Sun Jan 14 02:07:23 UTC 2024 I: starting to build mdanalysis/bookworm/amd64 on jenkins on '2024-01-14 02:07' Sun Jan 14 02:07:23 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_15/9926/console.log Sun Jan 14 02:07:23 UTC 2024 I: Downloading source for bookworm/mdanalysis=2.4.2+dfsg1-1 --2024-01-14 02:07:23-- http://cdn-fastly.deb.debian.org/debian/pool/main/m/mdanalysis/mdanalysis_2.4.2%2bdfsg1-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2901 (2.8K) [text/prs.lines.tag] Saving to: ‘mdanalysis_2.4.2+dfsg1-1.dsc’ 0K .. 100% 333M=0s 2024-01-14 02:07:23 (333 MB/s) - ‘mdanalysis_2.4.2+dfsg1-1.dsc’ saved [2901/2901] Sun Jan 14 02:07:23 UTC 2024 I: mdanalysis_2.4.2+dfsg1-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: mdanalysis Binary: python3-mdanalysis, python-mdanalysis-doc Architecture: any all Version: 2.4.2+dfsg1-1 Maintainer: Debichem Team Uploaders: Drew Parsons Homepage: https://www.mdanalysis.org/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/debichem-team/mdanalysis Vcs-Git: https://salsa.debian.org/debichem-team/mdanalysis.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@, python3-hypothesis, python3-pytest, python3-sklearn Build-Depends: debhelper-compat (= 13), cython3, dh-python, pybuild-plugin-pyproject, python3-all-dev, python3-setuptools, python3-numpy (>= 1.20.0~), python3-biopython (>= 1.80), python3-networkx (>= 2.0), python3-griddataformats (>= 0.4.0), python3-mmtf (>= 1.0.0), python3-joblib (>= 0.12), python3-scipy (>= 1.5.0), python3-matplotlib (>= 1.5.1), python3-mock, python3-netcdf4 (>= 1.0~), python3-tqdm (>= 4.43.0), python3-gsd (>= 1.9.3~), python3-duecredit, python3-h5py, python3-hypothesis, python3-pytest, python3-seaborn, python3-sklearn, python3-sphinx, python3-threadpoolctl, python3-packaging, python3-fasteners Build-Depends-Indep: python3-msmb-theme, python3-pybtex, python3-sphinx-rtd-theme, python3-sphinx-sitemap, python3-sphinxcontrib.bibtex, libjs-mathjax Package-List: python-mdanalysis-doc deb doc optional arch=all python3-mdanalysis deb python optional arch=any Checksums-Sha1: 6d13bb890605d944507d8be8951e1b21293fb345 46702388 mdanalysis_2.4.2+dfsg1.orig.tar.xz b760ce377b44cf357da62daa5b2e5919f51f9a82 8768 mdanalysis_2.4.2+dfsg1-1.debian.tar.xz Checksums-Sha256: 500281060fd0d99b8e4a5ebac2b69e54e3d4b2d60dae618d936039394e865b21 46702388 mdanalysis_2.4.2+dfsg1.orig.tar.xz a716d3b05e0de061e93b901f4780505c8c484e347af1f631f41821b2570ad830 8768 mdanalysis_2.4.2+dfsg1-1.debian.tar.xz Files: ce05ec2f2c4ac19a6fd45992052b9d1e 46702388 mdanalysis_2.4.2+dfsg1.orig.tar.xz 5eb135305e3576bc8c6ead0d6eee827a 8768 mdanalysis_2.4.2+dfsg1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAmO8c1wACgkQVz7x5L1a Afo5tBAAk+kMb8OUZGfQiQ2hMEhKw2gh+8JFAT2DONXgel0yswgRyUEa3Rg4KV71 um0GMw/PFxqjGJsSRXoGWYI5Tk4+xaEWFX5w8Gi4NBNahTB8cUxZt7iKxnmu0e7H 4gg4VyjqR+fdp+GBTD4UUXV3kt5NrcrFBy4Rr9HHcbQ3GA4oyn9Ck05VLcLKjh5g pJlprMJU68ZgaA0F2b6szi3oBygYmmQDeXp41vN1VGHfUFUpHGhdcaOYDO0oE13K 1dKZTwQPG5nY1F0buzqu2izV44f1dbIYfxfgA7OZgR3THYZKOC8oNwc4lnRDhlpD NJI6Tq5noh5xz3k8B/ofh9rHYXaK72Q16KeZrYPlI1Vi1o4GcKApK0PFprWi91UB WEnH+e5XHUyliKD1y12xOnnMX3s0Pkmrbwp/ioRSFQ5WZ7S1gkqiqv2kqaMXxVdd FGZ4NVeeSzx39ChRn8/KTja2FZ1qr9m6vhFMwYbbJlewaf2Gp4//9yIpx3giHLJV pgG0+N1wdm8XUYx5DN6LQ0LL5LK7DAL7QUViUD5ShJSKgIFuxc2+eYjcmv9lNIwa LtCjQ89rQCZjZY5ZvzVgZm1utio/4HtPSie6JcCQpM6fipeClTHJYk8nRc0FLxrB 5cIE0wD7vCOxj9PCDfrgeheP4iGPKoRFdxBCjpwnf8llC6naHVg= =S2SJ -----END PGP SIGNATURE----- Sun Jan 14 02:07:23 UTC 2024 I: Checking whether the package is not for us Sun Jan 14 02:07:23 UTC 2024 I: Starting 1st build on remote node ionos11-amd64.debian.net. Sun Jan 14 02:07:23 UTC 2024 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Sun Jan 14 04:00:58 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. 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: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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 [mdanalysis_2.4.2+dfsg1-1.dsc] I: copying [./mdanalysis_2.4.2+dfsg1.orig.tar.xz] I: copying [./mdanalysis_2.4.2+dfsg1-1.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Jan 9 20:04:44 2023 gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.4.2+dfsg1-1.dsc: no acceptable signature found dpkg-source: info: extracting mdanalysis in mdanalysis-2.4.2+dfsg1 dpkg-source: info: unpacking mdanalysis_2.4.2+dfsg1.orig.tar.xz dpkg-source: info: unpacking mdanalysis_2.4.2+dfsg1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying docs_use_built_module.patch dpkg-source: info: applying docs_no_logo.patch dpkg-source: info: applying docs_sphinx_warnings_are_not_errors.patch dpkg-source: info: applying docs_local_mathjax.patch 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: 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' 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='> ' 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' 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 I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 23 2023 more -rwsr-xr-x 1 root root 59704 Mar 23 2023 mount -rwxr-xr-x 1 root root 18744 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -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 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -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 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 -rwsr-xr-x 1 root root 35128 Mar 23 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -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 -> 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), cython3, dh-python, pybuild-plugin-pyproject, python3-all-dev, python3-setuptools, python3-numpy (>= 1.20.0~), python3-biopython (>= 1.80), python3-networkx (>= 2.0), python3-griddataformats (>= 0.4.0), python3-mmtf (>= 1.0.0), python3-joblib (>= 0.12), python3-scipy (>= 1.5.0), python3-matplotlib (>= 1.5.1), python3-mock, python3-netcdf4 (>= 1.0~), python3-tqdm (>= 4.43.0), python3-gsd (>= 1.9.3~), python3-duecredit, python3-h5py, python3-hypothesis, python3-pytest, python3-seaborn, python3-sklearn, python3-sphinx, python3-threadpoolctl, python3-packaging, python3-fasteners, python3-msmb-theme, python3-pybtex, python3-sphinx-rtd-theme, python3-sphinx-sitemap, python3-sphinxcontrib.bibtex, libjs-mathjax dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18148 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 cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python 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-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy (>= 1.20.0~); however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython (>= 1.80); however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx (>= 2.0); however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-griddataformats (>= 0.4.0); however: Package python3-griddataformats is not installed. pbuilder-satisfydepends-dummy depends on python3-mmtf (>= 1.0.0); however: Package python3-mmtf is not installed. pbuilder-satisfydepends-dummy depends on python3-joblib (>= 0.12); however: Package python3-joblib is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy (>= 1.5.0); however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib (>= 1.5.1); however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-mock; however: Package python3-mock is not installed. pbuilder-satisfydepends-dummy depends on python3-netcdf4 (>= 1.0~); however: Package python3-netcdf4 is not installed. pbuilder-satisfydepends-dummy depends on python3-tqdm (>= 4.43.0); however: Package python3-tqdm is not installed. pbuilder-satisfydepends-dummy depends on python3-gsd (>= 