cmd: autopkgtest --apt-upgrade --output-dir=artifact-dir --summary=artifact-dir/summary --no-built-binaries --needs-internet=run --copy=/etc/resolv.conf:/etc/resolv.conf /tmp/debusine-fetch-exec-upload-rd70jr62/python-biom-format-doc_2.1.16-1_all.deb /tmp/debusine-fetch-exec-upload-rd70jr62/python-click-doc_8.2.0-1_all.deb /tmp/debusine-fetch-exec-upload-rd70jr62/python3-biom-format_2.1.16-1+b3_arm64.deb /tmp/debusine-fetch-exec-upload-rd70jr62/python3-click_8.2.0-1_all.deb /tmp/debusine-fetch-exec-upload-rd70jr62/python-biom-format_2.1.16-1.dsc -- unshare --arch arm64 --release sid --tarball /var/lib/debusine/worker/system-images/1140263/system.tar.xz
output (contains stdout and stderr):
autopkgtest [15:20:52]: starting date and time: 2025-01-17 15:20:52+0000
autopkgtest [15:20:52]: version 5.38~bpo12+1
autopkgtest [15:20:52]: host debusine-worker-arm64-demeter-05; command line: /usr/bin/autopkgtest --apt-upgrade --output-dir=artifact-dir --summary=artifact-dir/summary --no-built-binaries --needs-internet=run --copy=/etc/resolv.conf:/etc/resolv.conf /tmp/debusine-fetch-exec-upload-rd70jr62/python-biom-format-doc_2.1.16-1_all.deb /tmp/debusine-fetch-exec-upload-rd70jr62/python-click-doc_8.2.0-1_all.deb /tmp/debusine-fetch-exec-upload-rd70jr62/python3-biom-format_2.1.16-1+b3_arm64.deb /tmp/debusine-fetch-exec-upload-rd70jr62/python3-click_8.2.0-1_all.deb /tmp/debusine-fetch-exec-upload-rd70jr62/python-biom-format_2.1.16-1.dsc -- unshare --arch arm64 --release sid --tarball /var/lib/debusine/worker/system-images/1140263/system.tar.xz
autopkgtest [15:20:57]: testbed dpkg architecture: arm64
autopkgtest [15:20:57]: testbed apt version: 2.9.20
autopkgtest [15:20:57]: @@@@@@@@@@@@@@@@@@@@ test bed setup
Get:1 http://deb.debian.org/debian sid InRelease [205 kB]
Get:2 http://deb.debian.org/debian sid/main arm64 Packages [9926 kB]
Get:3 http://deb.debian.org/debian sid/main Translation-en [7324 kB]
Get:4 http://deb.debian.org/debian sid/main arm64 Components [4694 kB]
Fetched 22.1 MB in 3s (6562 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following package was automatically installed and is no longer required:
libldap-2.5-0
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
libldap-common libldap2 libtext-charwidth-perl libtext-wrapi18n-perl
The following packages will be upgraded:
apt base-passwd binutils binutils-aarch64-linux-gnu binutils-common
bsdextrautils bsdutils dash diffutils dpkg dpkg-dev e2fsprogs gcc-14-base
gettext gettext-base gpg gpgconf gzip init-system-helpers libapt-pkg6.0t64
libatomic1 libaudit1 libbinutils libblkid1 libc-bin libc6 libcgi-pm-perl
libcom-err2 libcpanel-json-xs-perl libcrypt1 libctf-nobfd0 libctf0
libcurl3t64-gnutls libdebconfclient0 libdpkg-perl libext2fs2t64 libgcc-s1
libglib2.0-0t64 libgomp1 libgprofng0 libgssapi-krb5-2 libhtml-parser-perl
libicu72 libk5crypto3 libkrb5-3 libkrb5support0 liblz1 liblz4-1 libmount1
libsasl2-2 libsasl2-modules-db libsframe1 libsmartcols1 libss2 libssl3t64
libstdc++6 libsystemd0 libtext-markdown-discount-perl libudev1 libuuid1
libxs-parse-keyword-perl libxxhash0 libzstd1 login logsave mount openssl
openssl-provider-legacy sysvinit-utils tzdata ucf util-linux
72 upgraded, 4 newly installed, 0 to remove and 0 not upgraded.
