10.4 kB]
149s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240303-1ubuntu1 [3026 kB]
149s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240303-1ubuntu1 [1310 kB]
149s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240303-1ubuntu1 [2732 kB]
149s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240303-1ubuntu1 [1172 kB]
149s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240303-1ubuntu1 [1629 kB]
149s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240303-1ubuntu1 [155 kB]
149s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-17ubuntu2 [2687 kB]
149s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [21.9 MB]
149s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-17ubuntu2 [477 kB]
149s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B]
149s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B]
149s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-17ubuntu2 [2340 kB]
149s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [12.5 MB]
149s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-17ubuntu2 [14.5 kB]
149s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B]
149s Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B]
149s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 build-essential amd64 12.10ubuntu1 [4928 B]
149s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
149s Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
149s Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig-config amd64 2.15.0-1ubuntu1 [36.9 kB]
149s Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 libfontconfig1 amd64 2.15.0-1ubuntu1 [139 kB]
149s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig amd64 2.15.0-1ubuntu1 [180 kB]
149s Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.12.0-3 [238 kB]
149s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libpixman-1-0 amd64 0.42.2-1 [268 kB]
149s Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-render0 amd64 1.15-1 [16.3 kB]
149s Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-shm0 amd64 1.15-1 [5740 B]
149s Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB]
149s Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 libcairo2 amd64 1.18.0-1 [572 kB]
149s Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 libdatrie1 amd64 0.2.13-3 [20.9 kB]
149s Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate0 amd64 1.19-1 [43.7 kB]
149s Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran5 amd64 14-20240303-1ubuntu1 [924 kB]
149s Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 libgraphite2-3 amd64 1.3.14-2 [83.1 kB]
149s Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 libharfbuzz0b amd64 8.3.0-2 [469 kB]
149s Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 x11-common all 1:7.7+23ubuntu2 [23.4 kB]
149s Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libice6 amd64 2:1.0.10-1build2 [42.6 kB]
149s Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu1 [147 kB]
149s Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
149s Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.12.0-3 [2649 kB]
149s Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu1 [184 kB]
149s Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 libthai-data all 0.1.29-2 [158 kB]
149s Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 libthai0 amd64 0.1.29-2 [18.8 kB]
149s Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 libpango-1.0-0 amd64 1.51.0+ds-4 [228 kB]
149s Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 libpangoft2-1.0-0 amd64 1.51.0+ds-4 [42.1 kB]
149s Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 libpangocairo-1.0-0 amd64 1.51.0+ds-4 [29.0 kB]
149s Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper1 amd64 1.1.29 [13.4 kB]
149s Get:63 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper-utils amd64 1.1.29 [8658 B]
149s Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 libsharpyuv0 amd64 1.3.2-0.4 [15.6 kB]
149s Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 libsm6 amd64 2:1.2.3-1build2 [16.7 kB]
149s Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [984 kB]
149s Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 libjbig0 amd64 2.1-6.1ubuntu1 [29.3 kB]
149s Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 libwebp7 amd64 1.3.2-0.4 [230 kB]
149s Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 libtiff6 amd64 4.5.1+git230720-3ubuntu1 [232 kB]
149s Get:70 http://ftpmaster.internal/ubuntu noble/main amd64 libxft2 amd64 2.3.6-1 [44.5 kB]
149s Get:71 http://ftpmaster.internal/ubuntu noble/main amd64 libxss1 amd64 1:1.2.3-1build2 [8476 B]
149s Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 libtk8.6 amd64 8.6.13-2 [776 kB]
149s Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 libxt6 amd64 1:1.2.1-1.1 [173 kB]
149s Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 zip amd64 3.0-13 [176 kB]
149s Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 unzip amd64 6.0-28ubuntu3 [174 kB]
149s Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB]
149s Get:77 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-core amd64 4.3.2-1build1 [27.0 MB]
150s Get:78 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-learnbayes all 2.15.1-4build1 [963 kB]
150s Preconfiguring packages ...
150s Fetched 105 MB in 1s (145 MB/s)
150s Selecting previously unselected package libc-dev-bin.
150s (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.)
150s Preparing to unpack .../00-libc-dev-bin_2.39-0ubuntu2_amd64.deb ...