1.9.3~); however: Package python3-gsd is not installed. pbuilder-satisfydepends-dummy depends on python3-duecredit; however: Package python3-duecredit is not installed. pbuilder-satisfydepends-dummy depends on python3-h5py; however: Package python3-h5py is not installed. pbuilder-satisfydepends-dummy depends on python3-hypothesis; however: Package python3-hypothesis is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-seaborn; however: Package python3-seaborn is not installed. pbuilder-satisfydepends-dummy depends on python3-sklearn; however: Package python3-sklearn is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-threadpoolctl; however: Package python3-threadpoolctl is not installed. pbuilder-satisfydepends-dummy depends on python3-packaging; however: Package python3-packaging is not installed. pbuilder-satisfydepends-dummy depends on python3-fasteners; however: Package python3-fasteners is not installed. pbuilder-satisfydepends-dummy depends on python3-msmb-theme; however: Package python3-msmb-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-pybtex; however: Package python3-pybtex is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-rtd-theme; however: Package python3-sphinx-rtd-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-sitemap; however: Package python3-sphinx-sitemap is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.bibtex; however: Package python3-sphinxcontrib.bibtex is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax 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} blt{a} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-font-awesome{a} fonts-lato{a} fonts-lyx{a} fonts-mathjax{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libblas3{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libcurl3-gnutls{a} libcurl4{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libhdf5-103-1{a} libhdf5-hl-100{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblzf1{a} libmagic-mgc{a} libmagic1{a} libnetcdf19{a} libnghttp2-14{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libopenjp2-7{a} libpipeline1{a} libpng16-16{a} libproc2-0{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libsz2{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxsimd-dev{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} openssl{a} po-debconf{a} procps{a} pybuild-plugin-pyproject{a} python-babel-localedata{a} python-matplotlib-data{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-appdirs{a} python3-attr{a} python3-babel{a} python3-beniget{a} python3-biopython{a} python3-brotli{a} python3-build{a} python3-certifi{a} python3-cftime{a} python3-chardet{a} python3-charset-normalizer{a} python3-citeproc{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-docutils{a} python3-duecredit{a} python3-fasteners{a} python3-fonttools{a} python3-fs{a} python3-gast{a} python3-griddataformats{a} python3-gsd{a} python3-h5py{a} python3-h5py-serial{a} python3-hypothesis{a} python3-idna{a} python3-imagesize{a} python3-importlib-metadata{a} python3-iniconfig{a} python3-installer{a} python3-jinja2{a} python3-joblib{a} python3-kiwisolver{a} python3-latexcodec{a} python3-lib2to3{a} python3-lxml{a} python3-lz4{a} python3-markupsafe{a} python3-matplotlib{a} python3-minimal{a} python3-mmtf{a} python3-mock{a} python3-monotonic{a} python3-more-itertools{a} python3-mpmath{a} python3-mrcfile{a} python3-msgpack{a} python3-msmb-theme{a} python3-netcdf4{a} python3-networkx{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pbr{a} python3-pep517{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-pluggy{a} python3-ply{a} python3-py{a} python3-pybtex{a} python3-pybtex-docutils{a} python3-pygments{a} python3-pyparsing{a} python3-pytest{a} python3-pythran{a} python3-renderpm{a} python3-reportlab{a} python3-reportlab-accel{a} python3-requests{a} python3-roman{a} python3-scipy{a} python3-seaborn{a} python3-setuptools{a} python3-six{a} python3-sklearn{a} python3-sklearn-lib{a} python3-snowballstemmer{a} python3-sortedcontainers{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-sphinx-sitemap{a} python3-sphinxcontrib.bibtex{a} python3-sympy{a} python3-threadpoolctl{a} python3-tk{a} python3-toml{a} python3-tomli{a} python3-tqdm{a} python3-tz{a} python3-ufolib2{a} python3-urllib3{a} python3-wheel{a} python3-yaml{a} python3-zipp{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl isympy-common javascript-common libarchive-cpio-perl libglib2.0-data libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules lynx ncbi-blast+ psmisc publicsuffix python-biopython-doc python3-bottleneck python3-bs4 python3-click python3-gdal python3-html5lib python3-nose python3-numba python3-numexpr python3-odf python3-olefile python3-openpyxl python3-patsy python3-psutil python3-pydot python3-pygraphviz python3-simplejson python3-tables shared-mime-info wget xdg-user-dirs 0 packages upgraded, 250 newly installed, 0 to remove and 0 not upgraded. Need to get 180 MB of archives. After unpacking 912 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 fonts-lato all 2.0-2.1 [2696 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 mailcap all 3.70+nmu1 [32.0 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 mime-support all 3.66 [10.9 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 14 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 tzdata all 2023c-5+deb12u1 [296 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.11-1~deb12u2 [1419 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libfontenc1 amd64 1:1.1.4-1 [24.3 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 fonts-urw-base35 all 20200910-7 [10.8 MB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-4.1 [593 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 blt amd64 2.5.3+dfsg-4.1 [14.9 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 cython3 amd64 0.29.32-2+b1 [1302 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130+deb12u1 [104 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 docutils-common all 0.19+dfsg-6 [127 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 fonts-lyx all 2.3.7-1 [186 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libaec0 amd64 1.0.6-1+b1 [21.1 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-21 [9508 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-10+deb12u4 [385 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10+deb12u4 [390 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libsz2 amd64 1.0.6-1+b1 [7804 B] Get: 106 http://deb.debian.org/debian bookworm/main amd64 libhdf5-103-1 amd64 1.10.8+repack1-1 [1237 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-100 amd64 1.10.8+repack1-1 [67.8 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 libimagequant0 amd64 2.17.0-1 [32.5 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 libopenblas0-pthread amd64 0.3.21+ds-4 [6709 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1 [28.9 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 liblzf1 amd64 3.6-3 [10.2 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 libnetcdf19 amd64 1:4.9.0-3+b1 [476 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 libopenblas0 amd64 0.3.21+ds-4 [32.6 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 libopenblas-pthread-dev amd64 0.3.21+ds-4 [4971 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 libopenblas-dev amd64 0.3.21+ds-4 [44.9 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-2 [189 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6 [1988 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6 [4738 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B] Get: 132 http://deb.debian.org/debian