Need to get 41.0 MB of archives.
After this operation, 1438 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main arm64 bsdutils arm64 1:2.40.4-1 [105 kB]
Get:2 http://deb.debian.org/debian sid/main arm64 dash arm64 0.5.12-11 [92.8 kB]
Get:3 http://deb.debian.org/debian sid/main arm64 diffutils arm64 1:3.10-2 [378 kB]
Get:4 http://deb.debian.org/debian sid/main arm64 libatomic1 arm64 14.2.0-14 [10.1 kB]
Get:5 http://deb.debian.org/debian sid/main arm64 libgomp1 arm64 14.2.0-14 [124 kB]
Get:6 http://deb.debian.org/debian sid/main arm64 gcc-14-base arm64 14.2.0-14 [48.7 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 libgcc-s1 arm64 14.2.0-14 [54.1 kB]
Get:8 http://deb.debian.org/debian sid/main arm64 libstdc++6 arm64 14.2.0-14 [637 kB]
Get:9 http://deb.debian.org/debian sid/main arm64 libc6 arm64 2.40-5 [2459 kB]
Get:10 http://deb.debian.org/debian sid/main arm64 libxxhash0 arm64 0.8.3-2 [22.3 kB]
Get:11 http://deb.debian.org/debian sid/main arm64 liblz4-1 arm64 1.9.4-4 [55.3 kB]
Get:12 http://deb.debian.org/debian sid/main arm64 openssl-provider-legacy arm64 3.4.0-2 [299 kB]
Get:13 http://deb.debian.org/debian sid/main arm64 libzstd1 arm64 1.5.6+dfsg-2 [261 kB]
Get:14 http://deb.debian.org/debian sid/main arm64 libssl3t64 arm64 3.4.0-2 [2635 kB]
Get:15 http://deb.debian.org/debian sid/main arm64 libsystemd0 arm64 257.2-2 [418 kB]
Get:16 http://deb.debian.org/debian sid/main arm64 libudev1 arm64 257.2-2 [140 kB]
Get:17 http://deb.debian.org/debian sid/main arm64 libapt-pkg6.0t64 arm64 2.9.22 [977 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 dpkg arm64 1.22.14 [1522 kB]
Get:19 http://deb.debian.org/debian sid/main arm64 gzip arm64 1.13-1 [135 kB]
Get:20 http://deb.debian.org/debian sid/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB]
Get:21 http://deb.debian.org/debian sid/main arm64 libblkid1 arm64 2.40.4-1 [163 kB]
Get:22 http://deb.debian.org/debian sid/main arm64 libmount1 arm64 2.40.4-1 [191 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 libsmartcols1 arm64 2.40.4-1 [136 kB]
Get:24 http://deb.debian.org/debian sid/main arm64 mount arm64 2.40.4-1 [153 kB]
Get:25 http://deb.debian.org/debian sid/main arm64 libuuid1 arm64 2.40.4-1 [36.1 kB]
Get:26 http://deb.debian.org/debian sid/main arm64 util-linux arm64 2.40.4-1 [1173 kB]
Get:27 http://deb.debian.org/debian sid/main arm64 libdebconfclient0 arm64 0.277 [10.5 kB]
Get:28 http://deb.debian.org/debian sid/main arm64 base-passwd arm64 3.6.6 [52.9 kB]
Get:29 http://deb.debian.org/debian sid/main arm64 apt arm64 2.9.22 [1299 kB]
Get:30 http://deb.debian.org/debian sid/main arm64 init-system-helpers all 1.68 [38.7 kB]
Get:31 http://deb.debian.org/debian sid/main arm64 libc-bin arm64 2.40-5 [541 kB]
Get:32 http://deb.debian.org/debian sid/main arm64 sysvinit-utils arm64 3.13-1 [33.1 kB]
Get:33 http://deb.debian.org/debian sid/main arm64 logsave arm64 1.47.2-1 [23.8 kB]
Get:34 http://deb.debian.org/debian sid/main arm64 libext2fs2t64 arm64 1.47.2-1 [204 kB]
