Thu May 16 08:48:55 UTC 2024 I: starting to build python-biom-format/trixie/i386 on jenkins on '2024-05-16 08:48' Thu May 16 08:48:55 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_12/11358/console.log Thu May 16 08:48:55 UTC 2024 I: Downloading source for trixie/python-biom-format=2.1.15.2-3 --2024-05-16 08:48:56-- http://deb.debian.org/debian/pool/main/p/python-biom-format/python-biom-format_2.1.15.2-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1883 (1.8K) [text/prs.lines.tag] Saving to: ‘python-biom-format_2.1.15.2-3.dsc’ 0K . 100% 167M=0s 2024-05-16 08:48:56 (167 MB/s) - ‘python-biom-format_2.1.15.2-3.dsc’ saved [1883/1883] Thu May 16 08:48:56 UTC 2024 I: python-biom-format_2.1.15.2-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: python-biom-format Binary: python3-biom-format, python-biom-format-doc Architecture: any all Version: 2.1.15.2-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://biom-format.org/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/python-biom-format Vcs-Git: https://salsa.debian.org/med-team/python-biom-format.git Testsuite: autopkgtest, autopkgtest-pkg-python Build-Depends: debhelper-compat (= 13), dh-sequence-python3, help2man, bash-completion, cython3, python3-all-dev, python3-click, python3-h5py, python3-numpy, python3-numpydoc, python3-pandas, python3-setuptools, python3-scipy, python3-sphinx, python3-matplotlib, python3-pytest , python3-pytest-cov Package-List: python-biom-format-doc deb doc optional arch=all python3-biom-format deb python optional arch=any Checksums-Sha1: 39170d70ddc09f033f08829a084630e979e75ac6 11870335 python-biom-format_2.1.15.2.orig.tar.gz c78277bb0f31362538bc71117df12d4246adbde0 11464 python-biom-format_2.1.15.2-3.debian.tar.xz Checksums-Sha256: b4b710d70ab3365966d7fe5104eea73c3c927fe46de2be924aa82531432761e7 11870335 python-biom-format_2.1.15.2.orig.tar.gz 62b746fe97775a55d91caadcf20d4c60c304e816e843bda75c025caf923eeaab 11464 python-biom-format_2.1.15.2-3.debian.tar.xz Files: 4bb9c5c75c32075a3ba83422ebb8f849 11870335 python-biom-format_2.1.15.2.orig.tar.gz da2861837468170dc4ce26fe771563d7 11464 python-biom-format_2.1.15.2-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iHUEARYIAB0WIQSglbZu4JAkvuai8HIqJ5BL1yQ+2gUCZb/kGAAKCRAqJ5BL1yQ+ 2l/KAQC/WrkvVKATo2FUEx7kuu6YmraNsGekvwkEvxaNV1VFeQEA1AQQLTmznQBx eXBMjuujmK9B2DHN/kWkgolEgSDpeAQ= =OMZp -----END PGP SIGNATURE----- Thu May 16 08:48:56 UTC 2024 I: Checking whether the package is not for us Thu May 16 08:48:56 UTC 2024 I: Starting 1st build on remote node ionos12-i386.debian.net. Thu May 16 08:48:56 UTC 2024 I: Preparing to do remote build '1' on ionos12-i386.debian.net. Thu May 16 08:53:10 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed May 15 20:48:58 -12 2024 I: pbuilder-time-stamp: 1715849338 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [python-biom-format_2.1.15.2-3.dsc] I: copying [./python-biom-format_2.1.15.2.orig.tar.gz] I: copying [./python-biom-format_2.1.15.2-3.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Feb 4 19:23:04 2024 gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.15.2-3.dsc: no acceptable signature found dpkg-source: info: extracting python-biom-format in python-biom-format-2.1.15.2 dpkg-source: info: unpacking python-biom-format_2.1.15.2.orig.tar.gz dpkg-source: info: unpacking python-biom-format_2.1.15.2-3.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 dpkg-source: info: applying adjust-pd-df-interaction-with-greater-than.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/40526/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='329e057cae1143369dcdae30999a86a9' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='40526' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.4XswyG8H/pbuilderrc_Ozg2 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.4XswyG8H/b1 --logfile b1/build.log python-biom-format_2.1.15.2-3.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos12-i386 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 13 11:26 /bin -> usr/bin I: user script /srv/workspace/pbuilder/40526/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, help2man, bash-completion, cython3, python3-all-dev, python3-click, python3-h5py, python3-numpy, python3-numpydoc, python3-pandas, python3-setuptools, python3-scipy, python3-sphinx, python3-matplotlib, python3-pytest, python3-pytest-cov dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19684 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on bash-completion; however: Package bash-completion is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-click; however: Package python3-click is not installed. pbuilder-satisfydepends-dummy depends on python3-h5py; however: Package python3-h5py is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-numpydoc; however: Package python3-numpydoc is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-cov; however: Package python3-pytest-cov is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bash-completion{a} blt{a} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lyx{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhdf5-103-1t64{a} libhdf5-hl-100t64{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-hotkeys{a} libjs-jquery-isonscreen{a} libjs-jquery-metadata{a} libjs-jquery-tablesorter{a} libjs-jquery-throttle-debounce{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblocale-gettext-perl{a} liblzf1{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libopenjp2-7{a} libpipeline1{a} libpng16-16t64{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libsub-override-perl{a} libsz2{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} python-babel-localedata{a} python-matplotlib-data{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-appdirs{a} python3-attr{a} python3-babel{a} python3-brotli{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-click{a} python3-colorama{a} python3-contourpy{a} python3-coverage{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-docutils{a} python3-fonttools{a} python3-fs{a} python3-h5py{a} python3-h5py-serial{a} python3-idna{a} python3-imagesize{a} python3-iniconfig{a} python3-jinja2{a} python3-kiwisolver{a} python3-lib2to3{a} python3-lxml{a} python3-lz4{a} python3-markupsafe{a} python3-matplotlib{a} python3-minimal{a} python3-mpmath{a} python3-numpy{a} python3-numpydoc{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-pluggy{a} python3-pygments{a} python3-pyparsing{a} python3-pytest{a} python3-pytest-cov{a} python3-requests{a} python3-roman{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sympy{a} python3-tabulate{a} python3-tk{a} python3-tz{a} python3-ufolib2{a} python3-urllib3{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} x11-common{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl isympy-common javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules lynx publicsuffix python3-bottleneck python3-bs4 python3-cssselect python3-html5lib python3-numexpr python3-odf python3-olefile python3-openpyxl python3-tables shared-mime-info wget xdg-user-dirs 0 packages upgraded, 207 newly installed, 0 to remove and 0 not upgraded. Need to get 150 MB of archives. After unpacking 670 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libjs-jquery-hotkeys all 0~20130707+git2d51e3a9+dfsg-2.1 [11.5 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 liblocale-gettext-perl i386 1.07-7 [15.1 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 libpython3.11-minimal i386 3.11.9-1 [817 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.2-1 [107 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 python3.11-minimal i386 3.11.9-1 [1918 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.11.8-1 [26.3 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 tzdata all 2024a-4 [255 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-4 [69.3 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-4 [171 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 libpython3.11-stdlib i386 3.11.9-1 [1795 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 python3.11 i386 3.11.9-1 [602 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.11.8-1 [9336 B] Get: 16 http://deb.debian.org/debian trixie/main i386 python3 i386 3.11.8-1 [27.4 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 libpython3.12-minimal i386 3.12.3-1 [809 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 python3.12-minimal i386 3.12.3-1 [2224 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 sgml-base all 1.31 [15.4 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 bash-completion all 1:2.13.0-1 [302 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 openssl i386 3.2.1-3 [1364 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 ca-certificates all 20240203 [158 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3 [42.9 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-4 [1194 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40-8 [97.2 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.1-1 [1421 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 libtcl8.6 i386 8.6.14+dfsg-1 [1095 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libpng16-16t64 i386 1.6.43-5 [286 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 libfreetype6 i386 2.13.2+dfsg-1+b4 [449 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 fontconfig-config i386 2.15.0-1.1 [317 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 libfontconfig1 i386 2.15.0-1.1 [401 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libxau6 i386 1:1.0.9-1+b1 [18.5 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libbsd0 i386 0.12.2-1 [134 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 libxdmcp6 i386 1:1.1.2-3+b1 [24.8 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 libx11-6 i386 2:1.8.7-1+b1 [822 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 libxrender1 i386 1:0.9.10-1.1+b1 [28.8 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 libxft2 i386 2.3.6-1+b1 [55.3 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 x11-common all 1:7.7+23 [252 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 libxss1 i386 1:1.2.3-1+b1 [17.3 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 libtk8.6 i386 8.6.14-1 [826 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 tk8.6-blt2.5 i386 2.5.3+dfsg-7 [616 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 blt i386 2.5.3+dfsg-7 [6024 B] Get: 60 http://deb.debian.org/debian trixie/main i386 cython3 i386 3.0.10+dfsg-5 [3548 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 68 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.191-1+b1 [194 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b3 [727 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 python3-distutils all 3.12.3-1 [131 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 python3-setuptools all 68.1.2-2 [468 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 dh-python all 6.20240422 [107 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 xml-core all 0.19 [20.1 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 docutils-common all 0.20.1+dfsg-3 [128 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 fonts-lyx all 2.4.0~RC4-1 [189 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 help2man i386 1.49.3 [198 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 libaec0 i386 1.1.3-1 [24.5 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-3 [140 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.1~rc2-1 [22.8 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.20.1-6+b1 [36.1 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.20.1-6+b1 [83.2 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-3 [9432 B] Get: 91 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.20.1-6+b1 [360 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.20.1-6+b1 [145 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-6 [20.5 kB] Get: 94 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-6 [60.6 kB] Get: 95 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.17+dfsg-1 [198 kB] Get: 96 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.61.0-1+b1 [84.0 kB] Get: 97 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1 [57.4 kB] Get: 98 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b4 [62.0 kB] Get: 99 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.0-4.1+b2 [225 kB] Get: 100 http://deb.debian.org/debian trixie/main i386 libcurl4t64 i386 8.7.1-5 [478 kB] Get: 101 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.20-1 [46.9 kB] Get: 102 http://deb.debian.org/debian trixie/main i386 libexpat1-dev i386 2.6.2-1 [165 kB] Get: 103 http://deb.debian.org/debian trixie/main i386 libfribidi0 i386 1.0.13-3+b1 [71.8 kB] Get: 104 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14-20240330-1 [735 kB] Get: 105 http://deb.debian.org/debian trixie/main i386 libglib2.0-0t64 i386 2.80.2-1 [1555 kB] Get: 106 http://deb.debian.org/debian trixie/main i386 libgraphite2-3 i386 1.3.14-2 [77.7 kB] Get: 107 http://deb.debian.org/debian trixie/main i386 libharfbuzz0b i386 8.3.0-2+b1 [2234 kB] Get: 108 http://deb.debian.org/debian trixie/main i386 libsz2 i386 1.1.3-1 [7824 B] Get: 109 http://deb.debian.org/debian trixie/main i386 libhdf5-103-1t64 i386 1.10.10+repack-3.3 [1178 kB] Get: 110 http://deb.debian.org/debian trixie/main i386 libhdf5-hl-100t64 i386 1.10.10+repack-3.3 [74.4 kB] Get: 111 http://deb.debian.org/debian trixie/main i386 libimagequant0 i386 2.18.0-1+b1 [35.9 kB] Get: 112 http://deb.debian.org/debian trixie/main i386 libjbig0 i386 2.1-6.1+b1 [31.8 kB] Get: 113 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-3 [169 kB] Get: 114 http://deb.debian.org/debian trixie/main i386 libjs-jquery-isonscreen all 1.2.0-1.1 [3196 B] Get: 115 http://deb.debian.org/debian trixie/main i386 libjs-jquery-metadata all 12-4 [6532 B] Get: 116 http://deb.debian.org/debian trixie/main i386 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-3 [184 kB] Get: 117 http://deb.debian.org/debian trixie/main i386 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.2 kB] Get: 118 http://deb.debian.org/debian trixie/main i386 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 119 http://deb.debian.org/debian trixie/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 120 http://deb.debian.org/debian trixie/main i386 libjs-sphinxdoc all 7.2.6-6 [150 kB] Get: 121 http://deb.debian.org/debian trixie/main i386 libjson-perl all 4.10000-1 [87.5 kB] Get: 122 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.0-3 [2167 kB] Get: 123 http://deb.debian.org/debian trixie/main i386 liblbfgsb0 i386 3.0+dfsg.4-1+b1 [29.1 kB] Get: 124 http://deb.debian.org/debian trixie/main i386 liblcms2-2 i386 2.14-2+b1 [165 kB] Get: 125 http://deb.debian.org/debian trixie/main i386 liblerc4 i386 4.0.0+ds-4+b1 [180 kB] Get: 126 http://deb.debian.org/debian trixie/main i386 liblzf1 i386 3.6-4+b1 [10.1 kB] Get: 127 http://deb.debian.org/debian trixie/main i386 libopenjp2-7 i386 2.5.0-2+b3 [197 kB] Get: 128 http://deb.debian.org/debian trixie/main i386 libpython3.11t64 i386 3.11.9-1 [1982 kB] Get: 129 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg-3.1 [915 kB] Get: 130 http://deb.debian.org/debian trixie/main i386 libpython3.11-dev i386 3.11.9-1 [4632 kB] Get: 131 http://deb.debian.org/debian trixie/main i386 libpython3-dev i386 3.11.8-1 [9600 B] Get: 132 http://deb.debian.org/debian trixie/main i386 libpython3.12-stdlib i386 3.12.3-1 [1945 kB] Get: 133 http://deb.debian.org/debian trixie/main i386 libpython3.12t64 i386 3.12.3-1 [2141 kB] Get: 134 http://deb.debian.org/debian trixie/main i386 libpython3.12-dev i386 3.12.3-1 [5240 kB] Get: 135 http://deb.debian.org/debian trixie/main i386 libpython3-all-dev i386 3.11.8-1 [1068 B] Get: 136 http://deb.debian.org/debian trixie/main i386 libqhull-r8.0 i386 2020.2-6+b1 [256 kB] Get: 137 http://deb.debian.org/debian trixie/main i386 libraqm0 i386 0.10.1-1+b1 [14.7 kB] Get: 138 http://deb.debian.org/debian trixie/main i386 libsharpyuv0 i386 1.4.0-0.1 [113 kB] Get: 139 http://deb.debian.org/debian trixie/main i386 libwebp7 i386 1.4.0-0.1 [318 kB] Get: 140 http://deb.debian.org/debian trixie/main i386 libtiff6 i386 4.5.1+git230720-4 [338 kB] Get: 141 http://deb.debian.org/debian trixie/main i386 libwebpdemux2 i386 1.4.0-0.1 [111 kB] Get: 142 http://deb.debian.org/debian trixie/main i386 libwebpmux3 i386 1.4.0-0.1 [125 kB] Get: 143 http://deb.debian.org/debian trixie/main i386 libxslt1.1 i386 1.1.35-1+b1 [243 kB] Get: 144 http://deb.debian.org/debian trixie/main i386 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 145 http://deb.debian.org/debian trixie/main i386 python-matplotlib-data all 3.6.3-2 [2744 kB] Get: 146 http://deb.debian.org/debian trixie/main i386 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 147 http://deb.debian.org/debian trixie/main i386 python3.12 i386 3.12.3-1 [659 kB] Get: 148 http://deb.debian.org/debian trixie/main i386 python3-all i386 3.11.8-1 [1056 B] Get: 149 http://deb.debian.org/debian trixie/main i386 python3.11-dev i386 3.11.9-1 [501 kB] Get: 150 http://deb.debian.org/debian trixie/main i386 python3-dev i386 3.11.8-1 [26.1 kB] Get: 151 http://deb.debian.org/debian trixie/main i386 python3.12-dev i386 3.12.3-1 [499 kB] Get: 152 http://deb.debian.org/debian trixie/main i386 python3-all-dev i386 3.11.8-1 [1072 B] Get: 153 http://deb.debian.org/debian trixie/main i386 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 154 http://deb.debian.org/debian trixie/main i386 python3-attr all 23.2.0-2 [65.5 kB] Get: 155 http://deb.debian.org/debian trixie/main i386 python3-tz all 2024.1-2 [30.9 kB] Get: 156 http://deb.debian.org/debian trixie/main i386 python3-babel all 2.14.0-1 [111 kB] Get: 157 http://deb.debian.org/debian trixie/main i386 python3-brotli i386 1.1.0-2+b3 [323 kB] Get: 158 http://deb.debian.org/debian trixie/main i386 python3-certifi all 2023.11.17-1 [155 kB] Get: 159 http://deb.debian.org/debian trixie/main i386 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 160 http://deb.debian.org/debian trixie/main i386 python3-charset-normalizer all 3.3.2-1 [51.6 kB] Get: 161 http://deb.debian.org/debian trixie/main i386 python3-colorama all 0.4.6-4 [36.2 kB] Get: 162 http://deb.debian.org/debian trixie/main i386 python3-click all 8.1.7-1 [94.0 kB] Get: 163 http://deb.debian.org/debian trixie/main i386 python3-numpy i386 1:1.26.4+ds-8 [5469 kB] Get: 164 http://deb.debian.org/debian trixie/main i386 python3-contourpy i386 1.0.7-3 [295 kB] Get: 165 http://deb.debian.org/debian trixie/main i386 python3-coverage i386 7.2.7+dfsg1-1+b1 [170 kB] Get: 166 http://deb.debian.org/debian trixie/main i386 python3-cycler all 0.12.1-1 [9496 B] Get: 167 http://deb.debian.org/debian trixie/main i386 python3-six all 1.16.0-6 [16.3 kB] Get: 168 http://deb.debian.org/debian trixie/main i386 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 169 http://deb.debian.org/debian trixie/main i386 python3-decorator all 5.1.1-5 [15.1 kB] Get: 170 http://deb.debian.org/debian trixie/main i386 python3-roman all 3.3-3 [9880 B] Get: 171 http://deb.debian.org/debian trixie/main i386 python3-docutils all 0.20.1+dfsg-3 [389 kB] Get: 172 http://deb.debian.org/debian trixie/main i386 python3-scipy i386 1.11.4-6 [19.0 MB] Get: 173 http://deb.debian.org/debian trixie/main i386 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get: 174 http://deb.debian.org/debian trixie/main i386 python3-mpmath all 1.3.0-1 [419 kB] Get: 175 http://deb.debian.org/debian trixie/main i386 python3-sympy all 1.12-7 [3869 kB] Get: 176 http://deb.debian.org/debian trixie/main