I: pbuilder: network access will be disabled during build I: Current time: Thu Jan 8 01:38:44 +14 2026 I: pbuilder-time-stamp: 1767785924 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: Copying source file I: copying [pybel_0.15.5-1.dsc] I: copying [./pybel_0.15.5.orig.tar.gz] I: copying [./pybel_0.15.5-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Nov 30 02:03:40 2024 gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A gpgv: issuer "tchet@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./pybel_0.15.5-1.dsc: no acceptable signature found dpkg-source: info: extracting pybel in pybel-0.15.5 dpkg-source: info: unpacking pybel_0.15.5.orig.tar.gz dpkg-source: info: unpacking pybel_0.15.5-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying not_testing_what_fails.patch dpkg-source: info: applying more_click_is_not_packaged.patch dpkg-source: info: applying remove_psycopg2-binary I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/492424/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 7 11:39 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/492424/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/492424/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=f4fa62019b1b40968b70115d3fbfac0b LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=492424 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.oiEfLAQT/pbuilderrc_Kg7y --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oiEfLAQT/b2 --logfile b2/build.log pybel_0.15.5-1.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/492424/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: amd64 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, pybuild-plugin-pyproject, python3-all, python3-setuptools, python3-click-plugins, python3-humanize, python3-jinja2, python3-jsonschema, python3-networkx, python3-pandas, python3-pyparsing, python3-pystow, python3-pytest, python3-ratelimit, python3-requests-file, python3-sqlalchemy, python3-tabulate, python3-tqdm, python3-bioregistry, python3-bel-resources dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19969 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 pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-click-plugins; however: Package python3-click-plugins is not installed. pbuilder-satisfydepends-dummy depends on python3-humanize; however: Package python3-humanize is not installed. pbuilder-satisfydepends-dummy depends on python3-jinja2; however: Package python3-jinja2 is not installed. pbuilder-satisfydepends-dummy depends on python3-jsonschema; however: Package python3-jsonschema is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-pyparsing; however: Package python3-pyparsing is not installed. pbuilder-satisfydepends-dummy depends on python3-pystow; however: Package python3-pystow is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-ratelimit; however: Package python3-ratelimit is not installed. pbuilder-satisfydepends-dummy depends on python3-requests-file; however: Package python3-requests-file is not installed. pbuilder-satisfydepends-dummy depends on python3-sqlalchemy; however: Package python3-sqlalchemy is not installed. pbuilder-satisfydepends-dummy depends on python3-tabulate; however: Package python3-tabulate is not installed. pbuilder-satisfydepends-dummy depends on python3-tqdm; however: Package python3-tqdm is not installed. pbuilder-satisfydepends-dummy depends on python3-bioregistry; however: Package python3-bioregistry is not installed. pbuilder-satisfydepends-dummy depends on python3-bel-resources; however: Package python3-bel-resources 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} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libpipeline1{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} pybuild-plugin-pyproject{a} python3{a} python3-all{a} python3-annotated-types{a} python3-attr{a} python3-autocommand{a} python3-bel-resources{a} python3-bioregistry{a} python3-build{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-click{a} python3-click-plugins{a} python3-colorama{a} python3-curies{a} python3-dateutil{a} python3-dnspython{a} python3-email-validator{a} python3-greenlet{a} python3-humanize{a} python3-idna{a} python3-inflect{a} python3-iniconfig{a} python3-installer{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jinja2{a} python3-jsonschema{a} python3-jsonschema-specifications{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-multisplitby{a} python3-networkx{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pkg-resources{a} python3-pluggy{a} python3-pydantic{a} python3-pydantic-core{a} python3-pyparsing{a} python3-pyproject-hooks{a} python3-pystow{a} python3-pytest{a} python3-ratelimit{a} python3-referencing{a} python3-requests{a} python3-requests-file{a} python3-rpds-py{a} python3-setuptools{a} python3-sortedcontainers{a} python3-sqlalchemy{a} python3-tabulate{a} python3-toml{a} python3-tqdm{a} python3-trie{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-urllib3{a} python3-wheel{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: curl krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx python3-babel python3-bottleneck python3-bs4 python3-cryptography python3-gdal python3-h2 python3-html5lib python3-httpcore python3-httpx python3-json-pointer python3-lxml python3-matplotlib python3-numexpr python3-odf python3-openpyxl python3-pydot python3-pygments python3-pygraphviz python3-rfc3987 python3-scipy python3-sqlalchemy-ext python3-tables python3-uritemplate python3-webcolors python3-yaml wget 0 packages upgraded, 120 newly installed, 0 to remove and 0 not upgraded. Need to get 71.2 MB of archives. After unpacking 369 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-4 [256 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 46 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 60 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 74.1.2-2 [736 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20241024 [109 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 python3-toml all 0.10.2-1 [16.2 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 python3-wheel all 0.45.1-1 [56.7 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 python3-build all 1.2.2-1 [36.0 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 pybuild-plugin-pyproject all 6.20241024 [11.4 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.12.6-1 [1040 B] Get: 76 http://deb.debian.org/debian trixie/main amd64 python3-annotated-types all 0.7.0-1 [18.8 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 python3-multisplitby all 0.0.1-6 [4688 B] Get: 79 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 80 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.4.0-1+b1 [140 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.8-2 [41.6 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.2.3-3 [112 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 python3-requests-file all 2.0.0-1 [6424 B] Get: 86 http://deb.debian.org/debian trixie/main amd64 python3-colorama all 0.4.6-4 [36.2 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 python3-click all 8.1.7-2 [94.3 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 python3-bel-resources all 0.0.3-4 [13.5 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 python3-pydantic-core amd64 2.27.1-1 [1737 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 python3-dnspython all 2.6.1-1 [161 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 python3-email-validator all 2.2.0-1 [31.6 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 python3-pydantic amd64 2.10.2-1 [364 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 python3-trie all 0.4.0+ds-1 [7640 B] Get: 95 http://deb.debian.org/debian trixie/main amd64 python3-curies all 0.9.0-1 [38.3 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 python3-tqdm all 4.67.1-1 [91.0 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 python3-pystow all 0.5.5-1 [25.6 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 python3-bioregistry all 0.11.12-3 [3907 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 python3-click-plugins all 1.1.1-4 [9852 B] Get: 100 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 python3-greenlet amd64 3.1.0-1+b1 [179 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 python3-humanize all 4.11.0-1 [52.7 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 104 http://deb.debian.org/debian trixie/main amd64 python3-markupsafe amd64 2.1.5-1+b2 [13.9 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 python3-rpds-py amd64 0.21.0-2 [287 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 python3-referencing all 0.35.1-1 [23.5 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B] Get: 109 http://deb.debian.org/debian trixie/main amd64 python3-jsonschema all 4.19.2-5 [71.4 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 111 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [4738 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-5+b1 [7307 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 8.3.3-1 [249 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 python3-ratelimit all 2.2.1-2 [6108 B] Get: 119 http://deb.debian.org/debian trixie/main amd64 python3-sqlalchemy all 2.0.32+ds1-1 [1196 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB] Fetched 71.2 MB in 2s (29.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (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 ... 19969 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_amd64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:amd64 (3.12.7-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... 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 ... 20289 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-4_all.deb ... Unpacking tzdata (2024b-4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_amd64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (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 ... 21351 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../02-openssl_3.3.2-2_amd64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../03-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../05-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../08-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.40.2-11_amd64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../11-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. 