0s autopkgtest [17:16:40]: starting date and time: 2024-03-16 17:16:40+0000
  0s autopkgtest [17:16:40]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data
  0s autopkgtest [17:16:40]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.4dk1yuam/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-base,src:curl,src:glib2.0,src:libpng1.6,src:libpsl,src:libtirpc,src:libxt,src:openssl,src:orthanc-python,src:readline,src:wp2latex --apt-upgrade fastqtl --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 curl/8.5.0-2ubuntu7 glib2.0/2.79.3-3ubuntu5 libpng1.6/1.6.43-3 libpsl/0.21.2-1.1 libtirpc/1.3.4+ds-1.1 libxt/1:1.2.1-1.2 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3 readline/8.2-3.1 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-13.secgroup --name adt-noble-arm64-fastqtl-20240316-171639-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
100s autopkgtest [17:18:20]: testbed dpkg architecture: arm64
100s autopkgtest [17:18:20]: testbed apt version: 2.7.12
100s autopkgtest [17:18:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup
101s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
102s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3673 kB]
102s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB]
102s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
102s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB]
102s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB]
102s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
102s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB]
102s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
102s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3994 kB]
102s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
102s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB]
102s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
104s Fetched 9063 kB in 2s (4187 kB/s)
105s Reading package lists...
116s Reading package lists...
116s Building dependency tree...
116s Reading state information...
117s Calculating upgrade...
118s The following packages will be REMOVED:
118s   libglib2.0-0 libssl3
118s The following NEW packages will be installed:
118s   libglib2.0-0t64 libssl3t64 xdg-user-dirs
118s The following packages have been kept back:
118s   curl
118s The following packages will be upgraded:
118s   gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common
118s   ubuntu-minimal ubuntu-standard
118s 7 upgraded, 3 newly installed, 2 to remove and 1 not upgraded.
118s Need to get 4613 kB of archives.
118s After this operation, 211 kB of additional disk space will be used.
118s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB]
119s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB]
119s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB]
119s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB]
119s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB]
119s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B]
119s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB]
119s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB]
119s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB]
119s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB]
120s Fetched 4613 kB in 1s (4375 kB/s)
120s (Reading database ... 
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(Reading database ... 74758 files and directories currently installed.)
120s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ...
120s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ...
120s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested:
120s  udisks2 depends on libglib2.0-0 (>= 2.77.0).
120s  shared-mime-info depends on libglib2.0-0 (>= 2.75.3).
120s  python3-gi depends on libglib2.0-0 (>= 2.77.0).
120s  python3-dbus depends on libglib2.0-0 (>= 2.16.0).
120s  netplan.io depends on libglib2.0-0 (>= 2.70.0).
120s  netplan-generator depends on libglib2.0-0 (>= 2.70.0).
120s  libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0).
120s  libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0).
120s  libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3).
120s  libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56).
120s  libqmi-proxy depends on libglib2.0-0 (>= 2.30.0).
120s  libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0).
120s  libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0).
120s  libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0).
120s  libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3).
120s  libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0).
120s  libmbim-proxy depends on libglib2.0-0 (>= 2.56).
120s  libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56).
120s  libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3).
120s  libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3).
120s  libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3).
120s  libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0).
120s  libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0).
120s  libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0).
120s  libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2).
120s  libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3).
120s  libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2).
120s  libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2).
120s  libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2).
120s  libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2).
120s  libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2).
120s  libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2).
120s  libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2).
120s  fwupd depends on libglib2.0-0 (>= 2.79.0).
120s  bolt depends on libglib2.0-0 (>= 2.56.0).
120s 
120s (Reading database ... 
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(Reading database ... 74758 files and directories currently installed.)
120s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ...
120s Selecting previously unselected package libglib2.0-0t64:arm64.
120s (Reading database ... 
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(Reading database ... 74733 files and directories currently installed.)
120s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ...
120s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled...
120s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm'
120s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ...
120s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ...
120s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ...
121s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested:
121s  wget depends on libssl3 (>= 3.0.0).
121s  u-boot-tools depends on libssl3 (>= 3.0.0).
121s  tnftp depends on libssl3 (>= 3.0.0).
121s  tcpdump depends on libssl3 (>= 3.0.0).
121s  systemd-resolved depends on libssl3 (>= 3.0.0).
121s  systemd depends on libssl3 (>= 3.0.0).
121s  sudo depends on libssl3 (>= 3.0.0).
121s  sbsigntool depends on libssl3 (>= 3.0.0).