Get:35 http://deb.debian.org/debian sid/main arm64 e2fsprogs arm64 1.47.2-1 [563 kB]
Get:36 http://deb.debian.org/debian sid/main arm64 libaudit1 arm64 1:4.0.2-2+b1 [54.6 kB]
Get:37 http://deb.debian.org/debian sid/main arm64 libcrypt1 arm64 1:4.4.38-1 [91.8 kB]
Get:38 http://deb.debian.org/debian sid/main arm64 login arm64 1:4.16.0-2+really2.40.4-1 [86.7 kB]
Get:39 http://deb.debian.org/debian sid/main arm64 tzdata all 2024b-6 [257 kB]
Get:40 http://deb.debian.org/debian sid/main arm64 gettext-base arm64 0.23.1-1 [241 kB]
Get:41 http://deb.debian.org/debian sid/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B]
Get:42 http://deb.debian.org/debian sid/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B]
Get:43 http://deb.debian.org/debian sid/main arm64 ucf all 3.0048 [42.0 kB]
Get:44 http://deb.debian.org/debian sid/main arm64 libgprofng0 arm64 2.43.50.20250108-1 [668 kB]
Get:45 http://deb.debian.org/debian sid/main arm64 libctf0 arm64 2.43.50.20250108-1 [84.1 kB]
Get:46 http://deb.debian.org/debian sid/main arm64 libctf-nobfd0 arm64 2.43.50.20250108-1 [151 kB]
Get:47 http://deb.debian.org/debian sid/main arm64 binutils-aarch64-linux-gnu arm64 2.43.50.20250108-1 [2808 kB]
Get:48 http://deb.debian.org/debian sid/main arm64 libbinutils arm64 2.43.50.20250108-1 [660 kB]
Get:49 http://deb.debian.org/debian sid/main arm64 binutils arm64 2.43.50.20250108-1 [68.4 kB]
Get:50 http://deb.debian.org/debian sid/main arm64 binutils-common arm64 2.43.50.20250108-1 [2628 kB]
Get:51 http://deb.debian.org/debian sid/main arm64 libsframe1 arm64 2.43.50.20250108-1 [77.1 kB]
Get:52 http://deb.debian.org/debian sid/main arm64 dpkg-dev all 1.22.14 [1334 kB]
Get:53 http://deb.debian.org/debian sid/main arm64 libdpkg-perl all 1.22.14 [646 kB]
Get:54 http://deb.debian.org/debian sid/main arm64 gettext arm64 0.23.1-1 [1610 kB]
Get:55 http://deb.debian.org/debian sid/main arm64 gpg arm64 2.2.46-1+b1 [481 kB]
Get:56 http://deb.debian.org/debian sid/main arm64 gpgconf arm64 2.2.46-1+b1 [115 kB]
Get:57 http://deb.debian.org/debian sid/main arm64 libhtml-parser-perl arm64 3.83-1+b2 [97.5 kB]
Get:58 http://deb.debian.org/debian sid/main arm64 libcgi-pm-perl all 4.67-1 [217 kB]
Get:59 http://deb.debian.org/debian sid/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB]
Get:60 http://deb.debian.org/debian sid/main arm64 libcpanel-json-xs-perl arm64 4.39-1 [128 kB]
Get:61 http://deb.debian.org/debian sid/main arm64 libgssapi-krb5-2 arm64 1.21.3-4 [127 kB]
Get:62 http://deb.debian.org/debian sid/main arm64 libkrb5-3 arm64 1.21.3-4 [308 kB]
Get:63 http://deb.debian.org/debian sid/main arm64 libkrb5support0 arm64 1.21.3-4 [32.2 kB]
Get:64 http://deb.debian.org/debian sid/main arm64 libk5crypto3 arm64 1.21.3-4 [81.5 kB]
Get:65 http://deb.debian.org/debian sid/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8+b1 [20.3 kB]
Get:66 http://deb.debian.org/debian sid/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8+b1 [55.7 kB]
