Diff of the two buildlogs: -- --- b1/build.log 2024-01-08 12:01:08.089230449 +0000 +++ b2/build.log 2024-01-08 12:29:18.392021907 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jan 7 23:10:48 -12 2024 -I: pbuilder-time-stamp: 1704712248 +I: Current time: Mon Feb 10 08:24:23 +14 2025 +I: pbuilder-time-stamp: 1739125463 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/3050343/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3057240/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +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 9 18:25 /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/3057240/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3057240/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='851c480303bd4f36a29f06ecd6c6ebf7' - 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='3050343' - PS1='# ' - PS2='> ' + INVOCATION_ID=93dfa511070d4dafb9276f2ca69c0582 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=3057240 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.x9sBTo9j/pbuilderrc_l0Ox --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.x9sBTo9j/b1 --logfile b1/build.log mdanalysis_2.4.2+dfsg1-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.104:3128' + 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.x9sBTo9j/pbuilderrc_10xN --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.x9sBTo9j/b2 --logfile b2/build.log mdanalysis_2.4.2+dfsg1-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.104:3128 I: uname -a - Linux codethink02-arm64 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux I: ls -l /bin total 7104 -rwxr-xr-x 1 root root 1346480 Apr 23 2023 bash @@ -131,15 +163,15 @@ -rwxr-xr-x 1 root root 68456 Sep 20 2022 readlink -rwxr-xr-x 1 root root 68592 Sep 20 2022 rm -rwxr-xr-x 1 root root 68480 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 68392 Jul 28 23:46 run-parts + -rwxr-xr-x 1 root root 68392 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 134536 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Feb 9 18:25 sh -> /bin/bash -rwxr-xr-x 1 root root 68432 Sep 20 2022 sleep -rwxr-xr-x 1 root root 134088 Sep 20 2022 stty -rwsr-xr-x 1 root root 133312 Mar 23 2023 su -rwxr-xr-x 1 root root 68448 Sep 20 2022 sync -rwxr-xr-x 1 root root 539896 Apr 6 2023 tar - -rwxr-xr-x 1 root root 67904 Jul 28 23:46 tempfile + -rwxr-xr-x 1 root root 67904 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 134160 Sep 20 2022 touch -rwxr-xr-x 1 root root 68384 Sep 20 2022 true -rwxr-xr-x 1 root root 67664 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/3050343/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/3057240/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 arm64 python3-sphinx-sitemap all 2.2.0-2 [7252 B] Get: 249 http://deb.debian.org/debian bookworm/main arm64 python3-sphinxcontrib.bibtex all 2.5.0-1 [30.8 kB] Get: 250 http://deb.debian.org/debian bookworm/main arm64 python3-tqdm all 4.64.1-1 [97.7 kB] -Fetched 170 MB in 1s (170 MB/s) +Fetched 170 MB in 6s (30.7 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 ... 18171 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: Mon Jan 8 11:12:16 UTC 2024. -Universal Time is now: Mon Jan 8 11:12:16 UTC 2024. +Local time is now: Sun Feb 9 18:28:29 UTC 2025. +Universal Time is now: Sun Feb 9 18:28:29 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/3057240/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/3057240/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 @@ -2344,12 +2380,41 @@ INFO: compile options: '-D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/formats -I/usr/include/python3.11 -c' extra options: '-std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros' INFO: aarch64-linux-gnu-gcc: MDAnalysis/lib/formats/libmdaxdr.c -cc1: warning: '-fassociative-math' disabled; other options take precedence INFO: aarch64-linux-gnu-gcc: MDAnalysis/lib/formats/src/trr_seek.c -cc1: warning: '-fassociative-math' disabled; other options take precedence INFO: aarch64-linux-gnu-gcc: MDAnalysis/lib/formats/src/xdrfile.c INFO: aarch64-linux-gnu-gcc: MDAnalysis/lib/formats/src/xdrfile_trr.c +INFO: aarch64-linux-gnu-gcc: MDAnalysis/lib/formats/src/xdrfile_xtc.c +INFO: aarch64-linux-gnu-gcc: MDAnalysis/lib/formats/src/xtc_seek.c +cc1: warning: '-fassociative-math' disabled; other options take precedence +cc1: warning: '-fassociative-math' disabled; other options take precedence +cc1: warning: '-fassociative-math' disabled; other options take precedence cc1: warning: '-fassociative-math' disabled; other options take precedence +cc1: warning: '-fassociative-math' disabled; other options take precedence +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/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 -*- + | +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 /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 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 -*- + | 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 -*- @@ -2362,6 +2427,10 @@ /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: +/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': MDAnalysis/lib/formats/src/trr_seek.c:39:27: warning: unused variable 'totalframebytes' [-Wunused-variable] 39 | int result, framebytes, totalframebytes; @@ -2372,14 +2441,6 @@ MDAnalysis/lib/formats/src/trr_seek.c:38:9: warning: unused variable 'time' [-Wunused-variable] 38 | float time, lambda; | ^~~~ -cc1: warning: '-fassociative-math' disabled; other options take precedence -INFO: aarch64-linux-gnu-gcc: MDAnalysis/lib/formats/src/xdrfile_xtc.c -cc1: warning: '-fassociative-math' disabled; other options take precedence -INFO: aarch64-linux-gnu-gcc: MDAnalysis/lib/formats/src/xtc_seek.c -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 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 -*- @@ -2395,22 +2456,17 @@ 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/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 -*- - | +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: /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_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 /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: In function 'sizeofint': MDAnalysis/lib/formats/src/xdrfile.c:501:17: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 501 | while (size >= num && num_of_bits < 32) @@ -2434,17 +2490,9 @@ 706 | if (lastbits < num_of_bits) | ^ MDAnalysis/lib/formats/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': -cc1: warning: '-fassociative-math' disabled; other options take precedence -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.c:816:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 816 | if(size3>xfp->buf1size) | ^ -MDAnalysis/lib/formats/src/xdrfile_trr.c:407:8: note: 'plcholder' was declared here - 407 | int *plcholder; - | ^~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:868:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] 868 | 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'))) 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'))) 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'))) 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'))) +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://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'))) -loading intersphinx inventory from https://mdanalysis.org/pmda/objects.inv... -loading intersphinx inventory from https://networkx.org/documentation/stable/objects.inv... +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'))) +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'))) +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'))) 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://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'))) 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://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/pmda/objects.inv... +loading intersphinx inventory from https://networkx.org/documentation/stable/objects.inv... 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://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'))) loading intersphinx inventory from https://parmed.github.io/ParmEd/html/objects.inv... 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://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://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'))) +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'))) 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://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'))) 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-ti1x0bzr 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-pixicl4v 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: {'c3', 'oh', 'h1', 'ho', 'hc'}. 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: {'hc', 'h1', 'oh', 'c3', '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 -= 18270 passed, 573 skipped, 7 xfailed, 3 xpassed, 32335 warnings in 2108.55s (0:35:08) = += 18270 passed, 573 skipped, 7 xfailed, 3 xpassed, 32335 warnings in 821.57s (0:13:41) = --- 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: @@ -5659,13 +5695,13 @@ - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.4.2) [4] - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.4.2) [5] - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hbonds.hbond_autocorrel (v 2.4.2) [6] - - HOLE trajectory analysis with orderparameters, HOLE program / MDAnalysis.analysis.hole2 (v 2.4.2) [7, 8, 9] + - 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] - - Mean Squared Displacements with tidynamics, FCA fast correlation algorithm / MDAnalysis.analysis.msd (v 2.4.2) [11, 12] + - FCA fast correlation algorithm, Mean Squared Displacements with tidynamics / 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] - - MDAnalysis trajectory reader/writer of the H5MDformat, Specifications of the H5MD standard / MDAnalysis.coordinates.H5MD (v 1.1, 2.4.2) [15, 16] + - Specifications of the H5MD standard, MDAnalysis trajectory reader/writer of the H5MDformat / MDAnalysis.coordinates.H5MD (v 1.1, 2.4.2) [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 'python3-mdanalysis-dbgsym' in '../python3-mdanalysis-dbgsym_2.4.2+dfsg1-1_arm64.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-dbgsym' in '../python3-mdanalysis-dbgsym_2.4.2+dfsg1-1_arm64.deb'. dpkg-deb: building package 'python3-mdanalysis' in '../python3-mdanalysis_2.4.2+dfsg1-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../mdanalysis_2.4.2+dfsg1-1_arm64.buildinfo dpkg-genchanges --build=binary -O../mdanalysis_2.4.2+dfsg1-1_arm64.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/3057240/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3057240/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/3050343 and its subdirectories -I: Current time: Mon Jan 8 00:01:06 -12 2024 -I: pbuilder-time-stamp: 1704715266 +I: removing directory /srv/workspace/pbuilder/3057240 and its subdirectories +I: Current time: Mon Feb 10 08:52:16 +14 2025 +I: pbuilder-time-stamp: 1739127136