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Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../27-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../32-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../33-python3-more-itertools_10.5.0-1_all.deb ... Unpacking python3-more-itertools (10.5.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../34-python3-typing-extensions_4.12.2-2_all.deb ... Unpacking python3-typing-extensions (4.12.2-2) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../35-python3-typeguard_4.4.1-1_all.deb ... Unpacking python3-typeguard (4.4.1-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../36-python3-inflect_7.3.1-2_all.deb ... Unpacking python3-inflect (7.3.1-2) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../37-python3-jaraco.context_6.0.0-1_all.deb ... Unpacking python3-jaraco.context (6.0.0-1) ... Selecting previously unselected package python3-jaraco.functools. 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Preparing to unpack .../44-libgfortran5_14.2.0-8_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-8) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../45-liblapack3_3.12.0-4_amd64.deb ... Unpacking liblapack3:amd64 (3.12.0-4) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../46-python3-packaging_24.2-1_all.deb ... Unpacking python3-packaging (24.2-1) ... Selecting previously unselected package python3-pyproject-hooks. Preparing to unpack .../47-python3-pyproject-hooks_1.2.0-1_all.deb ... Unpacking python3-pyproject-hooks (1.2.0-1) ... Selecting previously unselected package python3-toml. Preparing to unpack .../48-python3-toml_0.10.2-1_all.deb ... Unpacking python3-toml (0.10.2-1) ... Selecting previously unselected package python3-wheel. Preparing to unpack .../49-python3-wheel_0.45.1-1_all.deb ... Unpacking python3-wheel (0.45.1-1) ... Selecting previously unselected package python3-build. 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Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Jan 7 11:42:01 UTC 2026. Universal Time is now: Wed Jan 7 11:42:01 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libgfortran5:amd64 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up netbase (6.4) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up openssl (3.3.2-2) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... 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 (1.14.0-1) ... Setting up liblapack3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up libpython3.12-stdlib:amd64 (3.12.7-3) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up python3-sortedcontainers (2.4.0-2) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b2) ... Setting up python3-wheel (0.45.1-1) ... Setting up python3-annotated-types (0.7.0-1) ... Setting up python3-tz (2024.1-2) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.2-1) ... Setting up python3-pyproject-hooks (1.2.0-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-certifi (2024.8.30+dfsg-1) ... Setting up python3-multisplitby (0.0.1-6) ... Setting up python3-greenlet (3.1.0-1+b1) ... Setting up python3-idna (3.8-2) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-installer (0.7.0+dfsg1-3) ... Setting up python3-urllib3 (2.2.3-3) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-rpds-py (0.21.0-2) ... Setting up python3-dnspython (2.6.1-1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-email-validator (2.2.0-1) ... Setting up python3-build (1.2.2-1) ... Setting up python3-trie (0.4.0+ds-1) ... Setting up python3-ratelimit (2.2.1-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (23.2.0-2) ... Setting up python3-pydantic-core (2.27.1-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-colorama (0.4.6-4) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3-pytest (8.3.3-1) ... Setting up python3-tqdm (4.67.1-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-tabulate (0.9.0-1) ... Setting up python3-all (3.12.6-1) ... Setting up python3-click (8.1.7-2) ... Setting up python3-sqlalchemy (2.0.32+ds1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pydantic (2.10.2-1) ... Setting up python3-click-plugins (1.1.1-4) ... Setting up python3-curies (0.9.0-1) ... Setting up python3-referencing (0.35.1-1) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-setuptools (74.1.2-2) ... Setting up python3-networkx (3.2.1-5) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up python3-pystow (0.5.5-1) ... Setting up python3-requests-file (2.0.0-1) ... Setting up python3-humanize (4.11.0-1) ... Setting up python3-jsonschema-specifications (2023.12.1-2) ... Setting up dh-python (6.20241024) ... Setting up pybuild-plugin-pyproject (6.20241024) ... Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5+b1) ... Setting up python3-bioregistry (0.11.12-3) ... Setting up python3-pandas (2.2.3+dfsg-5) ... Setting up python3-bel-resources (0.0.3-4) ... Setting up python3-jsonschema (4.19.2-5) ... Processing triggers for libc-bin (2.40-3) ... 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: user script /srv/workspace/pbuilder/492424/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/492424/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/pybel-0.15.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../pybel_0.15.5-1_source.changes dpkg-buildpackage: info: source package pybel dpkg-buildpackage: info: source version 0.15.5-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Alexandre Detiste dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from pybel-0.15.5/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/pybel-0.15.5' dh_auto_clean rm -rf src/PyBEL.egg-info/ src/pybel.egg-info/ make[1]: Leaving directory '/build/reproducible-path/pybel-0.15.5' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild dh_auto_build -O--buildsystem=pybuild I: pybuild plugin_pyproject:129: Building wheel for python3.12 with "build" module I: pybuild base:311: python3.12 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.12_pybel * Building wheel... running bdist_wheel running build running build_py creating build creating build/lib creating build/lib/pybel copying src/pybel/config.py -> build/lib/pybel copying src/pybel/version.py -> build/lib/pybel copying src/pybel/tokens.py -> build/lib/pybel copying src/pybel/grounding.py -> build/lib/pybel copying src/pybel/__main__.py -> build/lib/pybel copying src/pybel/cli.py -> build/lib/pybel copying src/pybel/utils.py -> build/lib/pybel copying src/pybel/typing.py -> build/lib/pybel copying src/pybel/repository.py -> build/lib/pybel copying src/pybel/__init__.py -> build/lib/pybel copying src/pybel/constants.py -> build/lib/pybel copying src/pybel/exceptions.py -> build/lib/pybel copying src/pybel/language.py -> build/lib/pybel copying src/pybel/canonicalize.py -> build/lib/pybel creating build/lib/pybel/parser copying src/pybel/parser/parse_control.py -> build/lib/pybel/parser copying src/pybel/parser/parse_concept.py -> build/lib/pybel/parser copying src/pybel/parser/baseparser.py -> build/lib/pybel/parser copying src/pybel/parser/parse_metadata.py -> build/lib/pybel/parser copying src/pybel/parser/utils.py -> build/lib/pybel/parser copying src/pybel/parser/parse_bel.py -> build/lib/pybel/parser copying src/pybel/parser/__init__.py -> build/lib/pybel/parser copying src/pybel/parser/constants.py -> build/lib/pybel/parser creating build/lib/pybel/manager copying src/pybel/manager/cache_manager.py -> build/lib/pybel/manager copying src/pybel/manager/utils.py -> build/lib/pybel/manager copying src/pybel/manager/query_manager.py -> build/lib/pybel/manager copying src/pybel/manager/models.py -> build/lib/pybel/manager copying src/pybel/manager/lookup_manager.py -> build/lib/pybel/manager copying src/pybel/manager/base_manager.py -> build/lib/pybel/manager copying src/pybel/manager/exc.py -> build/lib/pybel/manager copying src/pybel/manager/__init__.py -> build/lib/pybel/manager copying src/pybel/manager/citation_utils.py -> build/lib/pybel/manager copying src/pybel/manager/make_json_serializable.py -> build/lib/pybel/manager copying src/pybel/manager/database_io.py -> build/lib/pybel/manager creating build/lib/pybel/schema copying src/pybel/schema/__init__.py -> build/lib/pybel/schema creating build/lib/pybel/io copying src/pybel/io/umbrella_nodelink.py -> build/lib/pybel/io copying src/pybel/io/gpickle.py -> build/lib/pybel/io copying src/pybel/io/emmaa.py -> build/lib/pybel/io copying src/pybel/io/graphml.py -> build/lib/pybel/io copying src/pybel/io/indra.py -> build/lib/pybel/io copying src/pybel/io/api.py -> build/lib/pybel/io copying src/pybel/io/utils.py -> build/lib/pybel/io copying src/pybel/io/nodelink.py -> build/lib/pybel/io copying src/pybel/io/neo4j.py -> build/lib/pybel/io copying src/pybel/io/lines.py -> build/lib/pybel/io copying src/pybel/io/aws.py -> build/lib/pybel/io copying src/pybel/io/cx.py -> build/lib/pybel/io copying src/pybel/io/extras.py -> build/lib/pybel/io copying src/pybel/io/exc.py -> build/lib/pybel/io copying src/pybel/io/fraunhofer_orientdb.py -> build/lib/pybel/io copying src/pybel/io/pynpa.py -> build/lib/pybel/io copying src/pybel/io/jgif.py -> build/lib/pybel/io copying src/pybel/io/__init__.py -> build/lib/pybel/io copying src/pybel/io/jinja_utils.py -> build/lib/pybel/io copying src/pybel/io/spia.py -> build/lib/pybel/io copying src/pybel/io/sbel.py -> build/lib/pybel/io copying src/pybel/io/pykeen.py -> build/lib/pybel/io copying src/pybel/io/line_utils.py -> build/lib/pybel/io copying src/pybel/io/bel_commons_client.py -> build/lib/pybel/io copying src/pybel/io/graphdati.py -> build/lib/pybel/io copying src/pybel/io/hipathia.py -> build/lib/pybel/io copying src/pybel/io/biodati_client.py -> build/lib/pybel/io creating build/lib/pybel/struct copying src/pybel/struct/getters.py -> build/lib/pybel/struct copying src/pybel/struct/operations.py -> build/lib/pybel/struct copying src/pybel/struct/graph.py -> build/lib/pybel/struct copying src/pybel/struct/node_utils.py -> build/lib/pybel/struct copying src/pybel/struct/utils.py -> build/lib/pybel/struct copying src/pybel/struct/__init__.py -> build/lib/pybel/struct creating build/lib/pybel/testing copying src/pybel/testing/mocks.py -> build/lib/pybel/testing copying src/pybel/testing/utils.py -> build/lib/pybel/testing copying src/pybel/testing/mock_manager.py -> build/lib/pybel/testing copying src/pybel/testing/generate.py -> build/lib/pybel/testing copying src/pybel/testing/__init__.py -> build/lib/pybel/testing copying src/pybel/testing/constants.py -> build/lib/pybel/testing copying src/pybel/testing/cases.py -> build/lib/pybel/testing creating build/lib/pybel/dsl copying