Get:67 http://deb.debian.org/debian sid/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB]
Get:68 http://deb.debian.org/debian sid/main arm64 libcurl3t64-gnutls arm64 8.11.1-1+b1 [331 kB]
Get:69 http://deb.debian.org/debian sid/main arm64 libglib2.0-0t64 arm64 2.82.4-2 [1413 kB]
Get:70 http://deb.debian.org/debian sid/main arm64 libicu72 arm64 72.1-6 [9239 kB]
Get:71 http://deb.debian.org/debian sid/main arm64 libldap-common all 2.6.9+dfsg-1 [34.5 kB]
Get:72 http://deb.debian.org/debian sid/main arm64 liblz1 arm64 1.15-1 [37.8 kB]
Get:73 http://deb.debian.org/debian sid/main arm64 libss2 arm64 1.47.2-1 [28.4 kB]
Get:74 http://deb.debian.org/debian sid/main arm64 libtext-markdown-discount-perl arm64 0.17-1 [13.0 kB]
Get:75 http://deb.debian.org/debian sid/main arm64 libxs-parse-keyword-perl arm64 0.48-1 [64.2 kB]
Get:76 http://deb.debian.org/debian sid/main arm64 openssl arm64 3.4.0-2 [1385 kB]
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autopkgtest [15:21:24]: testbed running kernel: Linux 6.1.0-29-cloud-arm64 #1 SMP Debian 6.1.123-1 (2025-01-02)
autopkgtest [15:21:24]: @@@@@@@@@@@@@@@@@@@@ source /tmp/debusine-fetch-exec-upload-rd70jr62/python-biom-format_2.1.16-1.dsc
gpg: Signature made Mon May 27 20:43:46 2024 UTC
gpg: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpg: issuer "emollier@debian.org"
gpg: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for /tmp/autopkgtest.2X6XO0/python-biom-format_2.1.16-1.dsc: no acceptable signature found
dpkg-source: info: extracting python-biom-format in src
dpkg-source: info: unpacking python-biom-format_2.1.16.orig.tar.gz
dpkg-source: info: unpacking python-biom-format_2.1.16-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying ignore_local_dist-packages.patch
dpkg-source: info: applying no-web-adds.patch
dpkg-source: info: applying fix_future_import.patch
dpkg-source: info: applying sphinx_1.6.patch
dpkg-source: info: applying posix_shell.patch
autopkgtest [15:21:25]: testing package python-biom-format version 2.1.16-1
autopkgtest [15:21:26]: build not needed
autopkgtest [15:21:26]: test run-unit-test: preparing testbed
Reading package lists...
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apt-utils
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Starting pkgProblemResolver with broken count: 0
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Done
The following NEW packages will be installed:
libaec0 libblas3 libcurl4t64 libexpat1 libgfortran5 libhdf5-310
libhdf5-hl-310 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3
liblbfgsb0 liblzf1 libpython3-stdlib libpython3.13-minimal
libpython3.13-stdlib libsz2 media-types python-biom-format-doc python3
python3-biom-format python3-click python3-dateutil python3-decorator
python3-h5py python3-h5py-serial python3-minimal python3-numpy
python3-pandas python3-pandas-lib python3-scipy python3-tz python3.13
python3.13-minimal
0 upgraded, 34 newly installed, 0 to remove and 0 not upgraded.
Need to get 42.8 MB/43.2 MB of archives.