i386 python3-fs all 2.4.16-4 [95.4 kB] Get: 177 http://deb.debian.org/debian trixie/main i386 python3-lxml i386 5.1.0-1 [2065 kB] Get: 178 http://deb.debian.org/debian trixie/main i386 python3-lz4 i386 4.0.2+dfsg-1+b3 [25.6 kB] Get: 179 http://deb.debian.org/debian trixie/main i386 unicode-data all 15.1.0-1 [8547 kB] Get: 180 http://deb.debian.org/debian trixie/main i386 python3-fonttools i386 4.46.0-1 [1613 kB] Get: 181 http://deb.debian.org/debian trixie/main i386 python3-h5py-serial i386 3.10.0-1+b3 [1397 kB] Get: 182 http://deb.debian.org/debian trixie/main i386 python3-h5py all 3.10.0-1 [14.4 kB] Get: 183 http://deb.debian.org/debian trixie/main i386 python3-idna all 3.6-2 [37.0 kB] Get: 184 http://deb.debian.org/debian trixie/main i386 python3-imagesize all 1.4.1-1 [6688 B] Get: 185 http://deb.debian.org/debian trixie/main i386 python3-iniconfig all 1.1.1-2 [6396 B] Get: 186 http://deb.debian.org/debian trixie/main i386 python3-markupsafe i386 2.1.5-1 [14.4 kB] Get: 187 http://deb.debian.org/debian trixie/main i386 python3-jinja2 all 3.1.3-1 [119 kB] Get: 188 http://deb.debian.org/debian trixie/main i386 python3-kiwisolver i386 1.4.5-1 [84.8 kB] Get: 189 http://deb.debian.org/debian trixie/main i386 python3-pil i386 10.3.0-2 [566 kB] Get: 190 http://deb.debian.org/debian trixie/main i386 python3-tk i386 3.12.3-1 [110 kB] Get: 191 http://deb.debian.org/debian trixie/main i386 python3-pil.imagetk i386 10.3.0-2 [79.7 kB] Get: 192 http://deb.debian.org/debian trixie/main i386 python3-pyparsing all 3.1.2-1 [146 kB] Get: 193 http://deb.debian.org/debian trixie/main i386 python3-packaging all 24.0-1 [45.5 kB] Get: 194 http://deb.debian.org/debian trixie/main i386 python3-matplotlib i386 3.6.3-2 [8059 kB] Get: 195 http://deb.debian.org/debian trixie/main i386 sphinx-common all 7.2.6-6 [702 kB] Get: 196 http://deb.debian.org/debian trixie/main i386 python3-pygments all 2.17.2+dfsg-1 [818 kB] Get: 197 http://deb.debian.org/debian trixie/main i386 python3-urllib3 all 1.26.18-2 [116 kB] Get: 198 http://deb.debian.org/debian trixie/main i386 python3-requests all 2.31.0+dfsg-1 [68.6 kB] Get: 199 http://deb.debian.org/debian trixie/main i386 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 200 http://deb.debian.org/debian trixie/main i386 python3-sphinx all 7.2.6-6 [552 kB] Get: 201 http://deb.debian.org/debian trixie/main i386 python3-tabulate all 0.8.10-1 [38.8 kB] Get: 202 http://deb.debian.org/debian trixie/main i386 python3-numpydoc all 1.6.0-2 [49.6 kB] Get: 203 http://deb.debian.org/debian trixie/main i386 python3-pandas-lib i386 2.1.4+dfsg-8 [7491 kB] Get: 204 http://deb.debian.org/debian trixie/main i386 python3-pandas all 2.1.4+dfsg-8 [3015 kB] Get: 205 http://deb.debian.org/debian trixie/main i386 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 206 http://deb.debian.org/debian trixie/main i386 python3-pytest all 7.4.4-3 [239 kB] Get: 207 http://deb.debian.org/debian trixie/main i386 python3-pytest-cov all 5.0.0-1 [26.8 kB] Fetched 150 MB in 3s (55.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libjs-jquery. (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 ... 19684 files and directories currently installed.) Preparing to unpack .../0-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-hotkeys. Preparing to unpack .../1-libjs-jquery-hotkeys_0~20130707+git2d51e3a9+dfsg-2.1_all.deb ... Unpacking libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2.1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../2-liblocale-gettext-perl_1.07-7_i386.deb ... Unpacking liblocale-gettext-perl (1.07-7) ... Selecting previously unselected package libpython3.11-minimal:i386. Preparing to unpack .../3-libpython3.11-minimal_3.11.9-1_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.9-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../4-libexpat1_2.6.2-1_i386.deb ... Unpacking libexpat1:i386 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../5-python3.11-minimal_3.11.9-1_i386.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:i386 (3.11.9-1) ... Setting up libexpat1:i386 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (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 ... 20040 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_i386.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... 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Current default time zone: 'Etc/UTC' Local time is now: Thu May 16 08:49:46 UTC 2024. Universal Time is now: Thu May 16 08:49:46 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:i386 (2.80.2-1) ... No schema files found: doing nothing. Setting up libblas3:i386 (3.12.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libexpat1-dev:i386 (2.6.2-1) ... Setting up libjpeg62-turbo:i386 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up bash-completion (1:2.13.0-1) ... Setting up liblzf1:i386 (3.6-4+b1) ... Setting up libfribidi0:i386 (1.0.13-3+b1) ... Setting up libimagequant0:i386 (2.18.0-1+b1) ... Setting up fonts-dejavu-mono (2.37-8) ... 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Setting up libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2.1) ... Setting up python-matplotlib-data (3.6.3-2) ... Setting up openssl (3.2.1-3) ... Setting up libwebpmux3:i386 (1.4.0-0.1) ... Setting up libbsd0:i386 (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3+b3) ... Setting up liblocale-gettext-perl (1.07-7) ... Setting up libsz2:i386 (1.1.3-1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.12-minimal (3.12.3-1) ... Setting up libxdmcp6:i386 (1:1.1.2-3+b1) ... Setting up liblapack3:i386 (3.12.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up libxcb1:i386 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:i386 (1.4.0-0.1) ... Setting up libldap-2.5-0:i386 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:i386 (2.13.2+dfsg-1+b4) ... Setting up libjs-jquery-metadata (12-4) ... Setting up libjs-jquery-isonscreen (1.2.0-1.1) ... Setting up libgssapi-krb5-2:i386 (1.20.1-6+b1) ... Setting up libjs-sphinxdoc (7.2.6-6) ... Setting up libreadline8t64:i386 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-3) ... Setting up groff-base (1.23.0-4) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:i386 (1.1.35-1+b1) ... Setting up libx11-6:i386 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:i386 (8.3.0-2+b1) ... Setting up libfontconfig1:i386 (2.15.0-1.1) ... Setting up liblbfgsb0:i386 (3.0+dfsg.4-1+b1) ... Setting up libpython3.12-stdlib:i386 (3.12.3-1) ... Setting up libxrender1:i386 (1:0.9.10-1.1+b1) ... Setting up libcurl4t64:i386 (8.7.1-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:i386 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libpython3.11t64:i386 (3.11.9-1) ... Setting up libxext6:i386 (2:1.3.4-1+b1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3.12t64:i386 (3.12.3-1) ... Setting up libpython3.11-dev:i386 (3.11.9-1) ... Setting up libraqm0:i386 (0.10.1-1+b1) ... Setting up sphinx-common (7.2.6-6) ... Setting up libxss1:i386 (1:1.2.3-1+b1) ... Setting up libhdf5-103-1t64:i386 (1.10.10+repack-3.3) ... Setting up libpython3-stdlib:i386 (3.11.8-1) ... Setting up libhdf5-hl-100t64:i386 (1.10.10+repack-3.3) ... Setting up python3.11 (3.11.9-1) ... Setting up libxft2:i386 (2.3.6-1+b1) ... Setting up libpython3-dev:i386 (3.11.8-1) ... Setting up python3.11-dev (3.11.9-1) ... Setting up libtk8.6:i386 (8.6.14-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up libpython3.12-dev:i386 (3.12.3-1) ... Setting up python3-markupsafe (2.1.5-1) ... Setting up python3-tz (2024.1-2) ... Setting up python3-six (1.16.0-6) ... Setting up python3-pil:i386 (10.3.0-2) ... Setting up python3-roman (3.3-3) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.0-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-certifi (2023.11.17-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up libpython3-all-dev:i386 (3.11.8-1) ... Setting up python3-brotli (1.1.0-2+b3) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.5-1) ... Setting up python3-idna (3.6-2) ... Setting up python3.12-dev (3.12.3-1) ... Setting up cython3 (3.0.10+dfsg-5) ... Setting up python3-urllib3 (1.26.18-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-lxml:i386 (5.1.0-1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sympy (1.12-7) ... Setting up python3-attr (23.2.0-2) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-babel (2.14.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-colorama (0.4.6-4) ... Setting up python3-lz4 (4.0.2+dfsg-1+b3) ... Setting up python3-charset-normalizer (3.3.2-1) ... Setting up python3-pytest (7.4.4-3) ... Setting up python3-alabaster (0.7.12-1) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3-tabulate (0.8.10-1) ... Setting up python3-all (3.11.8-1) ... Setting up python3-coverage (7.2.7+dfsg1-1+b1) ... Setting up python3-tk:i386 (3.12.3-1) ... Setting up python3-pytest-cov (5.0.0-1) ... Setting up python3-click (8.1.7-1) ... Setting up python3-fs (2.4.16-4) ... Setting up python3-pygments (2.17.2+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-pil.imagetk:i386 (10.3.0-2) ... Setting up python3-dev (3.11.8-1) ... Setting up python3-requests (2.31.0+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-8) ... Setting up python3-contourpy (1.0.7-3) ... Setting up dh-python (6.20240422) ... Setting up python3-all-dev (3.11.8-1) ... Setting up python3-scipy (1.11.4-6) ... Setting up python3-pandas-lib:i386 (2.1.4+dfsg-8) ... Setting up python3-h5py-serial (3.10.0-1+b3) ... Setting up python3-pandas (2.1.4+dfsg-8) ... Setting up python3-h5py (3.10.0-1) ... Setting up python3-fonttools (4.46.0-1) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up python3-matplotlib (3.6.3-2) ... Processing triggers for libc-bin (2.38-10) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.20.1+dfsg-3) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.20.1+dfsg-3) ... Setting up python3-sphinx (7.2.6-6) ... Setting up python3-numpydoc (1.6.0-2) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/python-biom-format-2.1.15.