bookworm/main amd64 libpython3-all-dev amd64 3.11.2-1+b1 [1068 B] Get: 133 http://deb.debian.org/debian bookworm/main amd64 libqhull-r8.0 amd64 2020.2-5 [248 kB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 libraqm0 amd64 0.7.0-4.1 [10.6 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.4-0.2+deb12u1 [99.4 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.2+deb12u1 [109 kB] Get: 139 http://deb.debian.org/debian bookworm/main amd64 libxsimd-dev amd64 8.1.0-7 [88.8 kB] Get: 140 http://deb.debian.org/debian bookworm/main amd64 libxslt1.1 amd64 1.1.35-1 [242 kB] Get: 141 http://deb.debian.org/debian bookworm/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get: 142 http://deb.debian.org/debian bookworm/main amd64 python3-more-itertools all 8.10.0-2 [53.0 kB] Get: 143 http://deb.debian.org/debian bookworm/main amd64 python3-zipp all 1.0.0-6 [6696 B] Get: 144 http://deb.debian.org/debian bookworm/main amd64 python3-importlib-metadata all 4.12.0-1 [24.9 kB] Get: 145 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get: 146 http://deb.debian.org/debian bookworm/main amd64 python3-tomli all 2.0.1-2 [17.9 kB] Get: 147 http://deb.debian.org/debian bookworm/main amd64 python3-pep517 all 0.13.0-2 [17.4 kB] Get: 148 http://deb.debian.org/debian bookworm/main amd64 python3-toml all 0.10.2-1 [16.2 kB] Get: 149 http://deb.debian.org/debian bookworm/main amd64 python3-wheel all 0.38.4-2 [30.8 kB] Get: 150 http://deb.debian.org/debian bookworm/main amd64 python3-build all 0.9.0-1 [20.7 kB] Get: 151 http://deb.debian.org/debian bookworm/main amd64 python3-installer all 0.6.0+dfsg1-1 [18.1 kB] Get: 152 http://deb.debian.org/debian bookworm/main amd64 pybuild-plugin-pyproject all 5.20230130+deb12u1 [9184 B] Get: 153 http://deb.debian.org/debian bookworm/main amd64 python-babel-localedata all 2.10.3-1 [5615 kB] Get: 154 http://deb.debian.org/debian bookworm/main amd64 python-matplotlib-data all 3.6.3-1 [2744 kB] Get: 155 http://deb.debian.org/debian bookworm/main amd64 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 156 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Get: 157 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6 [615 kB] Get: 158 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB] Get: 159 http://deb.debian.org/debian bookworm/main amd64 python3-all-dev amd64 3.11.2-1+b1 [1072 B] Get: 160 http://deb.debian.org/debian bookworm/main amd64 python3-appdirs all 1.4.4-3 [13.0 kB] Get: 161 http://deb.debian.org/debian bookworm/main amd64 python3-attr all 22.2.0-1 [65.4 kB] Get: 162 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 163 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-4 [30.1 kB] Get: 164 http://deb.debian.org/debian bookworm/main amd64 python3-babel all 2.10.3-1 [103 kB] Get: 165 http://deb.debian.org/debian bookworm/main amd64 python3-gast all 0.5.2-2 [9364 B] Get: 166 http://deb.debian.org/debian bookworm/main amd64 python3-beniget all 0.4.1-3 [9920 B] Get: 167 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get: 168 http://deb.debian.org/debian bookworm/main amd64 python3-renderpm amd64 3.6.12-1+b1 [79.2 kB] Get: 169 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab-accel amd64 3.6.12-1+b1 [38.6 kB] Get: 170 http://deb.debian.org/debian bookworm/main amd64 python3-tk amd64 3.11.2-3 [98.3 kB] Get: 171 http://deb.debian.org/debian bookworm/main amd64 python3-pil.imagetk amd64 9.4.0-1.1+b1 [74.4 kB] Get: 172 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.4.0-1.1+b1 [472 kB] Get: 173 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab all 3.6.12-1 [564 kB] Get: 174 http://deb.debian.org/debian bookworm/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 175 http://deb.debian.org/debian bookworm/main amd64 python3-biopython amd64 1.80+dfsg-4+b1 [1593 kB] Get: 176 http://deb.debian.org/debian bookworm/main amd64 python3-brotli amd64 1.0.9-2+b6 [281 kB] Get: 177 http://deb.debian.org/debian bookworm/main amd64 python3-certifi all 2022.9.24-1 [153 kB] Get: 178 http://deb.debian.org/debian bookworm/main amd64 python3-cftime amd64 1.6.2-3+b1 [192 kB] Get: 179 http://deb.debian.org/debian bookworm/main amd64 python3-chardet all 5.1.0+dfsg-2 [110 kB] Get: 180 http://deb.debian.org/debian bookworm/main amd64 python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get: 181 http://deb.debian.org/debian bookworm/main amd64 python3-lxml amd64 4.9.2-1+b1 [1194 kB] Get: 182 http://deb.debian.org/debian bookworm/main amd64 python3-citeproc all 0.6.0-3 [96.7 kB] Get: 183 http://deb.debian.org/debian bookworm/main amd64 python3-contourpy amd64 1.0.7-1+b1 [176 kB] Get: 184 http://deb.debian.org/debian bookworm/main amd64 python3-cycler all 0.11.0-1 [8020 B] Get: 185 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get: 186 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.2-2 [78.3 kB] Get: 187 http://deb.debian.org/debian bookworm/main amd64 python3-decorator all 5.1.1-3 [14.9 kB] Get: 188 http://deb.debian.org/debian bookworm/main amd64 python3-roman all 3.3-3 [9880 B] Get: 189 http://deb.debian.org/debian bookworm/main amd64 python3-docutils all 0.19+dfsg-6 [382 kB] Get: 190 http://deb.debian.org/debian bookworm/main amd64 python3-idna all 3.3-1 [39.4 kB] Get: 191 http://deb.debian.org/debian bookworm/main amd64 python3-urllib3 all 1.26.12-1 [117 kB] Get: 192 http://deb.debian.org/debian bookworm/main amd64 python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get: 193 http://deb.debian.org/debian bookworm/main amd64 python3-duecredit all 0.9.1-1.1 [66.7 kB] Get: 194 http://deb.debian.org/debian bookworm/main amd64 python3-monotonic all 1.6-2 [5728 B] Get: 195 http://deb.debian.org/debian bookworm/main amd64 python3-fasteners all 0.17.3-2 [14.7 kB] Get: 196 http://deb.debian.org/debian bookworm/main amd64 python3-ply all 3.11-5 [65.8 kB] Get: 197 http://deb.debian.org/debian bookworm/main amd64 python3-pythran amd64 0.11.0+ds-7 [427 kB] Get: 198 http://deb.debian.org/debian bookworm/main amd64 python3-scipy amd64 1.10.1-2 [15.2 MB] Get: 199 http://deb.debian.org/debian bookworm/main amd64 python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB] Get: 200 http://deb.debian.org/debian bookworm/main amd64 python3-mpmath all 1.2.1-2 [418 kB] Get: 201 http://deb.debian.org/debian bookworm/main amd64 python3-sympy all 1.11.1-1 [4358 kB] Get: 202 http://deb.debian.org/debian bookworm/main amd64 python3-fs all 2.4.16-2 [95.2 kB] Get: 203 http://deb.debian.org/debian bookworm/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b2 [25.0 kB] Get: 204 http://deb.debian.org/debian bookworm/main amd64 unicode-data all 15.0.0-1 [7984 kB] Get: 205 http://deb.debian.org/debian bookworm/main amd64 python3-fonttools amd64 4.38.0-1+b1 [1012 kB] Get: 206 http://deb.debian.org/debian bookworm/main amd64 sphinx-rtd-theme-common all 1.2.0+dfsg-1 [997 kB] Get: 207 http://deb.debian.org/debian bookworm/main amd64 python3-mrcfile all 1.4.3-3 [113 kB] Get: 208 http://deb.debian.org/debian bookworm/main amd64 python3-griddataformats all 1.0.1-1 [2044 kB] Get: 209 http://deb.debian.org/debian bookworm/main amd64 python3-gsd amd64 2.7.0-2+b1 [84.5 kB] Get: 210 http://deb.debian.org/debian bookworm/main amd64 python3-h5py-serial amd64 3.7.0-8 [804 kB] Get: 211 http://deb.debian.org/debian bookworm/main amd64 python3-h5py all 3.7.0-8 [10.3 kB] Get: 212 http://deb.debian.org/debian bookworm/main amd64 python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 213 http://deb.debian.org/debian bookworm/main amd64 python3-hypothesis all 6.67.1-1 [270 kB] Get: 214 http://deb.debian.org/debian bookworm/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 