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Get:1 file:/tmp/autopkgtest.2X6XO0/binaries python-biom-format-doc 2.1.16-1 [67.3 kB]
Get:2 file:/tmp/autopkgtest.2X6XO0/binaries python3-click 8.2.0-1 [98.6 kB]
Get:3 file:/tmp/autopkgtest.2X6XO0/binaries python3-biom-format 2.1.16-1+b3 [160 kB]
Get:4 http://deb.debian.org/debian sid/main arm64 libpython3.13-minimal arm64 3.13.1-3 [852 kB]
Get:5 http://deb.debian.org/debian sid/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB]
Get:6 http://deb.debian.org/debian sid/main arm64 python3.13-minimal arm64 3.13.1-3 [1990 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 python3-minimal arm64 3.13.1-2 [27.0 kB]
Get:8 http://deb.debian.org/debian sid/main arm64 media-types all 10.1.0 [26.9 kB]
Get:9 http://deb.debian.org/debian sid/main arm64 libpython3.13-stdlib arm64 3.13.1-3 [1912 kB]
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Get:14 http://deb.debian.org/debian sid/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB]
Get:15 http://deb.debian.org/debian sid/main arm64 libcurl4t64 arm64 8.11.1-1+b1 [324 kB]
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Get:22 http://deb.debian.org/debian sid/main arm64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB]
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Get:26 http://deb.debian.org/debian sid/main arm64 python3-numpy arm64 1:1.26.4+ds-13 [3815 kB]
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Get:29 http://deb.debian.org/debian sid/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB]
Get:30 http://deb.debian.org/debian sid/main arm64 python3-tz all 2024.2-1 [31.0 kB]
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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
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update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
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Setting up libjs-sphinxdoc (8.1.3-4) ...
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Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5+b1) ...
Setting up python3-h5py-serial (3.12.1-1+b1) ...
Setting up python-biom-format-doc (2.1.16-1) ...
Setting up python3-pandas (2.2.3+dfsg-5) ...
Setting up python3-h5py (3.12.1-1) ...
Setting up python3-biom-format (2.1.16-1+b3) ...
Processing triggers for man-db (2.13.0-1) ...
Processing triggers for libc-bin (2.40-5) ...
autopkgtest [15:21:51]: test run-unit-test: [-----------------------
System information
==================
Platform: linux
Python version: 3.13.1 (main, Jan 3 2025, 10:26:34) [GCC 14.2.0]
Python executable: /usr/bin/python3
Dependency versions
===================
click version: 8.2.0
NumPy version: 1.26.4
SciPy version: 1.14.1
h5py version: 3.12.1
biom-format package information
===============================
biom-format version: 2.1.16
The input file is a valid BIOM-formatted file.
The input file is a valid BIOM-formatted file.
The input file is a valid BIOM-formatted file.
The input file is a valid BIOM-formatted file.
+ table=examples/min_sparse_otu_table_hdf5.biom
+ obsmd=examples/obs_md.txt
+ [ ! -f examples/min_sparse_otu_table_hdf5.biom ]
+ biom show-install-info
System information
==================
Platform: linux
Python version: 3.13.1 (main, Jan 3 2025, 10:26:34) [GCC 14.2.0]
Python executable: /usr/bin/python3
Dependency versions
===================
click version: 8.2.0
NumPy version: 1.26.4
SciPy version: 1.14.1
h5py version: 3.12.1
biom-format package information
===============================
biom-format version: 2.1.16
+ biom validate-table -i examples/min_sparse_otu_table_hdf5.biom
The input file is a valid BIOM-formatted file.
+ biom add-metadata -i examples/min_sparse_otu_table_hdf5.biom -o test_add_metadata.biom --observation-metadata-fp examples/obs_md.txt --sc-separated taxonomy
+ biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json
+ biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv
+ biom validate-table -i test_json.biom
The input file is a valid BIOM-formatted file.
+ biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5
+ biom validate-table -i test_hdf5.biom
The input file is a valid BIOM-formatted file.
+ biom convert -i test_json.biom -o test_tsv.txt --to-tsv
+ biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table
+ biom validate-table -i test_hdf5.biom
The input file is a valid BIOM-formatted file.
+ biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table
+ biom validate-table -i test_json.biom
The input file is a valid BIOM-formatted file.