150s Unpacking libc-dev-bin (2.39-0ubuntu2) ...
150s Selecting previously unselected package linux-libc-dev:amd64.
150s Preparing to unpack .../01-linux-libc-dev_6.8.0-11.11_amd64.deb ...
150s Unpacking linux-libc-dev:amd64 (6.8.0-11.11) ...
150s Selecting previously unselected package libcrypt-dev:amd64.
150s Preparing to unpack .../02-libcrypt-dev_1%3a4.4.36-4_amd64.deb ...
150s Unpacking libcrypt-dev:amd64 (1:4.4.36-4) ...
150s Selecting previously unselected package libtirpc-dev:amd64.
150s Preparing to unpack .../03-libtirpc-dev_1.3.4+ds-1build1_amd64.deb ...
150s Unpacking libtirpc-dev:amd64 (1.3.4+ds-1build1) ...
150s Selecting previously unselected package libnsl-dev:amd64.
150s Preparing to unpack .../04-libnsl-dev_1.3.0-3_amd64.deb ...
150s Unpacking libnsl-dev:amd64 (1.3.0-3) ...
151s Selecting previously unselected package rpcsvc-proto.
151s Preparing to unpack .../05-rpcsvc-proto_1.4.2-0ubuntu6_amd64.deb ...
151s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ...
151s Selecting previously unselected package libc6-dev:amd64.
151s Preparing to unpack .../06-libc6-dev_2.39-0ubuntu2_amd64.deb ...
151s Unpacking libc6-dev:amd64 (2.39-0ubuntu2) ...
151s Selecting previously unselected package libisl23:amd64.
151s Preparing to unpack .../07-libisl23_0.26-3_amd64.deb ...
151s Unpacking libisl23:amd64 (0.26-3) ...
151s Selecting previously unselected package libmpc3:amd64.
151s Preparing to unpack .../08-libmpc3_1.3.1-1_amd64.deb ...
151s Unpacking libmpc3:amd64 (1.3.1-1) ...
151s Selecting previously unselected package cpp-13-x86-64-linux-gnu.
151s Preparing to unpack .../09-cpp-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ...
151s Unpacking cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
151s Selecting previously unselected package cpp-13.
151s Preparing to unpack .../10-cpp-13_13.2.0-17ubuntu2_amd64.deb ...
151s Unpacking cpp-13 (13.2.0-17ubuntu2) ...
151s Selecting previously unselected package cpp-x86-64-linux-gnu.
151s Preparing to unpack .../11-cpp-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ...
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155s 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
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155s Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
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157s Setting up libcairo2:amd64 (1.18.0-1) ...
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157s Setting up cpp (4:13.2.0-7ubuntu1) ...
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157s Setting up libpangocairo-1.0-0:amd64 (1.51.0+ds-4) ...
157s Setting up g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
157s Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
157s Setting up gcc (4:13.2.0-7ubuntu1) ...
157s Setting up r-base-core (4.3.2-1build1) ...
157s 
157s Creating config file /etc/R/Renviron with new version
157s Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
157s Setting up g++-13 (13.2.0-17ubuntu2) ...
157s Setting up r-cran-learnbayes (2.15.1-4build1) ...
157s Setting up g++ (4:13.2.0-7ubuntu1) ...
157s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
157s Setting up build-essential (12.10ubuntu1) ...
157s Processing triggers for libc-bin (2.39-0ubuntu2) ...
158s Processing triggers for man-db (2.12.0-3) ...
159s Processing triggers for install-info (7.1-3) ...
160s Reading package lists...
160s Building dependency tree...
160s Reading state information...
160s Starting pkgProblemResolver with broken count: 0
160s Starting 2 pkgProblemResolver with broken count: 0
160s Done
161s The following NEW packages will be installed:
161s   autopkgtest-satdep
161s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
161s Need to get 0 B/696 B of archives.
161s After this operation, 0 B of additional disk space will be used.
161s Get:1 /tmp/autopkgtest.kZjTh8/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B]
161s Selecting previously unselected package autopkgtest-satdep.
161s (Reading database ... 
