Diff of the two buildlogs: -- --- b1/build.log 2024-01-14 04:00:58.079707500 +0000 +++ b2/build.log 2024-01-14 06:19:39.321054735 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jan 13 14:07:25 -12 2024 -I: pbuilder-time-stamp: 1705198045 +I: Current time: Sun Feb 16 00:24:14 +14 2025 +I: pbuilder-time-stamp: 1739615054 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -31,49 +31,81 @@ dpkg-source: info: applying docs_privacy.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1314727/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4128054/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 Feb 15 10:24 /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/4128054/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4128054/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + 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]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(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=16 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='802b094eb11546ec9dba2c2802fac4a2' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1314727' - PS1='# ' - PS2='> ' + INVOCATION_ID=c74bf6eed95d42ebb1a6a33a3317e912 + 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=4128054 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.jGQjWCYd/pbuilderrc_APPY --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.jGQjWCYd/b1 --logfile b1/build.log mdanalysis_2.4.2+dfsg1-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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.jGQjWCYd/pbuilderrc_fer5 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.jGQjWCYd/b2 --logfile b2/build.log mdanalysis_2.4.2+dfsg1-1.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://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash @@ -131,15 +163,15 @@ -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Jul 28 23:46 run-parts + -rwxr-xr-x 1 root root 27560 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Feb 15 10:24 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 23 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar - -rwxr-xr-x 1 root root 14520 Jul 28 23:46 tempfile + -rwxr-xr-x 1 root root 14520 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server @@ -159,7 +191,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/1314727/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/4128054/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -511,7 +543,7 @@ Get: 248 http://deb.debian.org/debian bookworm/main amd64 python3-sphinx-sitemap all 2.2.0-2 [7252 B] Get: 249 http://deb.debian.org/debian bookworm/main amd64 python3-sphinxcontrib.bibtex all 2.5.0-1 [30.8 kB] Get: 250 http://deb.debian.org/debian bookworm/main amd64 python3-tqdm all 4.64.1-1 [97.7 kB] -Fetched 180 MB in 1min 12s (2507 kB/s) +Fetched 180 MB in 11s (17.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package fonts-lato. (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 ... 18148 files and directories currently installed.) @@ -1308,8 +1340,8 @@ Setting up tzdata (2023c-5+deb12u1) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Jan 14 02:10:23 UTC 2024. -Universal Time is now: Sun Jan 14 02:10:23 UTC 2024. +Local time is now: Sat Feb 15 10:27:48 UTC 2025. +Universal Time is now: Sat Feb 15 10:27:48 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.0.0-1) ... @@ -1560,7 +1592,11 @@ fakeroot is already the newest version (1.31-1.2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/mdanalysis-2.4.2+dfsg1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../mdanalysis_2.4.2+dfsg1-1_source.changes +I: user script /srv/workspace/pbuilder/4128054/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/4128054/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/mdanalysis-2.4.2+dfsg1/ && 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 > ../mdanalysis_2.4.2+dfsg1-1_source.changes dpkg-buildpackage: info: source package mdanalysis dpkg-buildpackage: info: source version 2.4.2+dfsg1-1 dpkg-buildpackage: info: source distribution unstable @@ -2345,62 +2381,62 @@ extra options: '-std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros' INFO: x86_64-linux-gnu-gcc: MDAnalysis/lib/formats/libmdaxdr.c INFO: x86_64-linux-gnu-gcc: MDAnalysis/lib/formats/src/trr_seek.c -INFO: x86_64-linux-gnu-gcc: MDAnalysis/lib/formats/src/xdrfile.c -cc1: warning: '-fassociative-math' disabled; other options take precedence -INFO: x86_64-linux-gnu-gcc: MDAnalysis/lib/formats/src/xdrfile_trr.c cc1: warning: '-fassociative-math' disabled; other options take precedence +INFO: x86_64-linux-gnu-gcc: MDAnalysis/lib/formats/src/xdrfile.c cc1: warning: '-fassociative-math' disabled; other options take precedence -INFO: x86_64-linux-gnu-gcc: MDAnalysis/lib/formats/src/xdrfile_xtc.c -cc1: warning: '-fassociative-math' disabled; other options take precedence -INFO: x86_64-linux-gnu-gcc: MDAnalysis/lib/formats/src/xtc_seek.c cc1: warning: '-fassociative-math' disabled; other options take precedence -In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:30: +INFO: x86_64-linux-gnu-gcc: MDAnalysis/lib/formats/src/xdrfile_trr.c +In file included from MDAnalysis/lib/formats/src/trr_seek.c:30: /build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | -cc1: warning: '-fassociative-math' disabled; other options take precedence -In file included from