+ biom head -i examples/min_sparse_otu_table_hdf5.biom
# Constructed from biom file
#OTU ID Sample1 Sample2 Sample3 Sample4 Sample5
GG_OTU_1 0.0 0.0 1.0 0.0 0.0
GG_OTU_2 5.0 1.0 0.0 2.0 3.0
GG_OTU_3 0.0 0.0 1.0 4.0 0.0
GG_OTU_4 2.0 1.0 1.0 0.0 0.0
GG_OTU_5 0.0 1.0 1.0 0.0 0.0
+ biom table-ids -i examples/min_sparse_otu_table_hdf5.biom
Sample1
Sample2
Sample3
Sample4
Sample5
Sample6
+ biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p
+ cat
+ biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt
+ biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom
Num samples: 6
Num observations: 5
Total count: 27
Table density (fraction of non-zero values): 0.500
Counts/sample summary:
Min: 3.000
Max: 7.000
Median: 4.000
Mean: 4.500
Std. dev.: 1.500
Sample Metadata Categories: None provided
Observation Metadata Categories: None provided
Counts/sample detail:
Sample2: 3.000
Sample5: 3.000
Sample3: 4.000
Sample6: 4.000
Sample4: 6.000
Sample1: 7.000
+ cat
+ biom from-uc -i uctest -o test_uc.biom
If this message was shown, then all commands executed without failure
+ echo If this message was shown, then all commands executed without failure
autopkgtest [15:22:12]: test run-unit-test: -----------------------]
autopkgtest [15:22:12]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - -
run-unit-test PASS
autopkgtest [15:22:12]: test autodep8-python3: preparing testbed
autopkgtest [15:22:19]: testbed dpkg architecture: arm64
autopkgtest [15:22:19]: testbed apt version: 2.9.20
autopkgtest [15:22:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup
Get:1 http://deb.debian.org/debian sid InRelease [205 kB]
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Reading package lists...
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Building dependency tree...
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Calculating upgrade...
The following package was automatically installed and is no longer required:
libldap-2.5-0
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
libldap-common libldap2 libtext-charwidth-perl libtext-wrapi18n-perl
The following packages will be upgraded:
apt base-passwd binutils binutils-aarch64-linux-gnu binutils-common
bsdextrautils bsdutils dash diffutils dpkg dpkg-dev e2fsprogs gcc-14-base
gettext gettext-base gpg gpgconf gzip init-system-helpers libapt-pkg6.0t64
libatomic1 libaudit1 libbinutils libblkid1 libc-bin libc6 libcgi-pm-perl
libcom-err2 libcpanel-json-xs-perl libcrypt1 libctf-nobfd0 libctf0
libcurl3t64-gnutls libdebconfclient0 libdpkg-perl libext2fs2t64 libgcc-s1
libglib2.0-0t64 libgomp1 libgprofng0 libgssapi-krb5-2 libhtml-parser-perl
libicu72 libk5crypto3 libkrb5-3 libkrb5support0 liblz1 liblz4-1 libmount1
libsasl2-2 libsasl2-modules-db libsframe1 libsmartcols1 libss2 libssl3t64
libstdc++6 libsystemd0 libtext-markdown-discount-perl libudev1 libuuid1
libxs-parse-keyword-perl libxxhash0 libzstd1 login logsave mount openssl
openssl-provider-legacy sysvinit-utils tzdata ucf util-linux
72 upgraded, 4 newly installed, 0 to remove and 0 not upgraded.
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Setting up libbinutils:arm64 (2.43.50.20250108-1) ...
Setting up openssl (3.4.0-2) ...
Setting up libldap2:arm64 (2.6.9+dfsg-1) ...
Setting up gpg (2.2.46-1+b1) ...
Setting up login (1:4.16.0-2+really2.40.4-1) ...
Setting up libctf0:arm64 (2.43.50.20250108-1) ...
Setting up gettext (0.23.1-1) ...
Setting up libcgi-pm-perl (4.67-1) ...
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Setting up libglib2.0-0t64:arm64 (2.82.4-2) ...