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161s Preparing to unpack .../2-autopkgtest-satdep.deb ...
161s Unpacking autopkgtest-satdep (0) ...
161s Setting up autopkgtest-satdep (0) ...
163s (Reading database ... 76536 files and directories currently installed.)
163s Removing autopkgtest-satdep (0) ...
163s autopkgtest [23:58:35]: test run-unit-test: [-----------------------
163s 
163s R version 4.3.2 (2023-10-31) -- "Eye Holes"
163s Copyright (C) 2023 The R Foundation for Statistical Computing
163s Platform: x86_64-pc-linux-gnu (64-bit)
163s 
163s R is free software and comes with ABSOLUTELY NO WARRANTY.
163s You are welcome to redistribute it under certain conditions.
163s Type 'license()' or 'licence()' for distribution details.
163s 
163s R is a collaborative project with many contributors.
163s Type 'contributors()' for more information and
163s 'citation()' on how to cite R or R packages in publications.
163s 
163s Type 'demo()' for some demos, 'help()' for on-line help, or
163s 'help.start()' for an HTML browser interface to help.
163s Type 'q()' to quit R.
163s 
163s >   Stangle("BayesFactors.Rnw")
163s Writing to file BayesFactors.R 
163s >   source("BayesFactors.R", echo=TRUE)
163s 
163s > fire.counts <- c(75, 88, 84, 99, 79, 68, 86, 109, 
163s +     73, 85, 101, 85, 75, 81, 64, 77, 83, 83, 88, 83, 78, 83, 
163s +     78, 80, 82, 90, 74, 72, 69, .... [TRUNCATED] 
163s 
163s > hist(fire.counts, probability = TRUE, ylim = c(0, 
163s +     0.08))
163s 
163s > x <- 60:110
163s 
163s > lines(x, dpois(x, lambda = mean(fire.counts)), col = "red")
163s 
163s > lines(x, dnorm(x, mean = mean(fire.counts), sd = 12), 
163s +     col = "blue")
163s 
163s > lines(x, dnorm(x, mean = mean(fire.counts), sd = 6), 
163s +     col = "green")
163s 
163s > legend("topright", legend = c("M1: Poisson(theta)", 
163s +     "M2: N(theta, 12)", "M3: N(theta, 6)"), col = c("red", "blue", 
163s +     "green"), lty = 1)
163s 
163s > model.1 <- function(theta, y) {
163s +     sum(log(dpois(y, theta))) + dgamma(theta, shape = 280, rate = 4)
163s + }
163s 
163s > library(LearnBayes)
163s 
163s > log.pred.1 <- laplace(model.1, 80, fire.counts)$int
163s 
163s > log.pred.1
163s [1] -131.6253
163s 
163s > model.2 <- function(theta, y) {
163s +     sum(log(dnorm(y, theta, 6))) + dgamma(theta, shape = 280, 
163s +         rate = 4)
163s + }
163s 
163s > model.3 <- function(theta, y) {
163s +     sum(log(dnorm(y, theta, 12))) + dgamma(theta, shape = 280, 
163s +         rate = 4)
163s + }
163s 
163s > log.pred.2 <- laplace(model.2, 80, fire.counts)$int
163s 
163s > log.pred.3 <- laplace(model.3, 80, fire.counts)$int
163s 
163s > data.frame(Model = 1:3, log.pred = c(log.pred.1, log.pred.2, 
163s +     log.pred.3))
163s   Model  log.pred
163s 1     1 -131.6253
163s 2     2 -144.7554
163s 3     3 -132.9464
163s 
163s > exp(log.pred.1 - log.pred.3)
163s [1] 3.74751
163s > 
163s 
163s R version 4.3.2 (2023-10-31) -- "Eye Holes"
163s Copyright (C) 2023 The R Foundation for Statistical Computing
163s Platform: x86_64-pc-linux-gnu (64-bit)
163s 
163s R is free software and comes with ABSOLUTELY NO WARRANTY.
163s You are welcome to redistribute it under certain conditions.
163s Type 'license()' or 'licence()' for distribution details.
163s 
163s R is a collaborative project with many contributors.