121s  rsync depends on libssl3 (>= 3.0.0).
121s  python3-cryptography depends on libssl3 (>= 3.0.0).
121s  openssh-server depends on libssl3 (>= 3.0.10).
121s  openssh-client depends on libssl3 (>= 3.0.10).
121s  mtd-utils depends on libssl3 (>= 3.0.0).
121s  mokutil depends on libssl3 (>= 3.0.0).
121s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
121s  libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0).
121s  libssh-4:arm64 depends on libssl3 (>= 3.0.0).
121s  libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0).
121s  libsasl2-2:arm64 depends on libssl3 (>= 3.0.0).
121s  libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0).
121s  libnvme1 depends on libssl3 (>= 3.0.0).
121s  libkrb5-3:arm64 depends on libssl3 (>= 3.0.0).
121s  libkmod2:arm64 depends on libssl3 (>= 3.0.0).
121s  libfido2-1:arm64 depends on libssl3 (>= 3.0.0).
121s  libcurl4:arm64 depends on libssl3 (>= 3.0.0).
121s  libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0).
121s  kmod depends on libssl3 (>= 3.0.0).
121s  dhcpcd-base depends on libssl3 (>= 3.0.0).
121s  bind9-libs:arm64 depends on libssl3 (>= 3.0.0).
121s 
121s (Reading database ... 
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(Reading database ... 74758 files and directories currently installed.)
121s Removing libssl3:arm64 (3.0.10-1ubuntu4) ...
121s Selecting previously unselected package libssl3t64:arm64.
121s (Reading database ... 
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(Reading database ... 74747 files and directories currently installed.)
121s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu1_arm64.deb ...
121s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ...
121s Preparing to unpack .../1-libglib2.0-data_2.79.3-3ubuntu5_all.deb ...
121s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ...
121s Preparing to unpack .../2-libtirpc-common_1.3.4+ds-1.1_all.deb ...
121s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ...
121s Preparing to unpack .../3-readline-common_8.2-3.1_all.deb ...
121s Unpacking readline-common (8.2-3.1) over (8.2-3) ...
121s Preparing to unpack .../4-ubuntu-minimal_1.536_arm64.deb ...
121s Unpacking ubuntu-minimal (1.536) over (1.535) ...
121s Selecting previously unselected package xdg-user-dirs.
121s Preparing to unpack .../5-xdg-user-dirs_0.18-1_arm64.deb ...
121s Unpacking xdg-user-dirs (0.18-1) ...
121s Preparing to unpack .../6-ubuntu-standard_1.536_arm64.deb ...
121s Unpacking ubuntu-standard (1.536) over (1.535) ...
121s Setting up ubuntu-minimal (1.536) ...
121s Setting up xdg-user-dirs (0.18-1) ...
121s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ...
121s Setting up libtirpc-common (1.3.4+ds-1.1) ...
121s Setting up ubuntu-standard (1.536) ...
121s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ...
121s No schema files found: doing nothing.
121s Setting up libglib2.0-data (2.79.3-3ubuntu5) ...
121s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ...
121s Setting up openssl (3.0.13-0ubuntu1) ...
121s Setting up readline-common (8.2-3.1) ...
121s Processing triggers for man-db (2.12.0-3) ...
122s Processing triggers for install-info (7.1-3) ...
123s Processing triggers for libc-bin (2.39-0ubuntu2) ...
124s Reading package lists...
124s Building dependency tree...
124s Reading state information...
125s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
126s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
126s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
126s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
126s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease
131s Reading package lists...
132s Reading package lists...
132s Building dependency tree...
132s Reading state information...
133s Calculating upgrade...
133s The following packages have been kept back:
133s   curl
133s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
133s Reading package lists...
134s Building dependency tree...
134s Reading state information...
134s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
138s autopkgtest [17:18:58]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
138s autopkgtest [17:18:58]: @@@@@@@@@@@@@@@@@@@@ apt-source fastqtl
143s Get:1 http://ftpmaster.internal/ubuntu noble/universe fastqtl 2.184+v7+dfsg-4build1 (dsc) [2280 B]
143s Get:2 http://ftpmaster.internal/ubuntu noble/universe fastqtl 2.184+v7+dfsg-4build1 (tar) [17.1 MB]
143s Get:3 http://ftpmaster.internal/ubuntu noble/universe fastqtl 2.184+v7+dfsg-4build1 (diff) [21.0 kB]
144s gpgv: Signature made Tue Dec 19 15:01:14 2023 UTC
144s gpgv:                using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37
144s gpgv: Can't check signature: No public key
144s dpkg-source: warning: cannot verify inline signature for ./fastqtl_2.184+v7+dfsg-4build1.dsc: no acceptable signature found
147s autopkgtest [17:19:07]: testing package fastqtl version 2.184+v7+dfsg-4build1
147s autopkgtest [17:19:07]: build not needed
148s autopkgtest [17:19:08]: test run-sample-analysis: preparing testbed
150s Reading package lists...