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-biom-format_2.1.15.2-3_source.changes dpkg-buildpackage: info: source package python-biom-format dpkg-buildpackage: info: source version 2.1.15.2-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --with bash-completion,sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild pybuild --clean -i python{version} -p "3.12 3.11" I: pybuild base:311: python3.12 setup.py clean /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/python-biom-format-2.1.15.2/biom/_filter.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/python-biom-format-2.1.15.2/biom/_subsample.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/python-biom-format-2.1.15.2/biom/_transform.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling biom/_filter.pyx because it changed. Compiling biom/_transform.pyx because it changed. Compiling biom/_subsample.pyx because it changed. [1/3] Cythonizing biom/_filter.pyx [2/3] Cythonizing biom/_subsample.pyx [3/3] Cythonizing biom/_transform.pyx running clean removing '/build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build' (and everything under it) 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it I: pybuild base:311: python3.11 setup.py clean running clean removing '/build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build' (and everything under it) 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/python3-biom-format.substvars debian/python-biom-format-doc.substvars ./biom/_filter.c ./biom/_subsample.c ./biom/_transform.c debian/files rm -fr -- debian/python3-biom-format/ debian/tmp/ debian/python-biom-format-doc/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --with bash-completion,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild pybuild --configure -i python{version} -p "3.12 3.11" I: pybuild base:311: python3.12 setup.py config /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/python-biom-format-2.1.15.2/biom/_filter.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/python-biom-format-2.1.15.2/biom/_subsample.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/python-biom-format-2.1.15.2/biom/_transform.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling biom/_filter.pyx because it changed. Compiling biom/_transform.pyx because it changed. Compiling biom/_subsample.pyx because it changed. [1/3] Cythonizing biom/_filter.pyx [2/3] Cythonizing biom/_subsample.pyx [3/3] Cythonizing biom/_transform.pyx running config I: pybuild base:311: python3.11 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/python-biom-format-2.1.15.2' # arch USE_CYTHON=true dh_auto_build pybuild --build -i python{version} -p "3.12 3.11" I: pybuild base:311: /usr/bin/python3.12 setup.py build running build running build_py creating /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom copying biom/table.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom copying biom/err.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom copying biom/exception.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom copying biom/__init__.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom copying biom/parse.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom copying biom/util.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom creating /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests copying biom/tests/long_lines.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests copying biom/tests/test_err.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests copying biom/tests/test_util.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests copying biom/tests/__init__.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests copying biom/tests/test_table.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests copying biom/tests/test_parse.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests creating /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/cli copying biom/cli/table_validator.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/cli copying biom/cli/installation_informer.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/cli copying biom/cli/metadata_exporter.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/cli copying biom/cli/uc_processor.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/cli copying biom/cli/table_summarizer.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/cli copying biom/cli/table_converter.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/cli copying biom/cli/table_subsetter.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/cli copying biom/cli/table_head.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/cli copying biom/cli/table_normalizer.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/cli copying biom/cli/__init__.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/cli copying biom/cli/metadata_adder.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/cli copying biom/cli/table_ids.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/cli copying biom/cli/util.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/cli creating /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_subset_table.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_summarize_table.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_uc_processor.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_add_metadata.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/__init__.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_show_install_info.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_table_converter.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_validate_table.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_table_normalizer.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_cli creating /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_data copying biom/tests/test_data/__init__.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_data running egg_info creating biom_format.egg-info writing biom_format.egg-info/PKG-INFO writing dependency_links to biom_format.egg-info/dependency_links.txt writing entry points to biom_format.egg-info/entry_points.txt writing requirements to biom_format.egg-info/requires.txt writing top-level names to biom_format.egg-info/top_level.txt writing manifest file 'biom_format.egg-info/SOURCES.txt' dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative reading manifest file 'biom_format.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no directories found matching 'support_files' warning: no directories found matching 'tests/test_data' no previously-included directories found matching 'docs/_build' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '.git' found anywhere in distribution warning: no previously-included files matching '*.so' found anywhere in distribution warning: no previously-included files matching '.*.swp' found anywhere in distribution adding license file 'COPYING.txt' writing manifest file 'biom_format.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'biom.assets' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'biom.assets' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'biom.assets' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'biom.assets' to be distributed and are already explicitly excluding 'biom.assets' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'biom.tests.bench_tables' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'biom.tests.bench_tables' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'biom.tests.bench_tables' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'biom.tests.bench_tables' to be distributed and are already explicitly excluding 'biom.tests.bench_tables' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'biom.tests.test_cli.test_data' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'biom.tests.test_cli.test_data' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'biom.tests.test_cli.test_data' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'biom.tests.test_cli.test_data' to be distributed and are already explicitly excluding 'biom.tests.test_cli.test_data' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying biom/_filter.pyx -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom copying biom/_subsample.pyx -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom copying biom/_transform.pyx -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom creating /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/assets copying biom/assets/exercise_api.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/assets copying biom/assets/exercise_cli.sh -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/assets creating /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/bench_tables creating /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/json_obs_collapsed.biom -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/json_sample_collapsed.biom -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/test.biom -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/test.json -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_cli/test_data copying biom/tests/test_data/bad_table.txt -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_data copying biom/tests/test_data/bad_table.txt.