163s Type 'contributors()' for more information and
163s 'citation()' on how to cite R or R packages in publications.
163s 
163s Type 'demo()' for some demos, 'help()' for on-line help, or
163s 'help.start()' for an HTML browser interface to help.
163s Type 'q()' to quit R.
163s 
163s >   Stangle("BinomialInference.Rnw")
164s Writing to file BinomialInference.R 
164s >   source("BinomialInference.R", echo=TRUE)
164s 
164s > library(LearnBayes)
164s 
164s > beta.par <- beta.select(list(p = 0.5, x = 0.2), list(p = 0.75, 
164s +     x = 0.28))
164s 
164s > beta.par
164s [1]  2.95 10.82
164s 
164s > triplot(beta.par, c(6, 4))
164s 
164s > beta.post.par <- beta.par + c(6, 4)
164s 
164s > post.sample <- rbeta(1000, beta.post.par[1], beta.post.par[2])
164s 
164s > quantile(post.sample, c(0.05, 0.95))
164s        5%       95% 
164s 0.2232051 0.5419360 
164s 
164s > predplot(beta.par, 10, 6)
164s 
164s > n <- 20
164s 
164s > s <- 0:n
164s 
164s > pred.probs <- pbetap(beta.par, n, s)
164s 
164s > plot(s, pred.probs, type = "h")
164s 
164s > discint(cbind(s, pred.probs), 0.9)
164s $prob
164s [1] 0.9181962
164s 
164s $set
164s [1] 0 1 2 3 4 5 6 7 8
164s 
164s > 
164s 
164s R version 4.3.2 (2023-10-31) -- "Eye Holes"
164s Copyright (C) 2023 The R Foundation for Statistical Computing
164s Platform: x86_64-pc-linux-gnu (64-bit)
164s 
164s R is free software and comes with ABSOLUTELY NO WARRANTY.
164s You are welcome to redistribute it under certain conditions.
164s Type 'license()' or 'licence()' for distribution details.
164s 
164s R is a collaborative project with many contributors.
164s Type 'contributors()' for more information and
164s 'citation()' on how to cite R or R packages in publications.
164s 
164s Type 'demo()' for some demos, 'help()' for on-line help, or
164s 'help.start()' for an HTML browser interface to help.
164s Type 'q()' to quit R.
164s 
164s >   Stangle("DiscreteBayes.Rnw")
164s Writing to file DiscreteBayes.R 
164s >   source("DiscreteBayes.R", echo=TRUE)
164s 
164s > p <- seq(0, 1, by = 0.01)
164s 
164s > prior <- 1/101 + 0 * p
164s 
164s > plot(p, prior, type = "h", main = "Prior Distribution")
164s 
164s > library(LearnBayes)
164s 
164s > post <- pdisc(p, prior, c(20, 12))
164s 
164s > plot(p, post, type = "h", main = "Posterior Distribution")
164s 
164s > discint(cbind(p, post), 0.9)
164s $prob
164s [1] 0.9001245
164s 
164s $set
164s  [1] 0.49 0.50 0.51 0.52 0.53 0.54 0.55 0.56 0.57 0.58 0.59 0.60 0.61 0.62 0.63
164s [16] 0.64 0.65 0.66 0.67 0.68 0.69 0.70 0.71 0.72 0.73 0.74 0.75
164s 
164s 
164s > n <- 20
164s 
164s > s <- 0:20
164s 
164s > pred.probs <- pdiscp(p, post, n, s)
164s 
164s > plot(s, pred.probs, type = "h", main = "Predictive Distribution")
164s 
164s > prior <- rep(1/11, 11)
164s 
164s > names(prior) <- 20:30
164s 
164s > y <- c(24, 25, 31, 31, 22, 21, 26, 20, 16, 22)
164s 
164s > post <- discrete.bayes(dpois, prior, y)
164s 
164s > print(post)
164s           20           21           22           23           24           25 
164s 0.0086284462 0.0432554621 0.1263286996 0.2255195224 0.2566196329 0.1931041454 
164s           26           27           28           29           30 
164s 0.0992616593 0.0358720144 0.0093507519 0.0017989279 0.0002607378 
164s 
164s > plot(post)
164s 
164s > summary(post)
164s $mean
164s [1] 23.90475
164s 
164s $sd
164s [1] 1.538209
164s 
164s $coverage
164s [1] 0.9008337
164s 
164s $set
164s [1] 22 23 24 25 26
164s 
164s > 
164s 
164s R version 4.3.2 (2023-10-31) -- "Eye Holes"
164s Copyright (C) 2023 The R Foundation for Statistical Computing
164s Platform: x86_64-pc-linux-gnu (64-bit)
164s 
164s R is free software and comes with ABSOLUTELY NO WARRANTY.