150s Building dependency tree...
150s Reading state information...
151s Starting pkgProblemResolver with broken count: 0
151s Starting 2 pkgProblemResolver with broken count: 0
151s Done
152s The following additional packages will be installed:
152s   fastqtl fastqtl-doc libblas3 libboost-iostreams1.83.0
152s   libboost-program-options1.83.0 libdeflate0 libgsl27 libgslcblas0 libhts3
152s   libhtscodecs2 r-mathlib
152s Suggested packages:
152s   gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html
152s Recommended packages:
152s   r-cran-qvalue r-cran-tools r-cran-argparser r-base-core r-base-dev
152s The following NEW packages will be installed:
152s   autopkgtest-satdep fastqtl fastqtl-doc libblas3 libboost-iostreams1.83.0
152s   libboost-program-options1.83.0 libdeflate0 libgsl27 libgslcblas0 libhts3
152s   libhtscodecs2 r-mathlib
153s 0 upgraded, 12 newly installed, 0 to remove and 1 not upgraded.
153s Need to get 22.1 MB/22.1 MB of archives.
153s After this operation, 31.0 MB of additional disk space will be used.
153s Get:1 /tmp/autopkgtest.SqMa3s/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B]
153s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB]
153s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-2ubuntu1 [339 kB]
153s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-program-options1.83.0 arm64 1.83.0-2ubuntu1 [410 kB]
153s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libgslcblas0 arm64 2.7.1+dfsg-6ubuntu1 [72.5 kB]
153s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libgsl27 arm64 2.7.1+dfsg-6ubuntu1 [912 kB]
153s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
153s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB]
153s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB]
153s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-mathlib arm64 4.3.3-2build1 [2400 kB]
153s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 fastqtl arm64 2.184+v7+dfsg-4build1 [204 kB]
153s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 fastqtl-doc all 2.184+v7+dfsg-4build1 [17.0 MB]
155s Fetched 22.1 MB in 1s (17.1 MB/s)
155s Selecting previously unselected package libblas3:arm64.
155s (Reading database ... 
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(Reading database ... 74774 files and directories currently installed.)
155s Preparing to unpack .../00-libblas3_3.12.0-3_arm64.deb ...
155s Unpacking libblas3:arm64 (3.12.0-3) ...
155s Selecting previously unselected package libboost-iostreams1.83.0:arm64.
155s Preparing to unpack .../01-libboost-iostreams1.83.0_1.83.0-2ubuntu1_arm64.deb ...
155s Unpacking libboost-iostreams1.83.0:arm64 (1.83.0-2ubuntu1) ...
155s Selecting previously unselected package libboost-program-options1.83.0:arm64.
155s Preparing to unpack .../02-libboost-program-options1.83.0_1.83.0-2ubuntu1_arm64.deb ...
155s Unpacking libboost-program-options1.83.0:arm64 (1.83.0-2ubuntu1) ...
155s Selecting previously unselected package libgslcblas0:arm64.
155s Preparing to unpack .../03-libgslcblas0_2.7.1+dfsg-6ubuntu1_arm64.deb ...
155s Unpacking libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu1) ...
155s Selecting previously unselected package libgsl27:arm64.
155s Preparing to unpack .../04-libgsl27_2.7.1+dfsg-6ubuntu1_arm64.deb ...
155s Unpacking libgsl27:arm64 (2.7.1+dfsg-6ubuntu1) ...
155s Selecting previously unselected package libdeflate0:arm64.
155s Preparing to unpack .../05-libdeflate0_1.19-1_arm64.deb ...
155s Unpacking libdeflate0:arm64 (1.19-1) ...
155s Selecting previously unselected package libhtscodecs2:arm64.
155s Preparing to unpack .../06-libhtscodecs2_1.6.0-1_arm64.deb ...
155s Unpacking libhtscodecs2:arm64 (1.6.0-1) ...
155s Selecting previously unselected package libhts3:arm64.
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155s Unpacking r-mathlib (4.3.3-2build1) ...
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156s Preparing to unpack .../09-fastqtl_2.184+v7+dfsg-4build1_arm64.deb ...
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156s Selecting previously unselected package autopkgtest-satdep.