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_data copying biom/tests/test_data/empty.biom -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_data copying biom/tests/test_data/no-contents.biom -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_data copying biom/tests/test_data/test.biom -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_data copying biom/tests/test_data/test.json -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_data copying biom/tests/test_data/test.json.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_data copying biom/tests/test_data/test_grp_metadata.biom -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_data running build_ext building 'biom._filter' extension creating build creating build/temp.linux-i686-cpython-312 creating build/temp.linux-i686-cpython-312/biom i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.15.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c biom/_filter.c -o build/temp.linux-i686-cpython-312/biom/_filter.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from biom/_filter.c:1249: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.15.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/biom/_filter.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/_filter.cpython-312-i386-linux-gnu.so building 'biom._transform' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.15.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c biom/_transform.c -o build/temp.linux-i686-cpython-312/biom/_transform.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from biom/_transform.c:1249: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.15.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/biom/_transform.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/_transform.cpython-312-i386-linux-gnu.so building 'biom._subsample' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.15.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c biom/_subsample.c -o build/temp.linux-i686-cpython-312/biom/_subsample.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from biom/_subsample.c:1249: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.15.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/biom/_subsample.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/_subsample.cpython-312-i386-linux-gnu.so I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom copying biom/table.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom copying biom/err.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom copying biom/exception.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom copying biom/__init__.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom copying biom/parse.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom copying biom/util.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom creating /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests copying biom/tests/long_lines.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests copying biom/tests/test_err.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests copying biom/tests/test_util.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests copying biom/tests/__init__.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests copying biom/tests/test_table.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests copying biom/tests/test_parse.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests creating /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/cli copying biom/cli/table_validator.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/cli copying biom/cli/installation_informer.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/cli copying biom/cli/metadata_exporter.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/cli copying biom/cli/uc_processor.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/cli copying biom/cli/table_summarizer.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/cli copying biom/cli/table_converter.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/cli copying biom/cli/table_subsetter.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/cli copying biom/cli/table_head.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/cli copying biom/cli/table_normalizer.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/cli copying biom/cli/__init__.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/cli copying biom/cli/metadata_adder.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/cli copying biom/cli/table_ids.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/cli copying biom/cli/util.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/cli creating /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_subset_table.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_summarize_table.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_uc_processor.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_add_metadata.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/__init__.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_show_install_info.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_table_converter.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_validate_table.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_cli copying biom/tests/test_cli/test_table_normalizer.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_cli creating /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_data copying biom/tests/test_data/__init__.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_data running egg_info writing biom_format.egg-info/PKG-INFO writing dependency_links to biom_format.egg-info/dependency_links.txt writing entry points to biom_format.egg-info/entry_points.txt writing requirements to biom_format.egg-info/requires.txt writing top-level names to biom_format.egg-info/top_level.txt dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative reading manifest file 'biom_format.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no directories found matching 'support_files' warning: no directories found matching 'tests/test_data' no previously-included directories found matching 'docs/_build' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '.git' found anywhere in distribution warning: no previously-included files matching '*.so' found anywhere in distribution warning: no previously-included files matching '.*.swp' found anywhere in distribution adding license file 'COPYING.txt' writing manifest file 'biom_format.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'biom.assets' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'biom.assets' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'biom.assets' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'biom.assets' to be distributed and are already explicitly excluding 'biom.assets' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'biom.tests.bench_tables' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'biom.tests.bench_tables' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'biom.tests.bench_tables' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'biom.tests.bench_tables' to be distributed and are already explicitly excluding 'biom.tests.bench_tables' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'biom.tests.test_cli.test_data' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'biom.tests.test_cli.test_data' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'biom.tests.test_cli.test_data' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'biom.tests.test_cli.test_data' to be distributed and are already explicitly excluding 'biom.tests.test_cli.test_data' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying biom/_filter.pyx -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom copying biom/_subsample.pyx -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom copying biom/_transform.pyx -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom creating /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/assets copying biom/assets/exercise_api.py -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/assets copying biom/assets/exercise_cli.sh -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/assets creating /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.001_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.010_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.100_bench.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/bench_tables creating /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/json_obs_collapsed.biom -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/json_sample_collapsed.biom -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/test.biom -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/test.json -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_cli/test_data copying biom/tests/test_data/bad_table.txt -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_data copying biom/tests/test_data/bad_table.txt.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_data copying biom/tests/test_data/empty.biom -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_data copying biom/tests/test_data/no-contents.biom -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_data copying biom/tests/test_data/test.biom -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_data copying biom/tests/test_data/test.json -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_data copying biom/tests/test_data/test.json.gz -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_data copying biom/tests/test_data/test_grp_metadata.biom -> /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_data running build_ext building 'biom._filter' extension creating build/temp.linux-i686-cpython-311 creating build/temp.linux-i686-cpython-311/biom i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.15.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c biom/_filter.c -o build/temp.linux-i686-cpython-311/biom/_filter.