src/pybel/dsl/node_classes.py -> build/lib/pybel/dsl copying src/pybel/dsl/exc.py -> build/lib/pybel/dsl copying src/pybel/dsl/__init__.py -> build/lib/pybel/dsl copying src/pybel/dsl/constants.py -> build/lib/pybel/dsl copying src/pybel/dsl/edges.py -> build/lib/pybel/dsl copying src/pybel/dsl/namespaces.py -> build/lib/pybel/dsl creating build/lib/pybel/resources copying src/pybel/resources/update_resources.py -> build/lib/pybel/resources copying src/pybel/resources/__init__.py -> build/lib/pybel/resources copying src/pybel/resources/constants.py -> build/lib/pybel/resources copying src/pybel/resources/resources.py -> build/lib/pybel/resources creating build/lib/pybel/examples copying src/pybel/examples/vegf_example.py -> build/lib/pybel/examples copying src/pybel/examples/statin_example.py -> build/lib/pybel/examples copying src/pybel/examples/sialic_acid_example.py -> build/lib/pybel/examples copying src/pybel/examples/egf_example.py -> build/lib/pybel/examples copying src/pybel/examples/various_example.py -> build/lib/pybel/examples copying src/pybel/examples/homology_example.py -> build/lib/pybel/examples copying src/pybel/examples/ampk_example.py -> build/lib/pybel/examples copying src/pybel/examples/__init__.py -> build/lib/pybel/examples copying src/pybel/examples/tloc_example.py -> build/lib/pybel/examples copying src/pybel/examples/braf_example.py -> build/lib/pybel/examples creating build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/fragment.py -> build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/protein_substitution.py -> build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/truncation.py -> build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/gene_modification.py -> build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/variant.py -> build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/__init__.py -> build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/constants.py -> build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/fusion.py -> build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/gene_substitution.py -> build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/protein_modification.py -> build/lib/pybel/parser/modifiers copying src/pybel/parser/modifiers/location.py -> build/lib/pybel/parser/modifiers creating build/lib/pybel/io/hetionet copying src/pybel/io/hetionet/__main__.py -> build/lib/pybel/io/hetionet copying src/pybel/io/hetionet/cli.py -> build/lib/pybel/io/hetionet copying src/pybel/io/hetionet/hetionet.py -> build/lib/pybel/io/hetionet copying src/pybel/io/hetionet/__init__.py -> build/lib/pybel/io/hetionet copying src/pybel/io/hetionet/constants.py -> build/lib/pybel/io/hetionet creating build/lib/pybel/io/jupyter copying src/pybel/io/jupyter/__init__.py -> build/lib/pybel/io/jupyter copying src/pybel/io/jupyter/inline.py -> build/lib/pybel/io/jupyter copying src/pybel/io/jupyter/constants.py -> build/lib/pybel/io/jupyter copying src/pybel/io/jupyter/visualization.py -> build/lib/pybel/io/jupyter creating build/lib/pybel/io/tsv copying src/pybel/io/tsv/converters.py -> build/lib/pybel/io/tsv copying src/pybel/io/tsv/api.py -> build/lib/pybel/io/tsv copying src/pybel/io/tsv/__init__.py -> build/lib/pybel/io/tsv creating build/lib/pybel/io/triples copying src/pybel/io/triples/converters.py -> build/lib/pybel/io/triples copying src/pybel/io/triples/api.py -> build/lib/pybel/io/triples copying src/pybel/io/triples/__init__.py -> build/lib/pybel/io/triples creating build/lib/pybel/struct/filters copying src/pybel/struct/filters/node_filters.py -> build/lib/pybel/struct/filters copying src/pybel/struct/filters/utils.py -> build/lib/pybel/struct/filters copying src/pybel/struct/filters/node_predicate_builders.py -> build/lib/pybel/struct/filters copying src/pybel/struct/filters/typing.py -> build/lib/pybel/struct/filters copying src/pybel/struct/filters/edge_predicates.py -> build/lib/pybel/struct/filters copying src/pybel/struct/filters/edge_predicate_builders.py -> build/lib/pybel/struct/filters copying src/pybel/struct/filters/__init__.py -> build/lib/pybel/struct/filters copying src/pybel/struct/filters/edge_filters.py -> build/lib/pybel/struct/filters creating build/lib/pybel/struct/query copying src/pybel/struct/query/query.py -> build/lib/pybel/struct/query copying src/pybel/struct/query/exc.py -> build/lib/pybel/struct/query copying src/pybel/struct/query/seeding.py -> build/lib/pybel/struct/query copying src/pybel/struct/query/__init__.py -> build/lib/pybel/struct/query copying src/pybel/struct/query/constants.py -> build/lib/pybel/struct/query copying src/pybel/struct/query/selection.py -> build/lib/pybel/struct/query creating build/lib/pybel/struct/summary copying src/pybel/struct/summary/edge_summary.py -> build/lib/pybel/struct/summary copying src/pybel/struct/summary/errors.py -> build/lib/pybel/struct/summary copying src/pybel/struct/summary/node_summary.py -> build/lib/pybel/struct/summary copying src/pybel/struct/summary/__init__.py -> build/lib/pybel/struct/summary copying src/pybel/struct/summary/provenance.py -> build/lib/pybel/struct/summary copying src/pybel/struct/summary/supersummary.py -> build/lib/pybel/struct/summary creating build/lib/pybel/struct/grouping copying src/pybel/struct/grouping/annotations.py -> build/lib/pybel/struct/grouping copying src/pybel/struct/grouping/__init__.py -> build/lib/pybel/struct/grouping copying src/pybel/struct/grouping/provenance.py -> build/lib/pybel/struct/grouping creating build/lib/pybel/struct/mutation copying src/pybel/struct/mutation/utils.py -> build/lib/pybel/struct/mutation copying src/pybel/struct/mutation/induction_expansion.py -> build/lib/pybel/struct/mutation copying src/pybel/struct/mutation/__init__.py -> build/lib/pybel/struct/mutation copying src/pybel/struct/mutation/metadata.py -> build/lib/pybel/struct/mutation creating build/lib/pybel/struct/pipeline copying src/pybel/struct/pipeline/pipeline.py -> build/lib/pybel/struct/pipeline copying src/pybel/struct/pipeline/decorators.py -> build/lib/pybel/struct/pipeline copying src/pybel/struct/pipeline/exc.py -> build/lib/pybel/struct/pipeline copying src/pybel/struct/pipeline/__init__.py -> build/lib/pybel/struct/pipeline creating build/lib/pybel/struct/filters/node_predicates copying src/pybel/struct/filters/node_predicates/modifications.py -> build/lib/pybel/struct/filters/node_predicates copying src/pybel/struct/filters/node_predicates/activities.py -> build/lib/pybel/struct/filters/node_predicates copying src/pybel/struct/filters/node_predicates/misc.py -> build/lib/pybel/struct/filters/node_predicates copying src/pybel/struct/filters/node_predicates/utils.py -> build/lib/pybel/struct/filters/node_predicates copying src/pybel/struct/filters/node_predicates/__init__.py -> build/lib/pybel/struct/filters/node_predicates copying src/pybel/struct/filters/node_predicates/relations.py -> build/lib/pybel/struct/filters/node_predicates copying src/pybel/struct/filters/node_predicates/types.py -> build/lib/pybel/struct/filters/node_predicates creating build/lib/pybel/struct/mutation/deletion copying src/pybel/struct/mutation/deletion/protein_rna_origins.py -> build/lib/pybel/struct/mutation/deletion copying src/pybel/struct/mutation/deletion/deletion.py -> build/lib/pybel/struct/mutation/deletion copying src/pybel/struct/mutation/deletion/__init__.py -> build/lib/pybel/struct/mutation/deletion creating build/lib/pybel/struct/mutation/collapse copying src/pybel/struct/mutation/collapse/protein_rna_origins.py -> build/lib/pybel/struct/mutation/collapse copying src/pybel/struct/mutation/collapse/collapse.py -> build/lib/pybel/struct/mutation/collapse copying src/pybel/struct/mutation/collapse/__init__.py -> build/lib/pybel/struct/mutation/collapse creating build/lib/pybel/struct/mutation/inference copying src/pybel/struct/mutation/inference/protein_rna_origins.py -> build/lib/pybel/struct/mutation/inference copying src/pybel/struct/mutation/inference/transfer.py -> build/lib/pybel/struct/mutation/inference copying src/pybel/struct/mutation/inference/__init__.py -> build/lib/pybel/struct/mutation/inference creating build/lib/pybel/struct/mutation/expansion copying src/pybel/struct/mutation/expansion/upstream.py -> build/lib/pybel/struct/mutation/expansion copying src/pybel/struct/mutation/expansion/__init__.py -> build/lib/pybel/struct/mutation/expansion copying src/pybel/struct/mutation/expansion/neighborhood.py -> build/lib/pybel/struct/mutation/expansion creating build/lib/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/annotations.py -> build/lib/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/citation.py -> build/lib/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/utils.py -> build/lib/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/upstream.py -> build/lib/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/random_subgraph.py -> build/lib/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/__init__.py -> build/lib/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/paths.py -> build/lib/pybel/struct/mutation/induction copying src/pybel/struct/mutation/induction/neighborhood.py -> build/lib/pybel/struct/mutation/induction running egg_info creating src/pybel.egg-info writing src/pybel.egg-info/PKG-INFO writing dependency_links to src/pybel.egg-info/dependency_links.txt writing entry points to src/pybel.egg-info/entry_points.txt writing requirements to src/pybel.egg-info/requires.txt writing top-level names to src/pybel.egg-info/top_level.txt writing manifest file 'src/pybel.egg-info/SOURCES.txt' reading manifest file 'src/pybel.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching 'scripts' no previously-included directories found matching 'notebooks' warning: no files found matching '*.bel' under directory 'src/pybel/testing/bel' warning: no files found matching '*.belanno' under directory 'src/pybel/testing/belanno' warning: no files found matching '*.belns' under directory 'src/pybel/testing/belns' warning: no previously-included files matching '*.py[cod]' found anywhere in distribution warning: no previously-included files matching '__pycache__' found anywhere in distribution warning: no previously-included files matching '*.so' found anywhere in distribution warning: no previously-included files matching '*.dylib' found anywhere in distribution warning: no previously-included files matching '.DS_Store' found anywhere in distribution warning: no previously-included files matching '*.gpickle' found anywhere in distribution warning: no previously-included files found matching '.bumpversion.cfg' warning: no previously-included files found matching '.readthedocs.yml' warning: no previously-included files found matching '.flake8' warning: no previously-included files found matching 'tox.ini' warning: no previously-included files found matching 'CONTRIBUTING.md' warning: no previously-included files found matching 'CHANGELOG.rst' warning: no previously-included files found matching 'AUTHORS.rst' adding license file 'LICENSE' writing manifest file 'src/pybel.