164s You are welcome to redistribute it under certain conditions.
164s Type 'license()' or 'licence()' for distribution details.
164s 
164s R is a collaborative project with many contributors.
164s Type 'contributors()' for more information and
164s 'citation()' on how to cite R or R packages in publications.
164s 
164s Type 'demo()' for some demos, 'help()' for on-line help, or
164s 'help.start()' for an HTML browser interface to help.
164s Type 'q()' to quit R.
164s 
164s >   Stangle("MCMCintro.Rnw")
164s Writing to file MCMCintro.R 
164s >   source("MCMCintro.R", echo=TRUE)
164s 
164s > minmaxpost <- function(theta, data) {
164s +     mu <- theta[1]
164s +     sigma <- exp(theta[2])
164s +     dnorm(data$min, mu, sigma, log = TRUE) + dnorm(data$ma .... [TRUNCATED] 
164s 
164s > data <- list(n = 10, min = 52, max = 84)
164s 
164s > library(LearnBayes)
164s 
164s > fit <- laplace(minmaxpost, c(70, 2), data)
164s 
164s > fit
164s $mode
164s [1] 67.999960  2.298369
164s 
164s $var
164s               [,1]          [,2]
164s [1,]  1.920690e+01 -1.901459e-06
164s [2,] -1.901459e-06  6.031533e-02
164s 
164s $int
164s [1] -8.020139
164s 
164s $converge
164s [1] TRUE
164s 
164s 
164s > mycontour(minmaxpost, c(45, 95, 1.5, 4), data, xlab = expression(mu), 
164s +     ylab = expression(paste("log ", sigma)))
164s 
164s > mycontour(lbinorm, c(45, 95, 1.5, 4), list(m = fit$mode, 
164s +     v = fit$var), add = TRUE, col = "red")
164s 
164s > mcmc.fit <- rwmetrop(minmaxpost, list(var = fit$v, 
164s +     scale = 3), c(70, 2), 10000, data)
164s 
164s > mcmc.fit$accept
164s [1] 0.1767
164s 
164s > mycontour(minmaxpost, c(45, 95, 1.5, 4), data, xlab = expression(mu), 
164s +     ylab = expression(paste("log ", sigma)))
164s 
164s > points(mcmc.fit$par)
164s 
164s > mu <- mcmc.fit$par[, 1]
164s 
164s > sigma <- exp(mcmc.fit$par[, 2])
164s 
164s > P.75 <- mu + 0.674 * sigma
164s 
164s > plot(density(P.75), main = "Posterior Density of Upper Quartile")
165s > 
165s 
165s R version 4.3.2 (2023-10-31) -- "Eye Holes"
165s Copyright (C) 2023 The R Foundation for Statistical Computing
165s Platform: x86_64-pc-linux-gnu (64-bit)
165s 
165s R is free software and comes with ABSOLUTELY NO WARRANTY.
165s You are welcome to redistribute it under certain conditions.
165s Type 'license()' or 'licence()' for distribution details.
165s 
165s R is a collaborative project with many contributors.
165s Type 'contributors()' for more information and
165s 'citation()' on how to cite R or R packages in publications.
165s 
165s Type 'demo()' for some demos, 'help()' for on-line help, or
165s 'help.start()' for an HTML browser interface to help.
165s Type 'q()' to quit R.