215 http://deb.debian.org/debian bookworm/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 216 http://deb.debian.org/debian bookworm/main amd64 python3-markupsafe amd64 2.1.2-1+b1 [13.2 kB] Get: 217 http://deb.debian.org/debian bookworm/main amd64 python3-jinja2 all 3.1.2-1 [119 kB] Get: 218 http://deb.debian.org/debian bookworm/main amd64 python3-joblib all 1.2.0-4 [211 kB] Get: 219 http://deb.debian.org/debian bookworm/main amd64 python3-kiwisolver amd64 1.4.4-1+b1 [60.1 kB] Get: 220 http://deb.debian.org/debian bookworm/main amd64 python3-latexcodec all 2.0.1-2 [18.0 kB] Get: 221 http://deb.debian.org/debian bookworm/main amd64 python3-pyparsing all 3.0.9-1 [138 kB] Get: 222 http://deb.debian.org/debian bookworm/main amd64 python3-matplotlib amd64 3.6.3-1+b1 [6921 kB] Get: 223 http://deb.debian.org/debian bookworm/main amd64 python3-msgpack amd64 1.0.3-2+b1 [67.3 kB] Get: 224 http://deb.debian.org/debian bookworm/main amd64 python3-mmtf all 1.1.3-1 [17.0 kB] Get: 225 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB] Get: 226 http://deb.debian.org/debian bookworm/main amd64 python3-pbr all 5.10.0-2 [61.4 kB] Get: 227 http://deb.debian.org/debian bookworm/main amd64 python3-mock all 4.0.3-4 [64.0 kB] Get: 228 http://deb.debian.org/debian bookworm/main amd64 sphinx-common all 5.3.0-4 [653 kB] Get: 229 http://deb.debian.org/debian bookworm/main amd64 python3-pygments all 2.14.0+dfsg-1 [783 kB] Get: 230 http://deb.debian.org/debian bookworm/main amd64 python3-snowballstemmer all 2.2.0-2 [57.8 kB] Get: 231 http://deb.debian.org/debian bookworm/main amd64 python3-sphinx all 5.3.0-4 [549 kB] Get: 232 http://deb.debian.org/debian bookworm/main amd64 python3-sphinx-rtd-theme all 1.2.0+dfsg-1 [27.7 kB] Get: 233 http://deb.debian.org/debian bookworm/main amd64 python3-msmb-theme all 1.2.0-3 [33.7 kB] Get: 234 http://deb.debian.org/debian bookworm/main amd64 python3-netcdf4 amd64 1.6.2-1+b1 [465 kB] Get: 235 http://deb.debian.org/debian bookworm/main amd64 python3-networkx all 2.8.8-1 [1425 kB] Get: 236 http://deb.debian.org/debian bookworm/main amd64 python3-pandas-lib amd64 1.5.3+dfsg-2 [3499 kB] Get: 237 http://deb.debian.org/debian bookworm/main amd64 python3-pandas all 1.5.3+dfsg-2 [2885 kB] Get: 238 http://deb.debian.org/debian bookworm/main amd64 python3-pluggy all 1.0.0+repack-1 [19.7 kB] Get: 239 http://deb.debian.org/debian bookworm/main amd64 python3-py all 1.11.0-1 [89.2 kB] Get: 240 http://deb.debian.org/debian bookworm/main amd64 python3-yaml amd64 6.0-3+b2 [119 kB] Get: 241 http://deb.debian.org/debian bookworm/main amd64 python3-pybtex all 0.24.0-3 [74.5 kB] Get: 242 http://deb.debian.org/debian bookworm/main amd64 python3-pybtex-docutils all 1.0.2-1 [8064 B] Get: 243 http://deb.debian.org/debian bookworm/main amd64 python3-pytest all 7.2.1-2 [236 kB] Get: 244 http://deb.debian.org/debian bookworm/main amd64 python3-seaborn all 0.12.2-1 [215 kB] Get: 245 http://deb.debian.org/debian bookworm/main amd64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 246 http://deb.debian.org/debian bookworm/main amd64 python3-sklearn-lib amd64 1.2.1+dfsg-1 [2567 kB] Get: 247 http://deb.debian.org/debian bookworm/main amd64 python3-sklearn all 1.2.1+dfsg-1 [2103 kB] 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) 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.) Preparing to unpack .../fonts-lato_2.0-2.1_all.deb ... Unpacking fonts-lato (2.0-2.1) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... 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 ... 18490 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package mailcap. Preparing to unpack .../2-mailcap_3.70+nmu1_all.deb ... Unpacking mailcap (3.70+nmu1) ... Selecting previously unselected package mime-support. Preparing to unpack .../3-mime-support_3.66_all.deb ... Unpacking mime-support (3.66) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../5-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... 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 ... 18948 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package tzdata. Preparing to unpack .../002-tzdata_2023c-5+deb12u1_all.deb ... Unpacking tzdata (2023c-5+deb12u1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../003-libproc2-0_2%3a4.0.2-3_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../004-procps_2%3a4.0.2-3_amd64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../005-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../006-openssl_3.0.11-1~deb12u2_amd64.deb ... Unpacking openssl (3.0.11-1~deb12u2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../007-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../008-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../009-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../010-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../011-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../012-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../013-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../014-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../015-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../016-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../017-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../018-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../019-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../020-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. 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Setting up python3-msmb-theme (1.2.0-3) ... Processing triggers for ca-certificates (20230311) ... 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 Reading package lists... Building dependency tree... Reading state information... 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 dpkg-buildpackage: info: source package mdanalysis dpkg-buildpackage: info: source version 2.4.2+dfsg1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Drew Parsons dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from mdanalysis-2.4.2+dfsg1/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ fakeroot debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.4.2+dfsg1' rm -f .duecredit.p rm -f package/MDAnalysis/authors.py rm -f package/MDAnalysis/analysis/encore/clustering/affinityprop.c \ package/MDAnalysis/analysis/encore/cutils.c \ package/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c \ package/MDAnalysis/lib/_augment.cpp \ package/MDAnalysis/lib/_cutil.cpp \ package/MDAnalysis/lib/c_distances.c \ package/MDAnalysis/lib/c_distances_openmp.c \ package/MDAnalysis/lib/formats/cython_util.c \ package/MDAnalysis/lib/formats/libdcd.c \ package/MDAnalysis/lib/formats/libmdaxdr.c \ package/MDAnalysis/lib/nsgrid.cpp \ package/MDAnalysis/lib/qcprot.c rm -rf package/MDAnalysis.egg-info rm -f testsuite/MDAnalysisTests/data/.*_offsets.npz testsuite/MDAnalysisTests/data/*/.