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'pybel.apps' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybel.apps' 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 'pybel.apps' 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 'pybel.apps' to be distributed and are already explicitly excluding 'pybel.apps' 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:218: _Warning: Package 'pybel.io.jupyter.templates' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybel.io.jupyter.templates' 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 'pybel.io.jupyter.templates' 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 'pybel.io.jupyter.templates' to be distributed and are already explicitly excluding 'pybel.io.jupyter.templates' 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:218: _Warning: Package 'pybel.schema.node_types' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybel.schema.node_types' 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 'pybel.schema.node_types' 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 'pybel.schema.node_types' to be distributed and are already explicitly excluding 'pybel.schema.node_types' 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:218: _Warning: Package 'pybel.schema.node_types.variants' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybel.schema.node_types.variants' 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 'pybel.schema.node_types.variants' 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 'pybel.schema.node_types.variants' to be distributed and are already explicitly excluding 'pybel.schema.node_types.variants' 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:218: _Warning: Package 'pybel.schema.node_types.variants.hgvs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybel.schema.node_types.variants.hgvs' 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 'pybel.schema.node_types.variants.hgvs' 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 'pybel.schema.node_types.variants.hgvs' to be distributed and are already explicitly excluding 'pybel.schema.node_types.variants.hgvs' 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:218: _Warning: Package 'pybel.testing.resources.bel' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybel.testing.resources.bel' 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 'pybel.testing.resources.bel' 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 'pybel.testing.resources.bel' to be distributed and are already explicitly excluding 'pybel.testing.resources.bel' 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:218: _Warning: Package 'pybel.testing.resources.belanno' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybel.testing.resources.belanno' 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 'pybel.testing.resources.belanno' 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 'pybel.testing.resources.belanno' to be distributed and are already explicitly excluding 'pybel.testing.resources.belanno' 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:218: _Warning: Package 'pybel.testing.resources.belns' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybel.testing.resources.belns' 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 'pybel.testing.resources.belns' 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 'pybel.testing.resources.belns' to be distributed and are already explicitly excluding 'pybel.testing.resources.belns' 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) creating build/lib/pybel/apps copying src/pybel/apps/parser.py -> build/lib/pybel/apps copying src/pybel/schema/base_node.schema.json -> build/lib/pybel/schema copying src/pybel/schema/edge.schema.json -> build/lib/pybel/schema copying src/pybel/schema/entity.schema.json -> build/lib/pybel/schema copying src/pybel/schema/modifier.schema.json -> build/lib/pybel/schema creating build/lib/pybel/schema/node_types copying src/pybel/schema/node_types/base_abundance.schema.json -> build/lib/pybel/schema/node_types copying src/pybel/schema/node_types/fusion.schema.json -> build/lib/pybel/schema/node_types copying src/pybel/schema/node_types/fusion_range.schema.json -> build/lib/pybel/schema/node_types copying src/pybel/schema/node_types/list_abundance.schema.json -> build/lib/pybel/schema/node_types copying src/pybel/schema/node_types/reaction.schema.json -> build/lib/pybel/schema/node_types creating build/lib/pybel/schema/node_types/variants copying src/pybel/schema/node_types/variants/base_variant.schema.json -> build/lib/pybel/schema/node_types/variants copying src/pybel/schema/node_types/variants/fragment.schema.json -> build/lib/pybel/schema/node_types/variants copying src/pybel/schema/node_types/variants/gene_mod.schema.json -> build/lib/pybel/schema/node_types/variants copying src/pybel/schema/node_types/variants/protein_mod.schema.json -> build/lib/pybel/schema/node_types/variants creating build/lib/pybel/schema/node_types/variants/hgvs copying src/pybel/schema/node_types/variants/hgvs/base_hgvs.schema.json -> build/lib/pybel/schema/node_types/variants/hgvs copying src/pybel/schema/node_types/variants/hgvs/gene_hgvs.schema.json -> build/lib/pybel/schema/node_types/variants/hgvs copying src/pybel/schema/node_types/variants/hgvs/protein_hgvs.schema.json -> build/lib/pybel/schema/node_types/variants/hgvs copying src/pybel/schema/node_types/variants/hgvs/rna_hgvs.schema.json -> build/lib/pybel/schema/node_types/variants/hgvs creating build/lib/pybel/testing/resources creating build/lib/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/Cytotoxic T-cell Signaling-2.0-Hs.json -> build/lib/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/isolated.bel -> build/lib/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/misordered.bel -> build/lib/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/obo.bel -> build/lib/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/slushy.bel -> build/lib/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/test_bel.bel -> build/lib/pybel/testing/resources/bel copying src/pybel/testing/resources/bel/thorough.bel -> build/lib/pybel/testing/resources/bel creating build/lib/pybel/testing/resources/belanno copying src/pybel/testing/resources/belanno/cell-line.belanno -> build/lib/pybel/testing/resources/belanno copying src/pybel/testing/resources/belanno/confidence-1.0.0.belanno -> build/lib/pybel/testing/resources/belanno copying src/pybel/testing/resources/belanno/mesh-diseases.belanno -> build/lib/pybel/testing/resources/belanno copying src/pybel/testing/resources/belanno/species-taxonomy-id.belanno -> build/lib/pybel/testing/resources/belanno copying src/pybel/testing/resources/belanno/test_an_1.belanno -> build/lib/pybel/testing/resources/belanno creating build/lib/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/chebi-names.belns -> build/lib/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/disease-ontology.belns -> build/lib/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/go-names.belns -> build/lib/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/hgnc-names.belns -> build/lib/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/mesh-names.belns -> build/lib/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/test_ns_1.belns -> build/lib/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/test_ns_1_updated.belns -> build/lib/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/test_ns_2.belns -> build/lib/pybel/testing/resources/belns copying src/pybel/testing/resources/belns/test_ns_empty.belns -> build/lib/pybel/testing/resources/belns creating build/lib/pybel/io/jupyter/templates copying src/pybel/io/jupyter/templates/graph_template.html -> build/lib/pybel/io/jupyter/templates copying src/pybel/io/jupyter/templates/pybel_jupyter.js -> build/lib/pybel/io/jupyter/templates copying src/pybel/io/jupyter/templates/pybel_vis.js -> build/lib/pybel/io/jupyter/templates installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/pybel copying build/lib/pybel/config.py -> build/bdist.linux-x86_64/wheel/./pybel creating build/bdist.linux-x86_64/wheel/pybel/parser copying build/lib/pybel/parser/parse_control.py -> build/bdist.linux-x86_64/wheel/./pybel/parser copying build/lib/pybel/parser/parse_concept.py -> build/bdist.linux-x86_64/wheel/./pybel/parser copying build/lib/pybel/parser/baseparser.py -> build/bdist.linux-x86_64/wheel/./pybel/parser creating build/bdist.linux-x86_64/wheel/pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/fragment.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/protein_substitution.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/truncation.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/gene_modification.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/variant.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/constants.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/fusion.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/gene_substitution.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/protein_modification.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/modifiers/location.py -> build/bdist.linux-x86_64/wheel/./pybel/parser/modifiers copying build/lib/pybel/parser/parse_metadata.py -> build/bdist.linux-x86_64/wheel/./pybel/parser copying build/lib/pybel/parser/utils.py -> build/bdist.linux-x86_64/wheel/./pybel/parser copying build/lib/pybel/parser/parse_bel.py -> build/bdist.linux-x86_64/wheel/./pybel/parser copying build/lib/pybel/parser/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/parser copying build/lib/pybel/parser/constants.py -> build/bdist.linux-x86_64/wheel/./pybel/parser creating build/bdist.linux-x86_64/wheel/pybel/apps copying build/lib/pybel/apps/parser.py -> build/bdist.linux-x86_64/wheel/./pybel/apps copying build/lib/pybel/version.py -> build/bdist.linux-x86_64/wheel/./pybel copying build/lib/pybel/tokens.py -> build/bdist.linux-x86_64/wheel/./pybel creating build/bdist.linux-x86_64/wheel/pybel/manager copying build/lib/pybel/manager/cache_manager.