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from biom/_filter.c:1249: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.15.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/biom/_filter.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/_filter.cpython-311-i386-linux-gnu.so building 'biom._transform' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.15.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c biom/_transform.c -o build/temp.linux-i686-cpython-311/biom/_transform.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from biom/_transform.c:1249: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.15.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/biom/_transform.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/_transform.cpython-311-i386-linux-gnu.so building 'biom._subsample' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.15.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c biom/_subsample.c -o build/temp.linux-i686-cpython-311/biom/_subsample.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from biom/_subsample.c:1249: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-biom-format-2.1.15.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/biom/_subsample.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/_subsample.cpython-311-i386-linux-gnu.so # indep: PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b html doc build/html Running Sphinx v7.2.6 making output directory... done [autosummary] generating autosummary for: BIOM_LICENSE.rst, documentation/adding_metadata.rst, documentation/biom_conversion.rst, documentation/biom_format.rst, documentation/index.rst, documentation/quick_usage_examples.rst, documentation/summarizing_biom_tables.rst, documentation/table_objects.rst, index.rst WARNING: Failed to import biom.table. Possible hints: * KeyError: 'biom' * ModuleNotFoundError: No module named 'biom._filter' WARNING: Failed to import biom. Possible hints: * KeyError: 'biom' * ModuleNotFoundError: No module named 'biom._filter' building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 12 source files that are out of date updating environment: [new config] 12 added, 0 changed, 0 removed reading sources... [ 8%] BIOM_LICENSE reading sources... [ 17%] documentation/adding_metadata reading sources... [ 25%] documentation/biom_conversion reading sources... [ 33%] documentation/biom_format reading sources... [ 42%] documentation/format_versions/biom-1.0 reading sources... [ 50%] documentation/format_versions/biom-2.0 reading sources... [ 58%] documentation/format_versions/biom-2.1 reading sources... [ 67%] documentation/index reading sources... [ 75%] documentation/quick_usage_examples reading sources... [ 83%] documentation/summarizing_biom_tables reading sources... [ 92%] documentation/table_objects reading sources... [100%] index WARNING: autodoc: failed to import module 'biom'; the following exception was raised: No module named 'biom._filter' WARNING: autodoc: failed to import module 'table' from module 'biom'; the following exception was raised: No module named 'biom._filter' looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... done copying extra files... done done writing output... [ 8%] BIOM_LICENSE writing output... [ 17%] documentation/adding_metadata writing output... [ 25%] documentation/biom_conversion writing output... [ 33%] documentation/biom_format writing output... [ 42%] documentation/format_versions/biom-1.0 writing output... [ 50%] documentation/format_versions/biom-2.0 writing output... [ 58%] documentation/format_versions/biom-2.1 writing output... [ 67%] documentation/index writing output... [ 75%] documentation/quick_usage_examples writing output... [ 83%] documentation/summarizing_biom_tables writing output... [ 92%] documentation/table_objects writing output... [100%] index /build/reproducible-path/python-biom-format-2.1.15.2/doc/documentation/index.rst:11: WARNING: toctree contains reference to document 'documentation/quick_usage_examples' that doesn't have a title: no link will be generated /build/reproducible-path/python-biom-format-2.1.15.2/doc/documentation/index.rst:11: WARNING: toctree contains reference to document 'documentation/table_objects' that doesn't have a title: no link will be generated /build/reproducible-path/python-biom-format-2.1.15.2/doc/documentation/index.rst:11: WARNING: toctree contains reference to document 'documentation/quick_usage_examples' that doesn't have a title: no link will be generated /build/reproducible-path/python-biom-format-2.1.15.2/doc/documentation/index.rst:11: WARNING: toctree contains reference to document 'documentation/table_objects' that doesn't have a title: no link will be generated generating indices... done writing additional pages... search done copying images... [100%] _static/biom-format.png dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 8 warnings. The HTML pages are in build/html. PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b man doc build/man Running Sphinx v7.2.6 making output directory... done [autosummary] generating autosummary for: BIOM_LICENSE.rst, documentation/adding_metadata.rst, documentation/biom_conversion.rst, documentation/biom_format.rst, documentation/index.rst, documentation/quick_usage_examples.rst, documentation/summarizing_biom_tables.rst, documentation/table_objects.rst, index.rst WARNING: Failed to import biom.table. Possible hints: * KeyError: 'biom' * ModuleNotFoundError: No module named 'biom._filter' WARNING: Failed to import biom. Possible hints: * KeyError: 'biom' * ModuleNotFoundError: No module named 'biom._filter' building [mo]: targets for 0 po files that are out of date writing output... building [man]: all manpages updating environment: [new config] 12 added, 0 changed, 0 removed reading sources... [ 8%] BIOM_LICENSE reading sources... [ 17%] documentation/adding_metadata reading sources... [ 25%] documentation/biom_conversion reading sources... [ 33%] documentation/biom_format reading sources... [ 42%] documentation/format_versions/biom-1.0 reading sources... [ 50%] documentation/format_versions/biom-2.0 reading sources... [ 58%] documentation/format_versions/biom-2.1 reading sources... [ 67%] documentation/index reading sources... [ 75%] documentation/quick_usage_examples reading sources... [ 83%] documentation/summarizing_biom_tables reading sources... [ 92%] documentation/table_objects reading sources... [100%] index WARNING: autodoc: failed to import module 'biom'; the following exception was raised: No module named 'biom._filter' WARNING: autodoc: failed to import module 'table' from module 'biom'; the following exception was raised: No module named 'biom._filter' looking for now-outdated files... none found pickling environment... done checking consistency... done writing... biom.1 { documentation/index documentation/biom_format documentation/format_versions/biom-1.0 documentation/format_versions/biom-2.0 documentation/format_versions/biom-2.1 documentation/quick_usage_examples documentation/table_objects documentation/biom_conversion documentation/adding_metadata documentation/summarizing_biom_tables BIOM_LICENSE } done build succeeded, 4 warnings. The manual pages are in build/man. make[1]: Leaving directory '/build/reproducible-path/python-biom-format-2.1.15.2' dh_auto_test -O--buildsystem=pybuild pybuild --test --test-pytest -i python{version} -p "3.12 3.11" I: pybuild pybuild:308: cp -r /build/reproducible-path/python-biom-format-2.1.15.2/examples /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build I: pybuild base:311: cd /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build; python3.12 -m pytest ============================= test session starts ============================== platform linux -- Python 3.12.3, pytest-7.4.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build configfile: pytest.ini testpaths: biom plugins: cov-5.0.0 collected 376 items biom/tests/test_err.py ..................... [ 5%] biom/tests/test_parse.py ........................... [ 12%] biom/tests/test_table.py ............................................... [ 25%] ..sss................................................................... [ 44%] .....sss................................................................ [ 63%] ..............................F...F.F..F............................. [ 81%] biom/tests/test_util.py ..........F......... [ 87%] biom/tests/test_cli/test_add_metadata.py .... [ 88%] biom/tests/test_cli/test_show_install_info.py . [ 88%] biom/tests/test_cli/test_subset_table.py ..... [ 89%] biom/tests/test_cli/test_summarize_table.py .. [ 90%] biom/tests/test_cli/test_table_converter.py ...... [ 92%] biom/tests/test_cli/test_table_normalizer.py . [ 92%] biom/tests/test_cli/test_uc_processor.py ...... [ 93%] biom/tests/test_cli/test_validate_table.py ....................... [100%] =================================== FAILURES =================================== _______________________ SparseTableTests.test_subsample ________________________ obj = array([0]), method = 'repeat', args = (array([5], dtype=int64),) kwds = {'axis': None} bound = def _wrapfunc(obj, method, *args, **kwds): bound = getattr(obj, method, None) if bound is None: return _wrapit(obj, method, *args, **kwds) try: > return bound(*args, **kwds) E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:59: TypeError During handling of the above exception, another exception occurred: self = def test_subsample(self): table = Table(np.array([[0, 5, 0]]), ['O1'], ['S1', 'S2', 'S3']) > obs = table.subsample(5, axis='observation') /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_table.py:3244: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/table.py:2990: in subsample _subsample(data, n, with_replacement, rng) biom/_subsample.pyx:64: in biom._subsample._subsample ??? /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:466: in repeat return _wrapfunc(a, 'repeat', repeats, axis=axis) /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:68: in _wrapfunc return _wrapit(obj, method, *args, **kwds) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ obj = array([0]), method = 'repeat', args = (array([5], dtype=int64),) kwds = {'axis': None} wrap = def _wrapit(obj, method, *args, **kwds): try: wrap = obj.