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156s Unpacking autopkgtest-satdep (0) ...
156s Setting up libhtscodecs2:arm64 (1.6.0-1) ...
156s Setting up libboost-program-options1.83.0:arm64 (1.83.0-2ubuntu1) ...
156s Setting up fastqtl-doc (2.184+v7+dfsg-4build1) ...
156s Setting up libgslcblas0:arm64 (2.7.1+dfsg-6ubuntu1) ...
156s Setting up libdeflate0:arm64 (1.19-1) ...
156s Setting up libgsl27:arm64 (2.7.1+dfsg-6ubuntu1) ...
156s Setting up libblas3:arm64 (3.12.0-3) ...
156s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
156s Setting up libboost-iostreams1.83.0:arm64 (1.83.0-2ubuntu1) ...
156s Setting up r-mathlib (4.3.3-2build1) ...
156s Setting up libhts3:arm64 (1.18+ds-1) ...
156s Setting up fastqtl (2.184+v7+dfsg-4build1) ...
157s Setting up autopkgtest-satdep (0) ...
157s Processing triggers for man-db (2.12.0-3) ...
157s Processing triggers for libc-bin (2.39-0ubuntu2) ...
165s (Reading database ... 74906 files and directories currently installed.)
165s Removing autopkgtest-satdep (0) ...
166s autopkgtest [17:19:26]: test run-sample-analysis: [-----------------------
166s covariates.txt.gz
166s genotypes.vcf.gz
166s genotypes.vcf.gz.tbi
166s interaction.txt
166s phenotypes.bed.gz
166s phenotypes.bed.gz.tbi
166s 
166s Fast QTL
166s   * Authors : Olivier DELANEAU, Halit ONGEN, Alfonso BUIL & Manolis DERMITZAKIS
166s   * Contact : olivier.delaneau@gmail.com
166s   * Webpage : http://fastqtl.sourceforge.net/
166s   * Version : v2.184_gtex
166s 
166s Perform permutation based interaction analysis (used to calculate corrected p-values for MPs)
166s   * Perform 100 permutations
166s   * Test interaction with term from [interaction.txt]
166s   * Random number generator is seeded with 1
166s   * Considering variants within 1e+06 bp of the MPs
166s   * Using minor allele frequency threshold = 0.0000
166s   * Using minor allele sample threshold = 0
166s   * Using INFO field AF threshold = 0.0000
166s   * Chunk processed 1 / 100
166s 
166s Scanning phenotype data in [phenotypes.bed.gz]
166s   * 364 phenotypes
166s 
166s Reading phenotype data in [phenotypes.bed.gz]
166s   * region = 22:17517460-17646177
166s   * 373 samples included
166s   * 4 phenotypes included
166s 
166s Reading genotype data in [genotypes.vcf.gz] in VCF format
166s   * region = 22:16517460-18646177
167s   * 373 samples included
167s   * 8580 sites included
167s 
167s Reading covariates in [covariates.txt.gz]
167s   * 373 samples included
167s   * 4 covariate(s) included
167s 
167s Reading interaction term in [interaction.txt]
167s   * 373 samples included
167s 
167s Imputing missing genotypes
167s 
167s Imputing missing phenotypes
167s 
167s Initialize covariate 
167s 
167s Processing gene [ENSG00000237438.1]
167s   * Number of variants in cis = 7966
178s   * Beta distribution parameters = 1.0382 2287.7101
178s   * Progress = 25.0%
178s 
178s Processing gene [ENSG00000177663.8]
178s   * Number of variants in cis = 8165
189s   * Beta distribution parameters = 0.7994 2826.0721
189s   * Progress = 50.0%
189s 
189s Processing gene [ENSG00000183307.3]
189s   * Number of variants in cis = 8279
201s   * Beta distribution parameters = 0.9595 9906.5566
201s   * Progress = 75.0%
201s 
201s Processing gene [ENSG00000069998.8]
201s   * Number of variants in cis = 8466
213s   * Beta distribution parameters = 0.9606 4564.2130
213s   * Progress = 100.0%
213s 
213s Running time: 47 seconds
213s autopkgtest [17:20:13]: test run-sample-analysis: -----------------------]
214s autopkgtest [17:20:14]: test run-sample-analysis:  - - - - - - - - - - results - - - - - - - - - -
214s run-sample-analysis  PASS
214s autopkgtest [17:20:14]: @@@@@@@@@@@@@@@@@@@@ summary
214s run-sample-analysis  PASS
219s Creating nova instance adt-noble-arm64-fastqtl-20240316-171639-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...