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/manager/utils.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/manager/query_manager.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/manager/models.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/manager/lookup_manager.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/manager/base_manager.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/manager/exc.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/manager/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/manager/citation_utils.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/manager/make_json_serializable.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/manager/database_io.py -> build/bdist.linux-x86_64/wheel/./pybel/manager copying build/lib/pybel/grounding.py -> build/bdist.linux-x86_64/wheel/./pybel creating build/bdist.linux-x86_64/wheel/pybel/schema copying build/lib/pybel/schema/base_node.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema copying build/lib/pybel/schema/edge.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema creating build/bdist.linux-x86_64/wheel/pybel/schema/node_types copying build/lib/pybel/schema/node_types/reaction.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types copying build/lib/pybel/schema/node_types/fusion.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types creating build/bdist.linux-x86_64/wheel/pybel/schema/node_types/variants copying build/lib/pybel/schema/node_types/variants/gene_mod.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types/variants copying build/lib/pybel/schema/node_types/variants/protein_mod.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types/variants copying build/lib/pybel/schema/node_types/variants/fragment.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types/variants creating build/bdist.linux-x86_64/wheel/pybel/schema/node_types/variants/hgvs copying build/lib/pybel/schema/node_types/variants/hgvs/gene_hgvs.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types/variants/hgvs copying build/lib/pybel/schema/node_types/variants/hgvs/rna_hgvs.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types/variants/hgvs copying build/lib/pybel/schema/node_types/variants/hgvs/base_hgvs.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types/variants/hgvs copying build/lib/pybel/schema/node_types/variants/hgvs/protein_hgvs.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types/variants/hgvs copying build/lib/pybel/schema/node_types/variants/base_variant.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types/variants copying build/lib/pybel/schema/node_types/base_abundance.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types copying build/lib/pybel/schema/node_types/fusion_range.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types copying build/lib/pybel/schema/node_types/list_abundance.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema/node_types copying build/lib/pybel/schema/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/schema copying build/lib/pybel/schema/modifier.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema copying build/lib/pybel/schema/entity.schema.json -> build/bdist.linux-x86_64/wheel/./pybel/schema copying build/lib/pybel/__main__.py -> build/bdist.linux-x86_64/wheel/./pybel copying build/lib/pybel/cli.py -> build/bdist.linux-x86_64/wheel/./pybel copying build/lib/pybel/utils.py -> build/bdist.linux-x86_64/wheel/./pybel creating build/bdist.linux-x86_64/wheel/pybel/io copying build/lib/pybel/io/umbrella_nodelink.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/gpickle.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/emmaa.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/graphml.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/indra.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/api.py -> build/bdist.linux-x86_64/wheel/./pybel/io creating build/bdist.linux-x86_64/wheel/pybel/io/hetionet copying build/lib/pybel/io/hetionet/__main__.py -> build/bdist.linux-x86_64/wheel/./pybel/io/hetionet copying build/lib/pybel/io/hetionet/cli.py -> build/bdist.linux-x86_64/wheel/./pybel/io/hetionet copying build/lib/pybel/io/hetionet/hetionet.py -> build/bdist.linux-x86_64/wheel/./pybel/io/hetionet copying build/lib/pybel/io/hetionet/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/io/hetionet copying build/lib/pybel/io/hetionet/constants.py -> build/bdist.linux-x86_64/wheel/./pybel/io/hetionet copying build/lib/pybel/io/utils.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/nodelink.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/neo4j.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/lines.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/aws.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/cx.py -> build/bdist.linux-x86_64/wheel/./pybel/io creating build/bdist.linux-x86_64/wheel/pybel/io/jupyter copying build/lib/pybel/io/jupyter/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/io/jupyter copying build/lib/pybel/io/jupyter/inline.py -> build/bdist.linux-x86_64/wheel/./pybel/io/jupyter copying build/lib/pybel/io/jupyter/constants.py -> build/bdist.linux-x86_64/wheel/./pybel/io/jupyter creating build/bdist.linux-x86_64/wheel/pybel/io/jupyter/templates copying build/lib/pybel/io/jupyter/templates/pybel_jupyter.js -> build/bdist.linux-x86_64/wheel/./pybel/io/jupyter/templates copying build/lib/pybel/io/jupyter/templates/graph_template.html -> build/bdist.linux-x86_64/wheel/./pybel/io/jupyter/templates copying build/lib/pybel/io/jupyter/templates/pybel_vis.js -> build/bdist.linux-x86_64/wheel/./pybel/io/jupyter/templates copying build/lib/pybel/io/jupyter/visualization.py -> build/bdist.linux-x86_64/wheel/./pybel/io/jupyter copying build/lib/pybel/io/extras.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/exc.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/fraunhofer_orientdb.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/pynpa.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/jgif.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/jinja_utils.py -> build/bdist.linux-x86_64/wheel/./pybel/io creating build/bdist.linux-x86_64/wheel/pybel/io/tsv copying build/lib/pybel/io/tsv/converters.py -> build/bdist.linux-x86_64/wheel/./pybel/io/tsv copying build/lib/pybel/io/tsv/api.py -> build/bdist.linux-x86_64/wheel/./pybel/io/tsv copying build/lib/pybel/io/tsv/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/io/tsv copying build/lib/pybel/io/spia.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/sbel.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/pykeen.py -> build/bdist.linux-x86_64/wheel/./pybel/io creating build/bdist.linux-x86_64/wheel/pybel/io/triples copying build/lib/pybel/io/triples/converters.py -> build/bdist.linux-x86_64/wheel/./pybel/io/triples copying build/lib/pybel/io/triples/api.py -> build/bdist.linux-x86_64/wheel/./pybel/io/triples copying build/lib/pybel/io/triples/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/io/triples copying build/lib/pybel/io/line_utils.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/bel_commons_client.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/graphdati.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/hipathia.py -> build/bdist.linux-x86_64/wheel/./pybel/io copying build/lib/pybel/io/biodati_client.py -> build/bdist.linux-x86_64/wheel/./pybel/io creating build/bdist.linux-x86_64/wheel/pybel/struct creating build/bdist.linux-x86_64/wheel/pybel/struct/filters copying build/lib/pybel/struct/filters/node_filters.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters creating build/bdist.linux-x86_64/wheel/pybel/struct/filters/node_predicates copying build/lib/pybel/struct/filters/node_predicates/modifications.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters/node_predicates copying build/lib/pybel/struct/filters/node_predicates/activities.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters/node_predicates copying build/lib/pybel/struct/filters/node_predicates/misc.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters/node_predicates copying build/lib/pybel/struct/filters/node_predicates/utils.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters/node_predicates copying build/lib/pybel/struct/filters/node_predicates/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters/node_predicates copying build/lib/pybel/struct/filters/node_predicates/relations.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters/node_predicates copying build/lib/pybel/struct/filters/node_predicates/types.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters/node_predicates copying build/lib/pybel/struct/filters/utils.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters copying build/lib/pybel/struct/filters/node_predicate_builders.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters copying build/lib/pybel/struct/filters/typing.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters copying build/lib/pybel/struct/filters/edge_predicates.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters copying build/lib/pybel/struct/filters/edge_predicate_builders.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters copying build/lib/pybel/struct/filters/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters copying build/lib/pybel/struct/filters/edge_filters.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/filters copying build/lib/pybel/struct/getters.py -> build/bdist.linux-x86_64/wheel/./pybel/struct copying build/lib/pybel/struct/operations.py -> build/bdist.linux-x86_64/wheel/./pybel/struct creating build/bdist.linux-x86_64/wheel/pybel/struct/query copying build/lib/pybel/struct/query/query.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/query copying build/lib/pybel/struct/query/exc.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/query copying build/lib/pybel/struct/query/seeding.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/query copying build/lib/pybel/struct/query/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/query copying build/lib/pybel/struct/query/constants.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/query copying build/lib/pybel/struct/query/selection.