__array_wrap__ except AttributeError: wrap = None > result = getattr(asarray(obj), method)(*args, **kwds) E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:45: TypeError _________________ SparseTableTests.test_subsample_md_copy_bug __________________ obj = array([0]), method = 'repeat', args = (array([5], dtype=int64),) kwds = {'axis': None} bound = def _wrapfunc(obj, method, *args, **kwds): bound = getattr(obj, method, None) if bound is None: return _wrapit(obj, method, *args, **kwds) try: > return bound(*args, **kwds) E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:59: TypeError During handling of the above exception, another exception occurred: self = def test_subsample_md_copy_bug(self): """subsample would except when if metadata were present""" table = Table(np.array([[5, 5, 5]]), ['O1'], ['S1', 'S2', 'S3'], [{'foo': 'bar'}], [{1: 2}, {3: 4}, {5: 6}]) exp = table.copy() > obs = table.subsample(5) /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_table.py:3266: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/table.py:2990: in subsample _subsample(data, n, with_replacement, rng) biom/_subsample.pyx:64: in biom._subsample._subsample ??? /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:466: in repeat return _wrapfunc(a, 'repeat', repeats, axis=axis) /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:68: in _wrapfunc return _wrapit(obj, method, *args, **kwds) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ obj = array([0]), method = 'repeat', args = (array([5], dtype=int64),) kwds = {'axis': None} wrap = def _wrapit(obj, method, *args, **kwds): try: wrap = obj.__array_wrap__ except AttributeError: wrap = None > result = getattr(asarray(obj), method)(*args, **kwds) E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:45: TypeError ________ SparseTableTests.test_subsample_same_seed_without_replacement _________ obj = array([0]), method = 'repeat', args = (array([3], dtype=int64),) kwds = {'axis': None} bound = def _wrapfunc(obj, method, *args, **kwds): bound = getattr(obj, method, None) if bound is None: return _wrapit(obj, method, *args, **kwds) try: > return bound(*args, **kwds) E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:59: TypeError During handling of the above exception, another exception occurred: self = def test_subsample_same_seed_without_replacement(self): table = Table(np.array([[3, 1, 2], [0, 3, 4]]), ['O1', 'O2'], ['S1', 'S2', 'S3']) > exp = table.subsample(2, seed=1234) /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_table.py:3176: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/table.py:2990: in subsample _subsample(data, n, with_replacement, rng) biom/_subsample.pyx:64: in biom._subsample._subsample ??? /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:466: in repeat return _wrapfunc(a, 'repeat', repeats, axis=axis) /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:68: in _wrapfunc return _wrapit(obj, method, *args, **kwds) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ obj = array([0]), method = 'repeat', args = (array([3], dtype=int64),) kwds = {'axis': None} wrap = def _wrapit(obj, method, *args, **kwds): try: wrap = obj.__array_wrap__ except AttributeError: wrap = None > result = getattr(asarray(obj), method)(*args, **kwds) E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:45: TypeError ______ SparseTableTests.test_subsample_without_replacement_unique_results ______ obj = array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9]), method = 'repeat' args = (array([2, 1, 2, 1, 8, 6, 3, 3, 5, 5], dtype=int64),) kwds = {'axis': None} bound = def _wrapfunc(obj, method, *args, **kwds): bound = getattr(obj, method, None) if bound is None: return _wrapit(obj, method, *args, **kwds) try: > return bound(*args, **kwds) E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:59: TypeError During handling of the above exception, another exception occurred: self = def test_subsample_without_replacement_unique_results(self): """ As in scikit-bio. Given a vector of observations, the total number of unique subsamplings when n == sum(vector) - 1 should be equal to the number of unique categories of observations when the vector is subsampled without replacement. If the vector is subsamples *with* replacement, however, there should be more than 10 different possible subsamplings. """ a = np.array([[2, 1, 2, 1, 8, 6, 3, 3, 5, 5], ]).T dt = Table(data=a, sample_ids=['S1', ], observation_ids=[f'OTU{i:02d}' for i in range(10)]) actual = set() for i in range(1000): > obs = dt.subsample(35) /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_table.py:3290: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/table.py:2990: in subsample _subsample(data, n, with_replacement, rng) biom/_subsample.pyx:64: in biom._subsample._subsample ??? /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:466: in repeat return _wrapfunc(a, 'repeat', repeats, axis=axis) /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:68: in _wrapfunc return _wrapit(obj, method, *args, **kwds) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ obj = array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9]), method = 'repeat' args = (array([2, 1, 2, 1, 8, 6, 3, 3, 5, 5], dtype=int64),) kwds = {'axis': None} wrap = def _wrapit(obj, method, *args, **kwds): try: wrap = obj.__array_wrap__ except AttributeError: wrap = None > result = getattr(asarray(obj), method)(*args, **kwds) E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:45: TypeError ______________________ UtilTests.test_generate_subsamples ______________________ obj = array([0]), method = 'repeat', args = (array([3], dtype=int64),) kwds = {'axis': None} bound = def _wrapfunc(obj, method, *args, **kwds): bound = getattr(obj, method, None) if bound is None: return _wrapit(obj, method, *args, **kwds) try: > return bound(*args, **kwds) E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:59: TypeError During handling of the above exception, another exception occurred: self = def test_generate_subsamples(self): table = Table(np.array([[3, 1, 1], [0, 3, 3]]), ['O1', 'O2'], ['S1', 'S2', 'S3']) actual_o1 = set() actual_o2 = set() > for i, obs in zip(range(100), generate_subsamples(table, 3)): /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/tests/test_util.py:51: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/util.py:83: in generate_subsamples yield table.subsample(n, axis, by_id) /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build/biom/table.py:2990: in subsample _subsample(data, n, with_replacement, rng) biom/_subsample.pyx:64: in biom._subsample._subsample ??? /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:466: in repeat return _wrapfunc(a, 'repeat', repeats, axis=axis) /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:68: in _wrapfunc return _wrapit(obj, method, *args, **kwds) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ obj = array([0]), method = 'repeat', args = (array([3], dtype=int64),) kwds = {'axis': None} wrap = def _wrapit(obj, method, *args, **kwds): try: wrap = obj.__array_wrap__ except AttributeError: wrap = None > result = getattr(asarray(obj), method)(*args, **kwds) E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:45: TypeError =========================== short test summary info ============================ FAILED biom/tests/test_table.py::SparseTableTests::test_subsample - TypeError... FAILED biom/tests/test_table.py::SparseTableTests::test_subsample_md_copy_bug FAILED biom/tests/test_table.py::SparseTableTests::test_subsample_same_seed_without_replacement FAILED biom/tests/test_table.py::SparseTableTests::test_subsample_without_replacement_unique_results FAILED biom/tests/test_util.py::UtilTests::test_generate_subsamples - TypeErr... =================== 5 failed, 365 passed, 6 skipped in 9.64s =================== E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.12_biom-format/build; python3.12 -m pytest I: pybuild pybuild:308: cp -r /build/reproducible-path/python-biom-format-2.1.15.2/examples /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build I: pybuild base:311: cd /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build; python3.11 -m pytest ============================= test session starts ============================== platform linux -- Python 3.11.9, pytest-7.4.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build configfile: pytest.ini testpaths: biom plugins: cov-5.0.0 collected 376 items biom/tests/test_err.py ..................... [ 5%] biom/tests/test_parse.py ........................... [ 12%] biom/tests/test_table.py ............................................... [ 25%] ..sss................................................................... [ 44%] .....sss................................................................ [ 63%] ..............................F...F.F..F............................. [ 81%] biom/tests/test_util.py ..........F......... [ 87%] biom/tests/test_cli/test_add_metadata.py .... [ 88%] biom/tests/test_cli/test_show_install_info.py . [ 88%] biom/tests/test_cli/test_subset_table.py ..... [ 89%] biom/tests/test_cli/test_summarize_table.py .. [ 90%] biom/tests/test_cli/test_table_converter.py ...... [ 92%] biom/tests/test_cli/test_table_normalizer.py . [ 92%] biom/tests/test_cli/test_uc_processor.py ...... [ 93%] biom/tests/test_cli/test_validate_table.py ....................... [100%] =================================== FAILURES =================================== _______________________ SparseTableTests.test_subsample ________________________ obj = array([0]), method = 'repeat', args = (array([5], dtype=int64),) kwds = {'axis': None} bound = def _wrapfunc(obj, method, *args, **kwds): bound = getattr(obj, method, None) if bound is None: return _wrapit(obj, method, *args, **kwds) try: > return bound(*args, **kwds) E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:59: TypeError During handling of the above exception, another exception occurred: self = def test_subsample(self): table = Table(np.array([[0, 5, 0]]), ['O1'], ['S1', 'S2', 'S3']) > obs = table.subsample(5, axis='observation') /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_table.py:3244: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/table.py:2990: in subsample _subsample(data, n, with_replacement, rng) biom/_subsample.pyx:64: in biom._subsample._subsample ??? /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:466: in repeat return _wrapfunc(a, 'repeat', repeats, axis=axis) /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:68: in _wrapfunc return _wrapit(obj, method, *args, **kwds) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ obj = array([0]), method = 'repeat', args = (array([5], dtype=int64),) kwds = {'axis': None} wrap = def _wrapit(obj, method, *args, **kwds): try: wrap = obj.__array_wrap__ except AttributeError: wrap = None > result = getattr(asarray(obj), method)(*args, **kwds) E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:45: TypeError _________________ SparseTableTests.test_subsample_md_copy_bug __________________ obj = array([0]), method = 'repeat', args = (array([5], dtype=int64),) kwds = {'axis': None} bound = def _wrapfunc(obj, method, *args, **kwds): bound = getattr(obj, method, None) if bound is None: return _wrapit(obj, method, *args, **kwds) try: > return bound(*args, **kwds) E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:59: TypeError During handling of the above exception, another exception occurred: self = def test_subsample_md_copy_bug(self): """subsample would except when if metadata were present""" table = Table(np.array([[5, 5, 5]]), ['O1'], ['S1', 'S2', 'S3'], [{'foo': 'bar'}], [{1: 2}, {3: 4}, {5: 6}]) exp = table.copy() > obs = table.subsample(5) /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_table.py:3266: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/table.py:2990: in subsample _subsample(data, n, with_replacement, rng) biom/_subsample.pyx:64: in biom._subsample._subsample ??? /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:466: in repeat return _wrapfunc(a, 'repeat', repeats, axis=axis) /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:68: in _wrapfunc return _wrapit(obj, method, *args, **kwds) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ obj = array([0]), method = 'repeat', args = (array([5], dtype=int64),) kwds = {'axis': None} wrap = def _wrapit(obj, method, *args, **kwds): try: wrap = obj.__array_wrap__ except AttributeError: wrap = None > result = getattr(asarray(obj), method)(*args, **kwds) E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:45: TypeError ________ SparseTableTests.test_subsample_same_seed_without_replacement _________ obj = array([0]), method = 'repeat', args = (array([3], dtype=int64),) kwds = {'axis': None} bound = def _wrapfunc(obj, method, *args, **kwds): bound = getattr(obj, method, None) if bound is None: return _wrapit(obj, method, *args, **kwds) try: > return bound(*args, **kwds) E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:59: TypeError During handling of the above exception, another exception occurred: self = def test_subsample_same_seed_without_replacement(self): table = Table(np.array([[3, 1, 2], [0, 3, 4]]), ['O1', 'O2'], ['S1', 'S2', 'S3']) > exp = table.subsample(2, seed=1234) /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_table.py:3176: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/table.py:2990: in subsample _subsample(data, n, with_replacement, rng) biom/_subsample.pyx:64: in biom._subsample._subsample ??? /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:466: in repeat return _wrapfunc(a, 'repeat', repeats, axis=axis) /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:68: in _wrapfunc return _wrapit(obj, method, *args, **kwds) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ obj = array([0]), method = 'repeat', args = (array([3], dtype=int64),) kwds = {'axis': None} wrap = def _wrapit(obj, method, *args, **kwds): try: wrap = obj.__array_wrap__ except AttributeError: wrap = None > result = getattr(asarray(obj), method)(*args, **kwds) E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:45: TypeError ______ SparseTableTests.test_subsample_without_replacement_unique_results ______ obj = array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9]), method = 'repeat' args = (array([2, 1, 2, 1, 8, 6, 3, 3, 5, 5], dtype=int64),) kwds = {'axis': None} bound = def _wrapfunc(obj, method, *args, **kwds): bound = getattr(obj, method, None) if bound is None: return _wrapit(obj, method, *args, **kwds) try: > return bound(*args, **kwds) E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:59: TypeError During handling of the above exception, another exception occurred: self = def test_subsample_without_replacement_unique_results(self): """ As in scikit-bio. Given a vector of observations, the total number of unique subsamplings when n == sum(vector) - 1 should be equal to the number of unique categories of observations when the vector is subsampled without replacement. If the vector is subsamples *with* replacement, however, there should be more than 10 different possible subsamplings. """ a = np.array([[2, 1, 2, 1, 8, 6, 3, 3, 5, 5], ]).T dt = Table(data=a, sample_ids=['S1', ], observation_ids=[f'OTU{i:02d}' for i in range(10)]) actual = set() for i in range(1000): > obs = dt.subsample(35) /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_table.py:3290: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/table.py:2990: in subsample _subsample(data, n, with_replacement, rng) biom/_subsample.pyx:64: in biom._subsample._subsample ??? /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:466: in repeat return _wrapfunc(a, 'repeat', repeats, axis=axis) /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:68: in _wrapfunc return _wrapit(obj, method, *args, **kwds) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ obj = array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9]), method = 'repeat' args = (array([2, 1, 2, 1, 8, 6, 3, 3, 5, 5], dtype=int64),) kwds = {'axis': None} wrap = def _wrapit(obj, method, *args, **kwds): try: wrap = obj.__array_wrap__ except AttributeError: wrap = None > result = getattr(asarray(obj), method)(*args, **kwds) E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:45: TypeError ______________________ UtilTests.test_generate_subsamples ______________________ obj = array([0]), method = 'repeat', args = (array([3], dtype=int64),) kwds = {'axis': None} bound = def _wrapfunc(obj, method, *args, **kwds): bound = getattr(obj, method, None) if bound is None: return _wrapit(obj, method, *args, **kwds) try: > return bound(*args, **kwds) E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:59: TypeError During handling of the above exception, another exception occurred: self = def test_generate_subsamples(self): table = Table(np.array([[3, 1, 1], [0, 3, 3]]), ['O1', 'O2'], ['S1', 'S2', 'S3']) actual_o1 = set() actual_o2 = set() > for i, obs in zip(range(100), generate_subsamples(table, 3)): /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/tests/test_util.py:51: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/util.py:83: in generate_subsamples yield table.subsample(n, axis, by_id) /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build/biom/table.py:2990: in subsample _subsample(data, n, with_replacement, rng) biom/_subsample.pyx:64: in biom._subsample._subsample ??? /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:466: in repeat return _wrapfunc(a, 'repeat', repeats, axis=axis) /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:68: in _wrapfunc return _wrapit(obj, method, *args, **kwds) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ obj = array([0]), method = 'repeat', args = (array([3], dtype=int64),) kwds = {'axis': None} wrap = def _wrapit(obj, method, *args, **kwds): try: wrap = obj.__array_wrap__ except AttributeError: wrap = None > result = getattr(asarray(obj), method)(*args, **kwds) E TypeError: Cannot cast array data from dtype('int64') to dtype('int32') according to the rule 'safe' /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:45: TypeError =========================== short test summary info ============================ FAILED biom/tests/test_table.py::SparseTableTests::test_subsample - TypeError... FAILED biom/tests/test_table.py::SparseTableTests::test_subsample_md_copy_bug FAILED biom/tests/test_table.py::SparseTableTests::test_subsample_same_seed_without_replacement FAILED biom/tests/test_table.py::SparseTableTests::test_subsample_without_replacement_unique_results FAILED biom/tests/test_util.py::UtilTests::test_generate_subsamples - TypeErr... ================== 5 failed, 365 passed, 6 skipped in 10.20s =================== E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /build/reproducible-path/python-biom-format-2.1.15.2/.pybuild/cpython3_3.11_biom-format/build; python3.11 -m pytest rm -fr -- /tmp/dh-xdg-rundir-Tq3C_ag7 dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13 make: *** [debian/rules:19: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/40526 and its subdirectories Thu May 16 08:53:11 UTC 2024 W: No second build log, what happened?