165s 
165s >   Stangle("MultilevelModeling.Rnw")
165s Writing to file MultilevelModeling.R 
165s >   source("MultilevelModeling.R", echo=TRUE)
165s 
165s > d <- data.frame(Name = c("Clemente", "Robinson", "Howard", 
165s +     "Johnstone", "Berry", "Spencer", "Kessinger", "Alvarado", 
165s +     "Santo", "Swaboda ..." ... [TRUNCATED] 
165s 
165s > library(LearnBayes)
165s 
165s > laplace.fit <- laplace(betabinexch, c(0, 0), d[, c("Hits", 
165s +     "At.Bats")])
165s 
165s > laplace.fit
165s $mode
165s [1] -1.013462  4.436169
165s 
165s $var
165s              [,1]         [,2]
165s [1,]  0.009556755 -0.005509578
165s [2,] -0.005509578  0.702918198
165s 
165s $int
165s [1] -474.3837
165s 
165s $converge
165s [1] TRUE
165s 
165s 
165s > mcmc.fit <- rwmetrop(betabinexch, list(var = laplace.fit$var, 
165s +     scale = 2), c(0, 0), 5000, d[, c("Hits", "At.Bats")])
165s 
165s > mycontour(betabinexch, c(-1.5, -0.5, 2, 12), d[, c("Hits", 
165s +     "At.Bats")], xlab = "Logit ETA", ylab = "Log K")
165s 
165s > with(mcmc.fit, points(par))
165s 
165s > eta <- with(mcmc.fit, exp(par[, 1])/(1 + exp(par[, 
165s +     1])))
165s 
165s > K <- exp(mcmc.fit$par[, 2])
165s 
165s > p.estimate <- function(j, eta, K) {
165s +     yj <- d[j, "Hits"]
165s +     nj <- d[j, "At.Bats"]
165s +     p.sim <- rbeta(5000, yj + K * eta, nj - yj + K * (1 - .... [TRUNCATED] 
165s 
165s > E <- t(sapply(1:18, p.estimate, eta, K))
165s 
165s > rownames(E) <- d[, "Name"]
165s 
165s > round(E, 3)
165s               5%   50%   95%
165s Clemente   0.242 0.303 0.396
165s Robinson   0.239 0.296 0.385
165s Howard     0.232 0.288 0.374
165s Johnstone  0.227 0.283 0.365
165s Berry      0.220 0.277 0.352
165s Spencer    0.221 0.278 0.354
165s Kessinger  0.213 0.272 0.344
165s Alvarado   0.205 0.267 0.332
165s Santo      0.197 0.261 0.326
165s Swaboda    0.198 0.261 0.325
165s Petrocelli 0.185 0.255 0.314
165s Rodriguez  0.188 0.255 0.316
165s Scott      0.187 0.256 0.314
165s Unser      0.188 0.255 0.318
165s Williams   0.187 0.255 0.314
165s Campaneris 0.178 0.247 0.307
165s Munson     0.169 0.242 0.302
165s Alvis      0.159 0.236 0.295
165s 
165s > plot(d$Hits/45, E[, 2], pch = 19, ylim = c(0.15, 0.4), 
165s +     xlab = "Observed AVG", ylab = "True Probability", main = "90 Percent Probability Inter ..." ... [TRUNCATED] 
165s 
165s > for (j in 1:18) lines(d$Hits[j]/45 * c(1, 1), E[j, 
165s +     c(1, 3)])
165s 
165s > abline(a = 0, b = 1, col = "blue")
165s 
165s > abline(h = mean(d$Hits)/45, col = "red")
165s 
165s > legend("topleft", legend = c("Individual", "Combined"), 
165s +     lty = 1, col = c("blue", "red"))
165s > 
165s autopkgtest [23:58:37]: test run-unit-test: -----------------------]
166s autopkgtest [23:58:38]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
166s run-unit-test        PASS
166s autopkgtest [23:58:38]: @@@@@@@@@@@@@@@@@@@@ summary
166s run-unit-test        PASS
176s Creating nova instance adt-noble-i386-r-cran-learnbayes-20240322-235552-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-amd64-server-20240322.img (UUID 485815e0-0f91-4788-a5b5-e5301593a332)...