*_offsets.npz rm -rf testsuite/.pytest_cache make[1]: Leaving directory '/build/reproducible-path/mdanalysis-2.4.2+dfsg1' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build dh build --with python3,sphinxdoc --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:107: Building wheel for python3.11 with "build" module I: pybuild base:240: python3.11 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis * Building wheel... /usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar. if not hasattr(numpy, method): /usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar. obj = getattr(themodule, elem) Attempting to autodetect OpenMP support... Compiler supports OpenMP Will attempt to use Cython. Compiling MDAnalysis/lib/formats/libdcd.pyx because it changed. Compiling MDAnalysis/lib/c_distances.pyx because it changed. Compiling MDAnalysis/lib/c_distances_openmp.pyx because it changed. Compiling MDAnalysis/lib/qcprot.pyx because it changed. Compiling MDAnalysis/lib/formats/libmdaxdr.pyx because it changed. Compiling MDAnalysis/lib/formats/cython_util.pyx because it changed. Compiling MDAnalysis/analysis/encore/cutils.pyx because it changed. Compiling MDAnalysis/analysis/encore/clustering/affinityprop.pyx because it changed. Compiling MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx because it changed. Compiling MDAnalysis/lib/_cutil.pyx because it changed. Compiling MDAnalysis/lib/_augment.pyx because it changed. Compiling MDAnalysis/lib/nsgrid.pyx because it changed. Compiling MDAnalysis/coordinates/timestep.pyx because it changed. [ 1/13] Cythonizing MDAnalysis/analysis/encore/clustering/affinityprop.pyx [ 2/13] Cythonizing MDAnalysis/analysis/encore/cutils.pyx [ 3/13] Cythonizing MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx [ 4/13] Cythonizing MDAnalysis/coordinates/timestep.pyx [ 5/13] Cythonizing MDAnalysis/lib/_augment.pyx [ 6/13] Cythonizing MDAnalysis/lib/_cutil.pyx [ 7/13] Cythonizing MDAnalysis/lib/c_distances.pyx [ 8/13] Cythonizing MDAnalysis/lib/c_distances_openmp.pyx [ 9/13] Cythonizing MDAnalysis/lib/formats/cython_util.pyx [10/13] Cythonizing MDAnalysis/lib/formats/libdcd.pyx [11/13] Cythonizing MDAnalysis/lib/formats/libmdaxdr.pyx [12/13] Cythonizing MDAnalysis/lib/nsgrid.pyx [13/13] Cythonizing MDAnalysis/lib/qcprot.pyx /usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:203: UserWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) warnings.warn(msg) running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-cpython-311 creating build/lib.linux-x86_64-cpython-311/MDAnalysis copying MDAnalysis/authors.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis copying MDAnalysis/version.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis copying MDAnalysis/units.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis copying MDAnalysis/exceptions.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis copying MDAnalysis/due.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis copying MDAnalysis/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis creating build/lib.linux-x86_64-cpython-311/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/visualization copying MDAnalysis/visualization/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/visualization creating build/lib.linux-x86_64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/wrap.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/translate.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/rotate.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/fit.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/base.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/transformations creating build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/tables.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/guessers.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/core.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/base.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/GROParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology creating build/lib.linux-x86_64-cpython-311/MDAnalysis/tests copying MDAnalysis/tests/datafiles.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/tests copying MDAnalysis/tests/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/tests creating build/lib.linux-x86_64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/vmd.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/pymol.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/jmol.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/gromacs.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/charmm.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/base.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/selections creating build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/util.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/transformations.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/mdamath.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/log.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/distances.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/correlations.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib creating build/lib.linux-x86_64-cpython-311/MDAnalysis/core copying MDAnalysis/core/universe.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/core copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/core copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/core copying MDAnalysis/core/topology.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/core copying MDAnalysis/core/selection.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/core copying MDAnalysis/core/groups.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/core copying MDAnalysis/core/accessors.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/core copying MDAnalysis/core/_get_readers.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/core copying MDAnalysis/core/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/core creating build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/null.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/memory.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/core.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/chain.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/base.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/TNG.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates creating build/lib.linux-x86_64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/RDKit.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/converters creating build/lib.linux-x86_64-cpython-311/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/core.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/base.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/auxiliary creating build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/rms.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/rdf.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/psa.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/polymer.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/pca.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/msd.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/gnm.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/distances.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/dielectric.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/density.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/contacts.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/bat.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/base.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/align.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis creating build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/tpr creating build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats creating build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/legacy creating build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hydrogenbonds creating build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/utils.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/templates.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/hole.