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/query copying build/lib/pybel/struct/graph.py -> build/bdist.linux-x86_64/wheel/./pybel/struct copying build/lib/pybel/struct/node_utils.py -> build/bdist.linux-x86_64/wheel/./pybel/struct copying build/lib/pybel/struct/utils.py -> build/bdist.linux-x86_64/wheel/./pybel/struct creating build/bdist.linux-x86_64/wheel/pybel/struct/summary copying build/lib/pybel/struct/summary/edge_summary.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/summary copying build/lib/pybel/struct/summary/errors.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/summary copying build/lib/pybel/struct/summary/node_summary.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/summary copying build/lib/pybel/struct/summary/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/summary copying build/lib/pybel/struct/summary/provenance.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/summary copying build/lib/pybel/struct/summary/supersummary.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/summary creating build/bdist.linux-x86_64/wheel/pybel/struct/grouping copying build/lib/pybel/struct/grouping/annotations.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/grouping copying build/lib/pybel/struct/grouping/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/grouping copying build/lib/pybel/struct/grouping/provenance.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/grouping creating build/bdist.linux-x86_64/wheel/pybel/struct/mutation creating build/bdist.linux-x86_64/wheel/pybel/struct/mutation/deletion copying build/lib/pybel/struct/mutation/deletion/protein_rna_origins.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/deletion copying build/lib/pybel/struct/mutation/deletion/deletion.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/deletion copying build/lib/pybel/struct/mutation/deletion/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/deletion copying build/lib/pybel/struct/mutation/utils.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation creating build/bdist.linux-x86_64/wheel/pybel/struct/mutation/collapse copying build/lib/pybel/struct/mutation/collapse/protein_rna_origins.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/collapse copying build/lib/pybel/struct/mutation/collapse/collapse.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/collapse copying build/lib/pybel/struct/mutation/collapse/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/collapse creating build/bdist.linux-x86_64/wheel/pybel/struct/mutation/inference copying build/lib/pybel/struct/mutation/inference/protein_rna_origins.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/inference copying build/lib/pybel/struct/mutation/inference/transfer.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/inference copying build/lib/pybel/struct/mutation/inference/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/inference copying build/lib/pybel/struct/mutation/induction_expansion.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation creating build/bdist.linux-x86_64/wheel/pybel/struct/mutation/expansion copying build/lib/pybel/struct/mutation/expansion/upstream.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/expansion copying build/lib/pybel/struct/mutation/expansion/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/expansion copying build/lib/pybel/struct/mutation/expansion/neighborhood.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/expansion creating build/bdist.linux-x86_64/wheel/pybel/struct/mutation/induction copying build/lib/pybel/struct/mutation/induction/annotations.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/induction copying build/lib/pybel/struct/mutation/induction/citation.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/induction copying build/lib/pybel/struct/mutation/induction/utils.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/induction copying build/lib/pybel/struct/mutation/induction/upstream.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/induction copying build/lib/pybel/struct/mutation/induction/random_subgraph.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/induction copying build/lib/pybel/struct/mutation/induction/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/induction copying build/lib/pybel/struct/mutation/induction/paths.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/induction copying build/lib/pybel/struct/mutation/induction/neighborhood.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation/induction copying build/lib/pybel/struct/mutation/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation copying build/lib/pybel/struct/mutation/metadata.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/mutation copying build/lib/pybel/struct/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct creating build/bdist.linux-x86_64/wheel/pybel/struct/pipeline copying build/lib/pybel/struct/pipeline/pipeline.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/pipeline copying build/lib/pybel/struct/pipeline/decorators.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/pipeline copying build/lib/pybel/struct/pipeline/exc.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/pipeline copying build/lib/pybel/struct/pipeline/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/struct/pipeline copying build/lib/pybel/typing.py -> build/bdist.linux-x86_64/wheel/./pybel copying build/lib/pybel/repository.py -> build/bdist.linux-x86_64/wheel/./pybel creating build/bdist.linux-x86_64/wheel/pybel/testing copying build/lib/pybel/testing/mocks.py -> build/bdist.linux-x86_64/wheel/./pybel/testing copying build/lib/pybel/testing/utils.py -> build/bdist.linux-x86_64/wheel/./pybel/testing copying build/lib/pybel/testing/mock_manager.py -> build/bdist.linux-x86_64/wheel/./pybel/testing copying build/lib/pybel/testing/generate.py -> build/bdist.linux-x86_64/wheel/./pybel/testing copying build/lib/pybel/testing/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/testing copying build/lib/pybel/testing/constants.py -> build/bdist.linux-x86_64/wheel/./pybel/testing copying build/lib/pybel/testing/cases.py -> build/bdist.linux-x86_64/wheel/./pybel/testing creating build/bdist.linux-x86_64/wheel/pybel/testing/resources creating build/bdist.linux-x86_64/wheel/pybel/testing/resources/belns copying build/lib/pybel/testing/resources/belns/mesh-names.belns -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belns copying build/lib/pybel/testing/resources/belns/go-names.belns -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belns copying build/lib/pybel/testing/resources/belns/test_ns_2.belns -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belns copying build/lib/pybel/testing/resources/belns/test_ns_1.belns -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belns copying build/lib/pybel/testing/resources/belns/test_ns_empty.belns -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belns copying build/lib/pybel/testing/resources/belns/hgnc-names.belns -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belns copying build/lib/pybel/testing/resources/belns/test_ns_1_updated.belns -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belns copying build/lib/pybel/testing/resources/belns/disease-ontology.belns -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belns copying build/lib/pybel/testing/resources/belns/chebi-names.belns -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belns creating build/bdist.linux-x86_64/wheel/pybel/testing/resources/belanno copying build/lib/pybel/testing/resources/belanno/test_an_1.belanno -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belanno copying build/lib/pybel/testing/resources/belanno/mesh-diseases.belanno -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belanno copying build/lib/pybel/testing/resources/belanno/species-taxonomy-id.belanno -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belanno copying build/lib/pybel/testing/resources/belanno/confidence-1.0.0.belanno -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belanno copying build/lib/pybel/testing/resources/belanno/cell-line.belanno -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/belanno creating build/bdist.linux-x86_64/wheel/pybel/testing/resources/bel copying build/lib/pybel/testing/resources/bel/Cytotoxic T-cell Signaling-2.0-Hs.json -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/bel copying build/lib/pybel/testing/resources/bel/test_bel.bel -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/bel copying build/lib/pybel/testing/resources/bel/slushy.bel -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/bel copying build/lib/pybel/testing/resources/bel/isolated.bel -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/bel copying build/lib/pybel/testing/resources/bel/obo.bel -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/bel copying build/lib/pybel/testing/resources/bel/misordered.bel -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/bel copying build/lib/pybel/testing/resources/bel/thorough.bel -> build/bdist.linux-x86_64/wheel/./pybel/testing/resources/bel copying build/lib/pybel/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel copying build/lib/pybel/constants.py -> build/bdist.linux-x86_64/wheel/./pybel creating build/bdist.linux-x86_64/wheel/pybel/dsl copying build/lib/pybel/dsl/node_classes.py -> build/bdist.linux-x86_64/wheel/./pybel/dsl copying build/lib/pybel/dsl/exc.py -> build/bdist.linux-x86_64/wheel/./pybel/dsl copying build/lib/pybel/dsl/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/dsl copying build/lib/pybel/dsl/constants.py -> build/bdist.linux-x86_64/wheel/./pybel/dsl copying build/lib/pybel/dsl/edges.py -> build/bdist.linux-x86_64/wheel/./pybel/dsl copying build/lib/pybel/dsl/namespaces.py -> build/bdist.linux-x86_64/wheel/./pybel/dsl copying build/lib/pybel/exceptions.py -> build/bdist.linux-x86_64/wheel/./pybel copying build/lib/pybel/language.py -> build/bdist.linux-x86_64/wheel/./pybel creating build/bdist.linux-x86_64/wheel/pybel/resources copying build/lib/pybel/resources/update_resources.py -> build/bdist.linux-x86_64/wheel/./pybel/resources copying build/lib/pybel/resources/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/resources copying build/lib/pybel/resources/constants.py -> build/bdist.linux-x86_64/wheel/./pybel/resources copying build/lib/pybel/resources/resources.py -> build/bdist.linux-x86_64/wheel/./pybel/resources creating build/bdist.linux-x86_64/wheel/pybel/examples copying build/lib/pybel/examples/vegf_example.py -> build/bdist.linux-x86_64/wheel/./pybel/examples copying build/lib/pybel/examples/statin_example.py -> build/bdist.linux-x86_64/wheel/./pybel/examples copying build/lib/pybel/examples/sialic_acid_example.py -> build/bdist.linux-x86_64/wheel/./pybel/examples copying build/lib/pybel/examples/egf_example.py -> build/bdist.linux-x86_64/wheel/./pybel/examples copying build/lib/pybel/examples/various_example.py -> build/bdist.linux-x86_64/wheel/./pybel/examples copying build/lib/pybel/examples/homology_example.py -> build/bdist.linux-x86_64/wheel/./pybel/examples copying build/lib/pybel/examples/ampk_example.py -> build/bdist.linux-x86_64/wheel/./pybel/examples copying build/lib/pybel/examples/__init__.py -> build/bdist.linux-x86_64/wheel/./pybel/examples copying build/lib/pybel/examples/tloc_example.py -> build/bdist.linux-x86_64/wheel/./pybel/examples copying build/lib/pybel/examples/braf_example.py -> build/bdist.linux-x86_64/wheel/./pybel/examples copying build/lib/pybel/canonicalize.py -> build/bdist.linux-x86_64/wheel/./pybel running install_egg_info Copying src/pybel.egg-info to build/bdist.linux-x86_64/wheel/./pybel-0.15.5.