No schema files found: doing nothing.
Setting up libgprofng0:arm64 (2.43.50.20250108-1) ...
Setting up libgssapi-krb5-2:arm64 (1.21.3-4) ...
Setting up libcurl3t64-gnutls:arm64 (8.11.1-1+b1) ...
Setting up binutils-aarch64-linux-gnu (2.43.50.20250108-1) ...
Setting up binutils (2.43.50.20250108-1) ...
Setting up dpkg-dev (1.22.14) ...
Processing triggers for libc-bin (2.40-5) ...
Processing triggers for man-db (2.13.0-1) ...
Processing triggers for debianutils (5.21) ...
Reading package lists...
Building dependency tree...
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The following packages will be REMOVED:
libldap-2.5-0*
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The following NEW packages will be installed:
apt-utils
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 309 kB of archives.
After this operation, 1174 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main arm64 apt-utils arm64 2.9.22 [309 kB]
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Ign:1 file:/tmp/autopkgtest.2X6XO0/binaries InRelease
Get:2 file:/tmp/autopkgtest.2X6XO0/binaries Release [816 B]
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Get:4 file:/tmp/autopkgtest.2X6XO0/binaries Packages [6565 B]
Reading package lists...
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Done
The following NEW packages will be installed:
libaec0 libblas3 libcurl4t64 libexpat1 libgfortran5 libhdf5-310
libhdf5-hl-310 liblapack3 liblbfgsb0 liblzf1 libnsl2 libpython3-stdlib
libpython3.12-minimal libpython3.12-stdlib libpython3.13-minimal
libpython3.13-stdlib libsz2 libtirpc-common libtirpc3t64 media-types python3
python3-all python3-biom-format python3-click python3-dateutil
python3-decorator python3-h5py python3-h5py-serial python3-minimal
python3-numpy python3-pandas python3-pandas-lib python3-scipy python3-tz
python3.12 python3.12-minimal python3.13 python3.13-minimal
0 upgraded, 38 newly installed, 0 to remove and 0 not upgraded.
Need to get 47.8 MB/48.1 MB of archives.
After this operation, 279 MB of additional disk space will be used.
Get:1 file:/tmp/autopkgtest.2X6XO0/binaries python3-click 8.2.0-1 [98.6 kB]
Get:2 file:/tmp/autopkgtest.2X6XO0/binaries python3-biom-format 2.1.16-1+b3 [160 kB]
Get:3 http://deb.debian.org/debian sid/main arm64 libpython3.13-minimal arm64 3.13.1-3 [852 kB]
Get:4 http://deb.debian.org/debian sid/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB]
Get:5 http://deb.debian.org/debian sid/main arm64 python3.13-minimal arm64 3.13.1-3 [1990 kB]
Get:6 http://deb.debian.org/debian sid/main arm64 python3-minimal arm64 3.13.1-2 [27.0 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 media-types all 10.1.0 [26.9 kB]
Get:8 http://deb.debian.org/debian sid/main arm64 libpython3.13-stdlib arm64 3.13.1-3 [1912 kB]
Get:9 http://deb.debian.org/debian sid/main arm64 python3.13 arm64 3.13.1-3 [740 kB]
Get:10 http://deb.debian.org/debian sid/main arm64 libpython3-stdlib arm64 3.13.1-2 [9952 B]
Get:11 http://deb.debian.org/debian sid/main arm64 python3 arm64 3.13.1-2 [28.0 kB]
Get:12 http://deb.debian.org/debian sid/main arm64 libpython3.12-minimal arm64 3.12.8-5 [810 kB]
Get:13 http://deb.debian.org/debian sid/main arm64 python3.12-minimal arm64 3.12.8-5 [1934 kB]
Get:14 http://deb.debian.org/debian sid/main arm64 libaec0 arm64 1.1.3-1+b1 [22.5 kB]
Get:15 http://deb.debian.org/debian sid/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB]
Get:16 http://deb.debian.org/debian sid/main arm64 libcurl4t64 arm64 8.11.1-1+b1 [324 kB]
Get:17 http://deb.debian.org/debian sid/main arm64 libgfortran5 arm64 14.2.0-14 [361 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 libsz2 arm64 1.1.3-1+b1 [8044 B]