MDAnalysis/lib/formats/src/trr_seek.c:30: -/build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] +In file included from MDAnalysis/lib/formats/src/trr_seek.c:31: +/build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | -In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31: -/build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] +In file included from /build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:42: +/build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | -In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:38: +MDAnalysis/lib/formats/src/trr_seek.c: In function 'read_trr_n_frames': +MDAnalysis/lib/formats/src/trr_seek.c:39:27: warning: unused variable 'totalframebytes' [-Wunused-variable] + 39 | int result, framebytes, totalframebytes; + | ^~~~~~~~~~~~~~~ +MDAnalysis/lib/formats/src/trr_seek.c:38:15: warning: unused variable 'lambda' [-Wunused-variable] + 38 | float time, lambda; + | ^~~~~~ +MDAnalysis/lib/formats/src/trr_seek.c:38:9: warning: unused variable 'time' [-Wunused-variable] + 38 | float time, lambda; + | ^~~~ +INFO: x86_64-linux-gnu-gcc: MDAnalysis/lib/formats/src/xdrfile_xtc.c +cc1: warning: '-fassociative-math' disabled; other options take precedence +INFO: x86_64-linux-gnu-gcc: MDAnalysis/lib/formats/src/xtc_seek.c +cc1: warning: '-fassociative-math' disabled; other options take precedence +In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:30: /build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | -In file included from MDAnalysis/lib/formats/src/trr_seek.c:31: -/build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] +In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31: +/build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | -In file included from MDAnalysis/lib/formats/src/xtc_seek.c:25: +In file included from /build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43: /build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | -In file included from /build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43: +cc1: warning: '-fassociative-math' disabled; other options take precedence +In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:38: /build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | -In file included from /build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:42: +In file included from MDAnalysis/lib/formats/src/xdrfile.c:62: /build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | -MDAnalysis/lib/formats/src/trr_seek.c: In function 'read_trr_n_frames': In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:39: /build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | -MDAnalysis/lib/formats/src/trr_seek.c:39:27: warning: unused variable 'totalframebytes' [-Wunused-variable] - 39 | int result, framebytes, totalframebytes; - | ^~~~~~~~~~~~~~~ -MDAnalysis/lib/formats/src/trr_seek.c:38:15: warning: unused variable 'lambda' [-Wunused-variable] - 38 | float time, lambda; - | ^~~~~~ -MDAnalysis/lib/formats/src/trr_seek.c:38:9: warning: unused variable 'time' [-Wunused-variable] - 38 | float time, lambda; - | ^~~~ In file included from /build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:42: /build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- @@ -2412,22 +2448,7 @@ MDAnalysis/lib/formats/src/xdrfile_trr.c:86:43: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 86 | if (xdrfile_write_string(version, xd) != (strlen(version) + 1)) | ^~ -In file included from MDAnalysis/lib/formats/src/xtc_seek.c:26: -/build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] - 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- - | -In file included from /build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43: -/build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] - 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- - | -MDAnalysis/lib/formats/src/xdrfile_trr.c: In function 'write_trr': -MDAnalysis/lib/formats/src/xdrfile_trr.c:408:10: warning: 'plcholder' is used uninitialized [-Wuninitialized] - 408 | return do_trn(xd, 0, &step, &t, &lambda, box, &natoms, x, v, f, plcholder); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -MDAnalysis/lib/formats/src/xdrfile_trr.c:407:8: note: 'plcholder' was declared here - 407 | int *plcholder; - | ^~~~~~~~~ -In file included from MDAnalysis/lib/formats/src/xdrfile.c:62: +In file included from MDAnalysis/lib/formats/src/xtc_seek.c:25: /build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | @@ -2466,6 +2487,14 @@ MDAnalysis/lib/formats/src/xdrfile.c:794:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 794 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ +In file included from MDAnalysis/lib/formats/src/xtc_seek.c:26: +/build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] + 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- + | +In file included from /build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43: +/build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] + 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- + | MDAnalysis/lib/formats/src/xdrfile.c:791:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 791 | int smallidx, minidx, maxidx; | ^~~~~~ @@ -2498,6 +2527,13 @@ MDAnalysis/lib/formats/src/xdrfile.c:1368:44: warning: operand of '?:' changes signedness from 'int' to 'long unsigned int' due to unsignedness of other operand [-Wsign-compare] 1368 | maxidx = (LASTIDX: HTTPSConnectionPool(host='docs.h5py.org', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://docs.h5py.org/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.h5py.org', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory from https://docs.python.org/3/objects.inv... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory from https://docs.scipy.org/doc/scipy/objects.inv... -WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://docs.scipy.org/doc/scipy/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.scipy.org', port=443): Max retries exceeded with url: /doc/scipy/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory from https://gsd.readthedocs.io/en/stable/objects.inv... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://gsd.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='gsd.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://gsd.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='gsd.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory from https://matplotlib.org/stable/objects.inv... +WARNING: failed to reach any of the inventories with the following issues: +intersphinx inventory 'https://matplotlib.org/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='matplotlib.org', port=443): Max retries exceeded with url: /stable/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory from https://mdanalysis.org/GridDataFormats/objects.inv... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://mdanalysis.org/GridDataFormats/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /GridDataFormats/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://mdanalysis.org/GridDataFormats/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /GridDataFormats/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory from https://mdanalysis.org/pmda/objects.inv... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://matplotlib.org/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='matplotlib.org', port=443): Max retries exceeded with url: /stable/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) -WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://mdanalysis.org/pmda/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /pmda/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://docs.scipy.org/doc/scipy/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.scipy.org', port=443): Max retries exceeded with url: /doc/scipy/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory from https://networkx.org/documentation/stable/objects.inv... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://networkx.org/documentation/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='networkx.org', port=443): Max retries exceeded with url: /documentation/stable/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://networkx.org/documentation/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='networkx.org', port=443): Max retries exceeded with url: /documentation/stable/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory from https://numpy.org/doc/stable/objects.inv... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://numpy.org/doc/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='numpy.org', port=443): Max retries exceeded with url: /doc/stable/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://numpy.org/doc/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='numpy.org', port=443): Max retries exceeded with url: /doc/stable/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory from https://parmed.github.io/ParmEd/html/objects.inv... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://parmed.github.io/ParmEd/html/objects.inv' not fetchable due to : HTTPSConnectionPool(host='parmed.github.io', port=443): Max retries exceeded with url: /ParmEd/html/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://parmed.github.io/ParmEd/html/objects.inv' not fetchable due to : HTTPSConnectionPool(host='parmed.github.io', port=443): Max retries exceeded with url: /ParmEd/html/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory from https://rdkit.org/docs/objects.inv... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://rdkit.org/docs/objects.inv' not fetchable due to : HTTPSConnectionPool(host='rdkit.org', port=443): Max retries exceeded with url: /docs/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://rdkit.org/docs/objects.inv' not fetchable due to : HTTPSConnectionPool(host='rdkit.org', port=443): Max retries exceeded with url: /docs/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +WARNING: failed to reach any of the inventories with the following issues: +intersphinx inventory 'https://mdanalysis.org/pmda/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /pmda/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) locale_dir /build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exists building [mo]: targets for 0 po files that are out of date building [html]: targets for 164 source files that are out of date @@ -3442,7 +3478,7 @@ Didn't find DistanceMatrix.atoms in MDAnalysis.analysis.diffusionmap Didn't find DistanceMatrix.results.dist_matrix in MDAnalysis.analysis.diffusionmap reading sources... [ 5%] documentation_pages/analysis/dihedrals -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-nq72x1_i because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-1fnxmkjq