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hole2 creating build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hbonds creating build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore creating build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/data creating build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering running egg_info creating MDAnalysis.egg-info writing MDAnalysis.egg-info/PKG-INFO writing dependency_links to MDAnalysis.egg-info/dependency_links.txt writing requirements to MDAnalysis.egg-info/requires.txt writing top-level names to MDAnalysis.egg-info/top_level.txt writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' reading manifest file 'MDAnalysis.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching 'doc/html/html' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.pyd' found anywhere in distribution warning: no previously-included files matching '*~' found anywhere in distribution warning: no previously-included files matching '.git' found anywhere in distribution adding license file 'LICENSE' adding license file 'AUTHORS' writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.analysis.encore.clustering.include' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.clustering.include' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.analysis.encore.clustering.include' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.analysis.encore.clustering.include' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.analysis.encore.clustering.src' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.clustering.src' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.analysis.encore.clustering.src' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.analysis.encore.clustering.src' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.analysis.encore.dimensionality_reduction.include' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.include' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.analysis.encore.dimensionality_reduction.include' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.analysis.encore.dimensionality_reduction.include' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.analysis.encore.dimensionality_reduction.src' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.src' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.analysis.encore.dimensionality_reduction.src' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.analysis.encore.dimensionality_reduction.src' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.formats.include' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.formats.include' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.lib.formats.include' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.lib.formats.include' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.formats.src' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.formats.src' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.lib.formats.src' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.lib.formats.src' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.include' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.include' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.lib.include' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.lib.include' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.libmdanalysis' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.libmdanalysis' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.lib.libmdanalysis' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.lib.libmdanalysis' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.src.transformations' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.src.transformations' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'MDAnalysis.lib.src.transformations' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'MDAnalysis.lib.src.transformations' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/data copying MDAnalysis/lib/_augment.cpp -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/_augment.pyx -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/_cutil.cpp -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pxd -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pyx -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/c_distances.c -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pyx -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.cpp -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.pyx -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/qcprot.c -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/qcprot.pyx -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib creating build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/include copying MDAnalysis/lib/include/calc_distances.h -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/include creating build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/libmdanalysis copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/libmdanalysis creating build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/src creating build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/src/transformations copying MDAnalysis/coordinates/timestep.cpp -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pxd -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pyx -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/lib/formats/cython_util.c -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.c -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats creating build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/include creating build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/src copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/include copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/include creating build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/src copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/src copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering creating build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering/include copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering/include creating build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering/src copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering/src running build_ext building 'MDAnalysis.lib.formats.libdcd' extension INFO: C compiler: x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.4.2+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC creating build/temp.linux-x86_64-cpython-311 creating build/temp.linux-x86_64-cpython-311/MDAnalysis creating build/temp.linux-x86_64-cpython-311/MDAnalysis/lib creating build/temp.linux-x86_64-cpython-311/MDAnalysis/lib/formats INFO: compile options: '-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/usr/include/python3.11 -c' extra options: '-std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros' INFO: x86_64-linux-gnu-gcc: MDAnalysis/lib/formats/libdcd.c cc1: warning: '-fassociative-math' disabled; other options take precedence In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/formats/libdcd.c:781: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In file included from MDAnalysis/lib/formats/libdcd.c:791: MDAnalysis/lib/formats/include/readdcd.h: In function 'read_dcdstep': MDAnalysis/lib/formats/include/readdcd.h:549:17: warning: comparison of integer expressions of different signedness: 'fio_size_t' {aka 'long int'} and 'long unsigned int' [-Wsign-compare] 549 | if (readlen != (6*sizeof(int) + 3*N*sizeof(float))) | ^~ MDAnalysis/lib/formats/include/readdcd.h:562:21: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 562 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; | ^~ MDAnalysis/lib/formats/include/readdcd.h: In function 'write_dcdheader': MDAnalysis/lib/formats/include/readdcd.h:698:14: warning: unused variable 'tmbuf' [-Wunused-variable] 698 | struct tm *tmbuf; | ^~~~~ MDAnalysis/lib/formats/include/readdcd.h:697:10: warning: unused variable 'cur_time' [-Wunused-variable] 697 | time_t cur_time; | ^~~~~~~~ In file included from MDAnalysis/lib/formats/include/readdcd.h:25: MDAnalysis/lib/formats/include/endianswap.h: At top level: MDAnalysis/lib/formats/include/endianswap.h:96:13: warning: 'swap2_aligned' defined but not used [-Wunused-function] 96 | static void swap2_aligned(void *v, long ndata) { | ^~~~~~~~~~~~~ MDAnalysis/lib/formats/include/endianswap.h:32:13: warning: 'swap2_unaligned' defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ In file included from MDAnalysis/lib/formats/libdcd.c:790: MDAnalysis/lib/formats/include/fastio.h:453:12: warning: 'fio_write_str' defined but not used [-Wunused-function] 453 | static int fio_write_str(fio_fd fd, const char *str) { | ^~~~~~~~~~~~~ MDAnalysis/lib/formats/include/fastio.h:449:12: warning: 'fio_read_int32' defined but not used [-Wunused-function] 449 | static int fio_read_int32(fio_fd fd, int *i) { | ^~~~~~~~~~~~~~ In file included from /usr/include/python3.11/tupleobject.h:39, from /usr/include/python3.11/Python.h:59, from MDAnalysis/lib/formats/libdcd.c:39: In function '__Pyx_GetItemInt_Fast', inlined from '__pyx_pf_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_26seek' at MDAnalysis/lib/formats/libdcd.c:6677:17, inlined from '__pyx_pw_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_27seek' at MDAnalysis/lib/formats/libdcd.c:6534:13: /usr/include/python3.11/cpython/tupleobject.h:30:64: warning: array subscript -1 is below array bounds of 'PyObject *[1]' {aka 'struct _object *[1]'} [-Warray-bounds] 30 | #define PyTuple_GET_ITEM(op, index) (_PyTuple_CAST(op)->ob_item[index]) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ MDAnalysis/lib/formats/libdcd.c:28607:27: note: in expansion of macro 'PyTuple_GET_ITEM' 28607 | PyObject *r = PyTuple_GET_ITEM(o, n); | ^~~~~~~~~~~~~~~~ /usr/include/python3.11/cpython/tupleobject.h: In function '__pyx_pw_10MDAnalysis_3lib_7formats_6libdcd_7DCDFile_27seek': /usr/include/python3.11/cpython/tupleobject.h:10:15: note: while referencing 'ob_item' 10 | PyObject *ob_item[1]; | ^~~~~~~ INFO: x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.4.2+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/MDAnalysis/lib/formats/libdcd.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/libdcd.cpython-311-x86_64-linux-gnu.so building 'MDAnalysis.lib.c_distances' extension INFO: C compiler: x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.4.2+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/include -I/usr/include/python3.11 -c' extra options: '-std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros' INFO: x86_64-linux-gnu-gcc: MDAnalysis/lib/c_distances.c cc1: warning: '-fassociative-math' disabled; other options take precedence In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/c_distances.c:781: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ INFO: x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.4.2+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/MDAnalysis/lib/c_distances.o -L/usr/lib/x86_64-linux-gnu -lm -o build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/c_distances.cpython-311-x86_64-linux-gnu.so building 'MDAnalysis.lib.c_distances_openmp' extension INFO: C compiler: x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.4.2+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-DPARALLEL -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/MDAnalysis/lib/include -I/usr/include/python3.11 -c' extra options: '-fopenmp -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros' INFO: x86_64-linux-gnu-gcc: MDAnalysis/lib/c_distances_openmp.c cc1: warning: '-fassociative-math' disabled; other options take precedence In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/c_distances_openmp.c:792: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ INFO: x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.4.2+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/MDAnalysis/lib/c_distances_openmp.o -L/usr/lib/x86_64-linux-gnu -lm -lgomp -o build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/c_distances_openmp.cpython-311-x86_64-linux-gnu.so -fopenmp building 'MDAnalysis.lib.qcprot' extension INFO: C compiler: x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.4.2+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros' INFO: x86_64-linux-gnu-gcc: MDAnalysis/lib/qcprot.c cc1: warning: '-fassociative-math' disabled; other options take precedence In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/qcprot.c:775: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ MDAnalysis/lib/qcprot.c: In function '__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct': MDAnalysis/lib/qcprot.c:2383:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 2383 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { | ^ MDAnalysis/lib/qcprot.c:2591:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 2591 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { | ^ INFO: x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.4.2+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/MDAnalysis/lib/qcprot.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/qcprot.cpython-311-x86_64-linux-gnu.so building 'MDAnalysis.lib._transformations' extension INFO: C compiler: x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.4.2+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC creating build/temp.linux-x86_64-cpython-311/MDAnalysis/lib/src creating build/temp.linux-x86_64-cpython-311/MDAnalysis/lib/src/transformations INFO: compile options: '-I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros' INFO: x86_64-linux-gnu-gcc: MDAnalysis/lib/src/transformations/transformations.c cc1: warning: '-fassociative-math' disabled; other options take precedence In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/src/transformations/transformations.c:73: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ MDAnalysis/lib/src/transformations/transformations.c: In function 'py_superimposition_matrix': MDAnalysis/lib/src/transformations/transformations.c:1845: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 1845 | #pragma vector always | MDAnalysis/lib/src/transformations/transformations.c:1962: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 1962 | #pragma vector always | MDAnalysis/lib/src/transformations/transformations.c:1986: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 1986 | #pragma vector always | MDAnalysis/lib/src/transformations/transformations.c: In function 'axis2tuple': MDAnalysis/lib/src/transformations/transformations.c:2122:5: warning: 'PyUnicode_GetSize' is deprecated [-Wdeprecated-declarations] 2122 | if (PyUnicode_Check(axes) && (PyUnicode_GetSize(axes) == 4)) { | ^~ In file included from /usr/include/python3.11/Python.h:51, from MDAnalysis/lib/src/transformations/transformations.c:68: /usr/include/python3.11/unicodeobject.h:177:43: note: declared here 177 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_ssize_t) PyUnicode_GetSize( | ^~~~~~~~~~~~~~~~~ MDAnalysis/lib/src/transformations/transformations.c: In function 'py_vector_norm': MDAnalysis/lib/src/transformations/transformations.c:3427: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 3427 | #pragma vector always | MDAnalysis/lib/src/transformations/transformations.c:3508: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 3508 | #pragma