Get:19 http://deb.debian.org/debian sid/main arm64 libhdf5-310 arm64 1.14.5+repack-3 [1155 kB]
Get:20 http://deb.debian.org/debian sid/main arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [66.1 kB]
Get:21 http://deb.debian.org/debian sid/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB]
Get:22 http://deb.debian.org/debian sid/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b2 [25.6 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 liblzf1 arm64 3.6-4+b3 [10.1 kB]
Get:24 http://deb.debian.org/debian sid/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get:25 http://deb.debian.org/debian sid/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB]
Get:26 http://deb.debian.org/debian sid/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB]
Get:27 http://deb.debian.org/debian sid/main arm64 libpython3.12-stdlib arm64 3.12.8-5 [1904 kB]
Get:28 http://deb.debian.org/debian sid/main arm64 python3.12 arm64 3.12.8-5 [677 kB]
Get:29 http://deb.debian.org/debian sid/main arm64 python3-all arm64 3.13.1-2 [1056 B]
Get:30 http://deb.debian.org/debian sid/main arm64 python3-numpy arm64 1:1.26.4+ds-13 [3815 kB]
Get:31 http://deb.debian.org/debian sid/main arm64 python3-h5py-serial arm64 3.12.1-1+b1 [1244 kB]
Get:32 http://deb.debian.org/debian sid/main arm64 python3-h5py all 3.12.1-1 [15.0 kB]
Get:33 http://deb.debian.org/debian sid/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB]
Get:34 http://deb.debian.org/debian sid/main arm64 python3-tz all 2024.2-1 [31.0 kB]
Get:35 http://deb.debian.org/debian sid/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-5+b1 [6028 kB]
Get:36 http://deb.debian.org/debian sid/main arm64 python3-pandas all 2.2.3+dfsg-5 [3096 kB]
Get:37 http://deb.debian.org/debian sid/main arm64 python3-decorator all 5.1.1-5 [15.1 kB]
Get:38 http://deb.debian.org/debian sid/main arm64 python3-scipy arm64 1.14.1-3 [18.5 MB]
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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
Setting up liblzf1:arm64 (3.6-4+b3) ...
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Setting up liblapack3:arm64 (3.12.0-4) ...
update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
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Setting up python3-biom-format (2.1.16-1+b3) ...
Processing triggers for man-db (2.13.0-1) ...
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autopkgtest [15:23:24]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import biom; print(biom)" ; done
autopkgtest [15:23:24]: test autodep8-python3: [-----------------------
Testing with python3.12:
<module 'biom' from '/usr/lib/python3/dist-packages/biom/__init__.py'>
Testing with python3.13:
<module 'biom' from '/usr/lib/python3/dist-packages/biom/__init__.py'>
autopkgtest [15:23:26]: test autodep8-python3: -----------------------]
autopkgtest [15:23:26]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - -
autodep8-python3 PASS (superficial)
autopkgtest [15:23:26]: @@@@@@@@@@@@@@@@@@@@ summary
run-unit-test PASS
autodep8-python3 PASS (superficial)
aborted: False
returncode: 0
Files in working directory:
artifact-dir
artifact-dir/autodep8-python3-packages
artifact-dir/autodep8-python3-stdout
artifact-dir/binaries
artifact-dir/binaries/python-biom-format-doc.deb
artifact-dir/binaries/python-click-doc.deb
artifact-dir/binaries/python3-biom-format.deb
artifact-dir/binaries/python3-click.deb
artifact-dir/log
artifact-dir/run-unit-test-packages
artifact-dir/run-unit-test-stderr
artifact-dir/run-unit-test-stdout
artifact-dir/summary
artifact-dir/testbed-packages
artifact-dir/testinfo.json
artifact-dir/testpkg-version
--------------------