because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Didn't find Dihedral.results.angles in MDAnalysis.analysis.dihedrals Didn't find Ramachandran.results.angles in MDAnalysis.analysis.dihedrals Didn't find Janin.results.angles in MDAnalysis.analysis.dihedrals @@ -4602,7 +4638,7 @@ MDAnalysisTests/analysis/test_bat.py: 9 warnings MDAnalysisTests/coordinates/test_mol2.py: 3 warnings - /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/topology/MOL2Parser.py:234: UserWarning: Unknown elements found for some atoms: {'ho', 'hc', 'oh', 'h1', 'c3'}. These have been given an empty element record. + /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/topology/MOL2Parser.py:234: UserWarning: Unknown elements found for some atoms: {'oh', 'c3', 'h1', 'hc', 'ho'}. These have been given an empty element record. warnings.warn("Unknown elements found for some " MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox @@ -5000,7 +5036,7 @@ MDAnalysisTests/coordinates/test_dcd.py::test_write_no_natoms MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_time_unit MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_unit - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/DCD.py", line 467, in __del__ @@ -5062,7 +5098,7 @@ warnings.warn( MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderWithRealTrajectory::test_wrong_driver - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1512, in __del__ @@ -5145,7 +5181,7 @@ warnings.warn("Found missing chainIDs." MDAnalysisTests/coordinates/test_h5md.py::TestH5PYNotInstalled::test_reader_no_h5py - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1510, in __del__ @@ -5166,7 +5202,7 @@ MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_time_unit MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_unit - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1510, in __del__ @@ -5203,7 +5239,7 @@ warnings.warn(wmsg) MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterErrorsWarnings::test_zero_atoms_VE - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1592, in __del__ @@ -5277,7 +5313,7 @@ warnings.warn( MDAnalysisTests/coordinates/test_tng.py::test_pytng_not_present_raises - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1510, in __del__ @@ -5291,7 +5327,7 @@ warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_trj.py::test_trj_no_natoms - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1512, in __del__ @@ -5326,7 +5362,7 @@ warnings.warn("Timestep didn't have velocity information, " MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_long_title - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1592, in __del__ @@ -5364,7 +5400,7 @@ warnings.warn(wmsg) MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriter_2::test_no_container - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/XDR.py", line 325, in __del__ @@ -5377,7 +5413,7 @@ warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriter_2::test_no_container - /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: + /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/XDR.py", line 325, in __del__ @@ -5391,12 +5427,12 @@ MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_nonexistent_offsets_file MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_io_fails - /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/XDR.py:91: UserWarning: Failed to load offsets file /tmp/pytest-of-pbuilder1/pytest-0/xtc0/.adk_oplsaa.xtc_offsets.npz + /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/XDR.py:91: UserWarning: Failed to load offsets file /tmp/pytest-of-pbuilder2/pytest-0/xtc0/.adk_oplsaa.xtc_offsets.npz warnings.warn("Failed to load offsets file {}\n".format(filename)) MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_io_fails - /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/XDR.py:223: UserWarning: Reading offsets from /tmp/pytest-of-pbuilder1/pytest-0/xtc0/.adk_oplsaa.xtc_offsets.npz failed, reading offsets from trajectory instead. + /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/XDR.py:223: UserWarning: Reading offsets from /tmp/pytest-of-pbuilder2/pytest-0/xtc0/.adk_oplsaa.xtc_offsets.npz failed, reading offsets from trajectory instead. Consider setting 'refresh_offsets=True' when loading your Universe. warnings.warn("Reading offsets from {} failed, " @@ -5408,12 +5444,12 @@ MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_nonexistent_offsets_file MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_io_fails - /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/XDR.py:91: UserWarning: Failed to load offsets file /tmp/pytest-of-pbuilder1/pytest-0/xtc1/.adk_oplsaa.trr_offsets.npz + /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/XDR.py:91: UserWarning: Failed to load offsets file /tmp/pytest-of-pbuilder2/pytest-0/xtc1/.adk_oplsaa.trr_offsets.npz warnings.warn("Failed to load offsets file {}\n".format(filename)) MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_io_fails - /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/XDR.py:223: UserWarning: Reading offsets from /tmp/pytest-of-pbuilder1/pytest-0/xtc1/.adk_oplsaa.trr_offsets.npz failed, reading offsets from trajectory instead. + /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/XDR.py:223: UserWarning: Reading offsets from /tmp/pytest-of-pbuilder2/pytest-0/xtc1/.adk_oplsaa.trr_offsets.npz failed, reading offsets