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/pybel-0.15.5.dist-info/WHEEL creating '/build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.12_pybel/.tmp-d2qm5uc_/pybel-0.15.5-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'pybel/__init__.py' adding 'pybel/__main__.py' adding 'pybel/canonicalize.py' adding 'pybel/cli.py' adding 'pybel/config.py' adding 'pybel/constants.py' adding 'pybel/exceptions.py' adding 'pybel/grounding.py' adding 'pybel/language.py' adding 'pybel/repository.py' adding 'pybel/tokens.py' adding 'pybel/typing.py' adding 'pybel/utils.py' adding 'pybel/version.py' adding 'pybel/apps/parser.py' adding 'pybel/dsl/__init__.py' adding 'pybel/dsl/constants.py' adding 'pybel/dsl/edges.py' adding 'pybel/dsl/exc.py' adding 'pybel/dsl/namespaces.py' adding 'pybel/dsl/node_classes.py' adding 'pybel/examples/__init__.py' adding 'pybel/examples/ampk_example.py' adding 'pybel/examples/braf_example.py' adding 'pybel/examples/egf_example.py' adding 'pybel/examples/homology_example.py' adding 'pybel/examples/sialic_acid_example.py' adding 'pybel/examples/statin_example.py' adding 'pybel/examples/tloc_example.py' adding 'pybel/examples/various_example.py' adding 'pybel/examples/vegf_example.py' adding 'pybel/io/__init__.py' adding 'pybel/io/api.py' adding 'pybel/io/aws.py' adding 'pybel/io/bel_commons_client.py' adding 'pybel/io/biodati_client.py' adding 'pybel/io/cx.py' adding 'pybel/io/emmaa.py' adding 'pybel/io/exc.py' adding 'pybel/io/extras.py' adding 'pybel/io/fraunhofer_orientdb.py' adding 'pybel/io/gpickle.py' adding 'pybel/io/graphdati.py' adding 'pybel/io/graphml.py' adding 'pybel/io/hipathia.py' adding 'pybel/io/indra.py' adding 'pybel/io/jgif.py' adding 'pybel/io/jinja_utils.py' adding 'pybel/io/line_utils.py' adding 'pybel/io/lines.py' adding 'pybel/io/neo4j.py' adding 'pybel/io/nodelink.py' adding 'pybel/io/pykeen.py' adding 'pybel/io/pynpa.py' adding 'pybel/io/sbel.py' adding 'pybel/io/spia.py' adding 'pybel/io/umbrella_nodelink.py' adding 'pybel/io/utils.py' adding 'pybel/io/hetionet/__init__.py' adding 'pybel/io/hetionet/__main__.py' adding 'pybel/io/hetionet/cli.py' adding 'pybel/io/hetionet/constants.py' adding 'pybel/io/hetionet/hetionet.py' adding 'pybel/io/jupyter/__init__.py' adding 'pybel/io/jupyter/constants.py' adding 'pybel/io/jupyter/inline.py' adding 'pybel/io/jupyter/visualization.py' adding 'pybel/io/jupyter/templates/graph_template.html' adding 'pybel/io/jupyter/templates/pybel_jupyter.js' adding 'pybel/io/jupyter/templates/pybel_vis.js' adding 'pybel/io/triples/__init__.py' adding 'pybel/io/triples/api.py' adding 'pybel/io/triples/converters.py' adding 'pybel/io/tsv/__init__.py' adding 'pybel/io/tsv/api.py' adding 'pybel/io/tsv/converters.py' adding 'pybel/manager/__init__.py' adding 'pybel/manager/base_manager.py' adding 'pybel/manager/cache_manager.py' adding 'pybel/manager/citation_utils.py' adding 'pybel/manager/database_io.py' adding 'pybel/manager/exc.py' adding 'pybel/manager/lookup_manager.py' adding 'pybel/manager/make_json_serializable.py' adding 'pybel/manager/models.py' adding 'pybel/manager/query_manager.py' adding 'pybel/manager/utils.py' adding 'pybel/parser/__init__.py' adding 'pybel/parser/baseparser.py' adding 'pybel/parser/constants.py' adding 'pybel/parser/parse_bel.py' adding 'pybel/parser/parse_concept.py' adding 'pybel/parser/parse_control.py' adding 'pybel/parser/parse_metadata.py' adding 'pybel/parser/utils.py' adding 'pybel/parser/modifiers/__init__.py' adding 'pybel/parser/modifiers/constants.py' adding 'pybel/parser/modifiers/fragment.py' adding 'pybel/parser/modifiers/fusion.py' adding 'pybel/parser/modifiers/gene_modification.py' adding 'pybel/parser/modifiers/gene_substitution.py' adding 'pybel/parser/modifiers/location.py' adding 'pybel/parser/modifiers/protein_modification.py' adding 'pybel/parser/modifiers/protein_substitution.py' adding 'pybel/parser/modifiers/truncation.py' adding 'pybel/parser/modifiers/variant.py' adding 'pybel/resources/__init__.py' adding 'pybel/resources/constants.py' adding 'pybel/resources/resources.py' adding 'pybel/resources/update_resources.py' adding 'pybel/schema/__init__.py' adding 'pybel/schema/base_node.schema.json' adding 'pybel/schema/edge.schema.json' adding 'pybel/schema/entity.schema.json' adding 'pybel/schema/modifier.schema.json' adding 'pybel/schema/node_types/base_abundance.schema.json' adding 'pybel/schema/node_types/fusion.schema.json' adding 'pybel/schema/node_types/fusion_range.schema.json' adding 'pybel/schema/node_types/list_abundance.schema.json' adding 'pybel/schema/node_types/reaction.schema.json' adding 'pybel/schema/node_types/variants/base_variant.schema.json' adding 'pybel/schema/node_types/variants/fragment.schema.json' adding 'pybel/schema/node_types/variants/gene_mod.schema.json' adding 'pybel/schema/node_types/variants/protein_mod.schema.json' adding 'pybel/schema/node_types/variants/hgvs/base_hgvs.schema.json' adding 'pybel/schema/node_types/variants/hgvs/gene_hgvs.schema.json' adding 'pybel/schema/node_types/variants/hgvs/protein_hgvs.schema.json' adding 'pybel/schema/node_types/variants/hgvs/rna_hgvs.schema.json' adding 'pybel/struct/__init__.py' adding 'pybel/struct/getters.py' adding 'pybel/struct/graph.py' adding 'pybel/struct/node_utils.py' adding 'pybel/struct/operations.py' adding 'pybel/struct/utils.py' adding 'pybel/struct/filters/__init__.py' adding 'pybel/struct/filters/edge_filters.py' adding 'pybel/struct/filters/edge_predicate_builders.py' adding 'pybel/struct/filters/edge_predicates.py' adding 'pybel/struct/filters/node_filters.py' adding 'pybel/struct/filters/node_predicate_builders.py' adding 'pybel/struct/filters/typing.py' adding 'pybel/struct/filters/utils.py' adding 'pybel/struct/filters/node_predicates/__init__.py' adding 'pybel/struct/filters/node_predicates/activities.py' adding 'pybel/struct/filters/node_predicates/misc.py' adding 'pybel/struct/filters/node_predicates/modifications.py' adding 'pybel/struct/filters/node_predicates/relations.py' adding 'pybel/struct/filters/node_predicates/types.py' adding 'pybel/struct/filters/node_predicates/utils.py' adding 'pybel/struct/grouping/__init__.py' adding 'pybel/struct/grouping/annotations.py' adding 'pybel/struct/grouping/provenance.py' adding 'pybel/struct/mutation/__init__.py' adding 'pybel/struct/mutation/induction_expansion.py' adding 'pybel/struct/mutation/metadata.py' adding 'pybel/struct/mutation/utils.py' adding 'pybel/struct/mutation/collapse/__init__.py' adding 'pybel/struct/mutation/collapse/collapse.py' adding 'pybel/struct/mutation/collapse/protein_rna_origins.py' adding 'pybel/struct/mutation/deletion/__init__.py' adding 'pybel/struct/mutation/deletion/deletion.py' adding 'pybel/struct/mutation/deletion/protein_rna_origins.py' adding 'pybel/struct/mutation/expansion/__init__.py' adding 'pybel/struct/mutation/expansion/neighborhood.py' adding 'pybel/struct/mutation/expansion/upstream.py' adding 'pybel/struct/mutation/induction/__init__.py' adding 'pybel/struct/mutation/induction/annotations.py' adding 'pybel/struct/mutation/induction/citation.py' adding 'pybel/struct/mutation/induction/neighborhood.py' adding 'pybel/struct/mutation/induction/paths.py' adding 'pybel/struct/mutation/induction/random_subgraph.py' adding 'pybel/struct/mutation/induction/upstream.py' adding 'pybel/struct/mutation/induction/utils.py' adding 'pybel/struct/mutation/inference/__init__.py' adding 'pybel/struct/mutation/inference/protein_rna_origins.py' adding 'pybel/struct/mutation/inference/transfer.py' adding 'pybel/struct/pipeline/__init__.py' adding 'pybel/struct/pipeline/decorators.py' adding 'pybel/struct/pipeline/exc.py' adding 'pybel/struct/pipeline/pipeline.py' adding 'pybel/struct/query/__init__.py' adding 'pybel/struct/query/constants.py' adding 'pybel/struct/query/exc.py' adding 'pybel/struct/query/query.py' adding 'pybel/struct/query/seeding.py' adding 'pybel/struct/query/selection.py' adding 'pybel/struct/summary/__init__.py' adding 'pybel/struct/summary/edge_summary.py' adding 'pybel/struct/summary/errors.py' adding 'pybel/struct/summary/node_summary.py' adding 'pybel/struct/summary/provenance.py' adding 'pybel/struct/summary/supersummary.py' adding 'pybel/testing/__init__.py' adding 'pybel/testing/cases.py' adding 'pybel/testing/constants.py' adding 'pybel/testing/generate.py' adding 'pybel/testing/mock_manager.py' adding 'pybel/testing/mocks.py' adding 'pybel/testing/utils.py' adding 'pybel/testing/resources/bel/Cytotoxic T-cell Signaling-2.0-Hs.json' adding 'pybel/testing/resources/bel/isolated.bel' adding 'pybel/testing/resources/bel/misordered.bel' adding 'pybel/testing/resources/bel/obo.bel' adding 'pybel/testing/resources/bel/slushy.bel' adding 'pybel/testing/resources/bel/test_bel.bel' adding 'pybel/testing/resources/bel/thorough.bel' adding 'pybel/testing/resources/belanno/cell-line.belanno' adding 'pybel/testing/resources/belanno/confidence-1.0.0.belanno' adding 'pybel/testing/resources/belanno/mesh-diseases.belanno' adding 'pybel/testing/resources/belanno/species-taxonomy-id.belanno' adding 'pybel/testing/resources/belanno/test_an_1.belanno' adding 'pybel/testing/resources/belns/chebi-names.belns' adding 'pybel/testing/resources/belns/disease-ontology.belns' adding 'pybel/testing/resources/belns/go-names.belns' adding 'pybel/testing/resources/belns/hgnc-names.belns' adding 'pybel/testing/resources/belns/mesh-names.belns' adding 'pybel/testing/resources/belns/test_ns_1.belns' adding 'pybel/testing/resources/belns/test_ns_1_updated.belns' adding 'pybel/testing/resources/belns/test_ns_2.belns' adding 'pybel/testing/resources/belns/test_ns_empty.belns' adding 'pybel-0.15.5.dist-info/LICENSE' adding 'pybel-0.15.5.dist-info/METADATA' adding 'pybel-0.15.5.dist-info/WHEEL' adding 'pybel-0.15.5.dist-info/entry_points.txt' adding 'pybel-0.15.5.dist-info/top_level.txt' adding 'pybel-0.15.5.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Successfully built pybel-0.15.5-py3-none-any.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.12 with "installer" module dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.12_pybel/build; python3.12 -m pytest --ignore=tests/test_grounding.py -k ' not test_seeding and not test_import and not test_manager_graph and not test_insert_namespace_persistent and not test_parse_metadata and not test_bel_simple and not test_bel_thorough and not test_update_matrix_activation and not test_update_matrix_activation_phosphorylation and not test_update_matrix_activation_ubiquination and not test_update_matrix_association and not test_update_matrix_expression and not test_update_matrix_inhibition and not test_update_matrix_inhibition_phosphorylation and not test_update_matrix_inhibition_ubiquination and not test_update_matrix_pmods and not test_update_matrix_repression and not test_reset_citation and not test_set_regex and not test_get_random_path ' ============================= test session starts ============================== platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 rootdir: /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.12_pybel/build configfile: pyproject.toml plugins: typeguard-4.4.1 collected 727 items / 171 deselected / 556 selected tests/test_bel_repository.py . [ 0%] tests/test_canonicalization.py .......................... [ 4%] tests/test_dsl.py ........................ [ 9%] tests/test_io/test_hipathia/test_export.py .... [ 9%] tests/test_io/test_hipathia/test_hipathia.py . [ 10%] tests/test_io/test_jgif.py . [ 10%] tests/test_io/test_jupyter.py .. [ 10%] tests/test_io/test_pynpa.py ..... [ 11%] tests/test_io/test_spia.py ... [ 12%] tests/test_io/test_triples.py .. [ 12%] tests/test_io/test_umbrella_nodelink.py .. [ 12%] tests/test_manager/test_citation_utils.py ........ssssss. [ 15%] tests/test_manager/test_connection.py .......... [ 17%] tests/test_manager/test_manager_definitions.py .. [ 17%] tests/test_manager/test_manager_drop.py .......... [ 19%] tests/test_manager/test_manager_model.py ....... [ 20%] tests/test_parse/test_parse_bel.py ..................................... [ 27%] ............................................ [ 35%] tests/test_parse/test_parse_bel_relations.py ........................... [ 40%] ........ [ 41%] tests/test_parse/test_parse_bel_variants.py ............................ [ 46%] .......... [ 48%] tests/test_parse/test_parse_control.py ................................. [ 54%] [ 54%] tests/test_parse/test_parse_identifier.py .................... [ 57%] tests/test_parse/test_parse_utils.py .......... [ 59%] tests/test_parse/test_user_api.py .... [ 60%] tests/test_schema.py ........... [ 62%] tests/test_struct/test_filters/test_edge_predicate_builders.py .... [ 63%] tests/test_struct/test_filters/test_edge_predicates.py . [ 63%] tests/test_struct/test_filters/test_node_predicate_builders.py ....... [ 64%] tests/test_struct/test_filters/test_node_predicates.py ................. [ 67%] ............... [ 70%] tests/test_struct/test_filters/test_node_selection.py . [ 70%] tests/test_struct/test_filters/test_struct_filters.py .................. [ 73%] .... [ 74%] tests/test_struct/test_getters.py . [ 74%] tests/test_struct/test_grouping.py ... [ 75%] tests/test_struct/test_node_utils.py .... [ 75%] tests/test_struct/test_query/test_mocks.py ... [ 76%] tests/test_struct/test_query/test_query.py ................. [ 79%] tests/test_struct/test_query/test_struct_pipeline.py ............ [ 81%] tests/test_struct/test_struct_graph.py .......... [ 83%] tests/test_struct/test_struct_operations.py ....................... [ 87%] tests/test_struct/test_summary/test_errors.py .. [ 87%] tests/test_struct/test_summary/test_provenance.py . [ 88%] tests/test_struct/test_summary/test_struct_summary_edges.py ...... [ 89%] tests/test_struct/test_summary/test_summary_nodes.py .......... [ 91%] tests/test_struct/test_transformations/test_collapse.py ...... [ 92%] tests/test_struct/test_transformations/test_deletions.py ......... [ 93%] tests/test_struct/test_transformations/test_expansion.py .... [ 94%] tests/test_struct/test_transformations/test_induction.py .......... [ 96%] tests/test_struct/test_transformations/test_metadata.py ... [ 96%] tests/test_struct/test_transformations/test_random.py ...... [ 97%] tests/test_struct/test_transformations/test_transfer.py ... [ 98%] tests/test_tokens.py . [ 98%] tests/test_utils.py ........ [100%] =============================== warnings summary =============================== pybel/io/api.py:9 /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.12_pybel/build/pybel/io/api.py:9: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import iter_entry_points pybel/manager/models.py:91 /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.12_pybel/build/pybel/manager/models.py:91: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9) Base = declarative_base() pybel/schema/__init__.py:30 /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.12_pybel/build/pybel/schema/__init__.py:30: DeprecationWarning: jsonschema.RefResolver is deprecated as of v4.18.0, in favor of the https://github.com/python-jsonschema/referencing library, which provides more compliant referencing behavior as well as more flexible APIs for customization. A future release will remove RefResolver. Please file a feature request (on referencing) if you are missing an API for the kind of customization you need. RESOLVER = jsonschema.RefResolver(base_uri=schema_uri, referrer=__file__) tests/test_io/test_spia.py::TestSpia::test_spia_matrix_complexes tests/test_io/test_spia.py::TestSpia::test_spia_matrix_composites /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.12_pybel/build/pybel/io/spia.py:178: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy spia_matrices["activation"][u_name][v_name] = 1 tests/test_io/test_spia.py::TestSpia::test_spia_matrix_complexes tests/test_io/test_spia.py::TestSpia::test_spia_matrix_composites /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.12_pybel/build/pybel/io/spia.py:174: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy spia_matrices["activation_phosphorylation"][u_name][v_name] = 1 tests/test_io/test_spia.py::TestSpia::test_spia_matrix_complexes tests/test_io/test_spia.py::TestSpia::test_spia_matrix_composites /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.12_pybel/build/pybel/io/spia.py:193: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy spia_matrices["inhibition"][u_name][v_name] = 1 tests/test_manager/test_manager_definitions.py: 1 warning tests/test_manager/test_manager_drop.py: 23 warnings /usr/lib/python3/dist-packages/sqlalchemy/sql/schema.py:3594: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC). return util.wrap_callable(lambda ctx: fn(), fn) # type: ignore tests/test_manager/test_manager_drop.py::TestReconstituteNodeTuples::test_simple /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.12_pybel/build/pybel/manager/cache_manager.py:421: LegacyAPIWarning: The Query.get() method is considered legacy as of the 1.x series of SQLAlchemy and becomes a legacy construct in 2.0. The method is now available as Session.get() (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9) network = self.session.query(Network).get(network_id) tests/test_manager/test_manager_model.py::TestNetwork::test_dump tests/test_manager/test_manager_model.py::TestNetwork::test_network tests/test_manager/test_manager_model.py::TestNetwork::test_to_json /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.12_pybel/build/tests/test_manager/test_manager_model.py:33: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC). self.created = datetime.datetime.utcnow() tests/test_parse/test_parse_bel.py: 82 warnings tests/test_parse/test_parse_bel_relations.py: 2 warnings /build/reproducible-path/pybel-0.15.5/.pybuild/cpython3_3.12_pybel/build/pybel/struct/graph.py:913: DeprecationWarning: use node.as_bel() warnings.warn("use node.as_bel()", DeprecationWarning) tests/test_struct/test_struct_graph.py: 1778 warnings /usr/lib/python3/dist-packages/bioregistry/schema_utils.py:61: PydanticDeprecatedSince20: The `parse_obj` method is deprecated; use `model_validate` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.10/migration/ return {prefix: Resource.parse_obj(value) for prefix, value in data.items()} tests/test_struct/test_struct_graph.py: 7112 warnings /usr/lib/python3/dist-packages/bioregistry/schema/struct.py:648: PydanticDeprecatedSince20: The `dict` method is deprecated; use `model_dump` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.10/migration/ return self.dict().get(metaprefix) or dict() -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ======== 550 passed, 6 skipped, 171 deselected, 9011 warnings in 58.18s ======== create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/pybel-0.15.5' dh_auto_install I: pybuild plugin_pyproject:178: Copying package built for python3.12 to destdir # eliminate lintian warning for d in $(find /build/reproducible-path/pybel-0.15.5/debian/python3-pybel/usr/lib -maxdepth 1 -type d -name "python3.*"); \ do \ chmod -x $d/dist-packages/pybel/testing/resources/bel/*.json ; \ done find debian -type f -name graph_template.html \ | xargs sed -i \ -e 's;https://cdn[js]*\..*/jquery.min.js;file:///usr/share/javascript/jquery/jquery.min.js;g' \ -e 's;https://cdn[js]*\..*/d3.min.js;file:///usr/share/javascript/d3/d3.min.js;g' \ make[1]: Leaving directory '/build/reproducible-path/pybel-0.15.5' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-pybel' in '../python3-pybel_0.15.5-1_all.deb'. dpkg-genbuildinfo --build=binary -O../pybel_0.15.5-1_amd64.buildinfo dpkg-genchanges --build=binary -O../pybel_0.15.5-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from pybel-0.15.5/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/492424/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/492424/tmp/hooks/B01_cleanup finished 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/492424 and its subdirectories I: Current time: Thu Jan 8 01:45:54 +14 2026 I: pbuilder-time-stamp: 1767786354