from trajectory instead. Consider setting 'refresh_offsets=True' when loading your Universe. warnings.warn("Reading offsets from {} failed, " @@ -5587,19 +5623,19 @@ See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. MDAnalysisTests/utils/test_pickleio.py::test_pickle_with_write_mode[unpicklable_f0] - /usr/lib/python3/dist-packages/_pytest/python.py:195: ResourceWarning: unclosed file <_io.FileIO name=local('/tmp/pytest-of-pbuilder1/pytest-0/test_pickle_with_write_mode_un0/pickle/test.pdb') mode='wb' closefd=True> + /usr/lib/python3/dist-packages/_pytest/python.py:195: ResourceWarning: unclosed file <_io.FileIO name=local('/tmp/pytest-of-pbuilder2/pytest-0/test_pickle_with_write_mode_un0/pickle/test.pdb') mode='wb' closefd=True> result = testfunction(**testargs) Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. MDAnalysisTests/utils/test_pickleio.py::test_pickle_with_write_mode[unpicklable_f1] - /usr/lib/python3/dist-packages/_pytest/python.py:195: ResourceWarning: unclosed file <_io.FileIO name=local('/tmp/pytest-of-pbuilder1/pytest-0/test_pickle_with_write_mode_un1/pickle/test.pdb') mode='xb' closefd=True> + /usr/lib/python3/dist-packages/_pytest/python.py:195: ResourceWarning: unclosed file <_io.FileIO name=local('/tmp/pytest-of-pbuilder2/pytest-0/test_pickle_with_write_mode_un1/pickle/test.pdb') mode='xb' closefd=True> result = testfunction(**testargs) Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. MDAnalysisTests/utils/test_pickleio.py::test_pickle_with_write_mode[unpicklable_f2] - /usr/lib/python3/dist-packages/_pytest/python.py:195: ResourceWarning: unclosed file <_io.FileIO name=local('/tmp/pytest-of-pbuilder1/pytest-0/test_pickle_with_write_mode_un2/pickle/test.pdb') mode='ab' closefd=True> + /usr/lib/python3/dist-packages/_pytest/python.py:195: ResourceWarning: unclosed file <_io.FileIO name=local('/tmp/pytest-of-pbuilder2/pytest-0/test_pickle_with_write_mode_un2/pickle/test.pdb') mode='ab' closefd=True> result = testfunction(**testargs) Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. @@ -5610,7 +5646,7 @@ return umath.absolute(a) * self.tolerance >= umath.absolute(b) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -= 18271 passed, 573 skipped, 7 xfailed, 2 xpassed, 32335 warnings in 4702.70s (1:18:22) = += 18271 passed, 573 skipped, 7 xfailed, 2 xpassed, 32335 warnings in 6635.45s (1:50:35) = --- Logging error --- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/duecredit/utils.py", line 190, in wrapped_func @@ -5650,7 +5686,7 @@ Call stack: File "/usr/lib/python3/dist-packages/duecredit/utils.py", line 192, in wrapped_func lgr.warning("DueCredit internal failure while running %s: %r. " -Message: "DueCredit internal failure while running : PermissionError(13, 'Permission denied'). Please report to developers at https://github.com/duecredit/duecredit/issues" +Message: "DueCredit internal failure while running : PermissionError(13, 'Permission denied'). Please report to developers at https://github.com/duecredit/duecredit/issues" Arguments: () DueCredit Report: @@ -5662,10 +5698,10 @@ - HOLE program, HOLE trajectory analysis with orderparameters / MDAnalysis.analysis.hole2 (v 2.4.2) [7, 8, 9] - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.4.2) [10] - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.4.2) [2] - - FCA fast correlation algorithm, Mean Squared Displacements with tidynamics / MDAnalysis.analysis.msd (v 2.4.2) [11, 12] + - Mean Squared Displacements with tidynamics, FCA fast correlation algorithm / MDAnalysis.analysis.msd (v 2.4.2) [11, 12] - Cumulative overlap / MDAnalysis.analysis.pca (v 2.4.2) [13] - Path Similarity Analysis algorithm and implementation / MDAnalysis.analysis.psa (v 2.4.2) [14] - - Specifications of the H5MD standard, MDAnalysis trajectory reader/writer of the H5MDformat / MDAnalysis.coordinates.H5MD (v 2.4.2, 1.1) [15, 16] + - MDAnalysis trajectory reader/writer of the H5MDformat, Specifications of the H5MD standard / MDAnalysis.coordinates.H5MD (v 2.4.2, 1.1) [15, 16] - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.4.2) [17] - The TNG paper / MDAnalysis.coordinates.TNG (v 2.4.2) [18] - QCProt implementation / MDAnalysis.lib.qcprot (v 2.4.2) [19, 20] @@ -5714,8 +5750,8 @@ dpkg-gencontrol: warning: package python-mdanalysis-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'python-mdanalysis-doc' in '../python-mdanalysis-doc_2.4.2+dfsg1-1_all.deb'. dpkg-deb: building package 'python3-mdanalysis-dbgsym' in '../python3-mdanalysis-dbgsym_2.4.2+dfsg1-1_amd64.deb'. +dpkg-deb: building package 'python-mdanalysis-doc' in '../python-mdanalysis-doc_2.4.2+dfsg1-1_all.deb'. dpkg-deb: building package 'python3-mdanalysis' in '../python3-mdanalysis_2.4.2+dfsg1-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../mdanalysis_2.4.2+dfsg1-1_amd64.buildinfo dpkg-genchanges --build=binary -O../mdanalysis_2.4.2+dfsg1-1_amd64.changes @@ -5725,12 +5761,14 @@ 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/4128054/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4128054/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/1314727 and its subdirectories -I: Current time: Sat Jan 13 16:00:56 -12 2024 -I: pbuilder-time-stamp: 1705204856 +I: removing directory /srv/workspace/pbuilder/4128054 and its subdirectories +I: Current time: Sun Feb 16 02:42:49 +14 2025 +I: pbuilder-time-stamp: 1739623369