vector always | MDAnalysis/lib/src/transformations/transformations.c: In function 'py_unit_vector': MDAnalysis/lib/src/transformations/transformations.c:3610: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 3610 | #pragma vector always | MDAnalysis/lib/src/transformations/transformations.c:3615: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 3615 | #pragma vector always | MDAnalysis/lib/src/transformations/transformations.c:3679: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 3679 | #pragma vector always | MDAnalysis/lib/src/transformations/transformations.c:3684: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 3684 | #pragma vector always | MDAnalysis/lib/src/transformations/transformations.c: At top level: MDAnalysis/lib/src/transformations/transformations.c:910:1: warning: 'PyConverter_DoubleVector4Copy' defined but not used [-Wunused-function] 910 | PyConverter_DoubleVector4Copy( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MDAnalysis/lib/src/transformations/transformations.c:804:1: warning: 'PyConverter_DoubleArrayOrNone' defined but not used [-Wunused-function] 804 | PyConverter_DoubleArrayOrNone( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MDAnalysis/lib/src/transformations/transformations.c:774:1: warning: 'PyConverter_DoubleArray' defined but not used [-Wunused-function] 774 | PyConverter_DoubleArray( | ^~~~~~~~~~~~~~~~~~~~~~~ INFO: x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.4.2+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/MDAnalysis/lib/src/transformations/transformations.o -L/usr/lib/x86_64-linux-gnu -lm -o build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/_transformations.cpython-311-x86_64-linux-gnu.so building 'MDAnalysis.lib.formats.libmdaxdr' extension INFO: C compiler: x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.4.2+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC creating build/temp.linux-x86_64-cpython-311/MDAnalysis/lib/formats/src 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: 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 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: /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] 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 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/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/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 /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_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 -*- | 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 -*- | MDAnalysis/lib/formats/src/xdrfile_trr.c: In function 'do_trnheader': MDAnalysis/lib/formats/src/xdrfile_trr.c:78:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 78 | if (slen != strlen(version) + 1) | ^~ 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: /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) | ^~ MDAnalysis/lib/formats/src/xdrfile.c: In function 'sizeofints': MDAnalysis/lib/formats/src/xdrfile.c:547:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 547 | while (bytes[num_of_bytes] >= num) | ^~ MDAnalysis/lib/formats/src/xdrfile.c: In function 'encodeints': MDAnalysis/lib/formats/src/xdrfile.c:656:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 656 | if (num_of_bits >= num_of_bytes * 8) | ^~ MDAnalysis/lib/formats/src/xdrfile.c:658:31: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 658 | for (i = 0; i < num_of_bytes; i++) | ^ MDAnalysis/lib/formats/src/xdrfile.c:666:31: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 666 | for (i = 0; i < num_of_bytes-1; i++) | ^ MDAnalysis/lib/formats/src/xdrfile.c: In function 'decodebits': MDAnalysis/lib/formats/src/xdrfile.c:706:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 706 | if (lastbits < num_of_bits) | ^ MDAnalysis/lib/formats/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': 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.c:868:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] 868 | maxidx = (LASTIDXxfp->buf1size) | ^ MDAnalysis/lib/formats/src/xdrfile.c:1135:25: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 1135 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) | ^ MDAnalysis/lib/formats/src/xdrfile.c:1141:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] 1141 | maxidx = (LASTIDXxfp->buf1size) | ^ MDAnalysis/lib/formats/src/xdrfile.c:1368:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] 1368 | maxidx = (LASTIDXxfp->buf1size) { | ^ MDAnalysis/lib/formats/src/xdrfile.c:1619:25: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 1619 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { | ^ MDAnalysis/lib/formats/src/xdrfile.c:1624:26: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] 1624 | maxidx = (LASTIDX build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/data copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/data copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/data copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/data creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/cutils.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/cutils.pyx -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/cutils.c -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering/src copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering/src/ap.c -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering/src creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering/include copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering/include/ap.h -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering/include copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/clustering creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/encore creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hbonds copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hbonds copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hbonds creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hole2 copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hole2 copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hole2/hole.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hole2 copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hole2/templates.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hole2 copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hole2/utils.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hole2 creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hydrogenbonds creating build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/legacy copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/legacy copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/legacy copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/align.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/base.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/bat.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/contacts.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/density.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/dielectric.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/distances.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/gnm.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/msd.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/nucleicacids.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/pca.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/polymer.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/psa.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/rdf.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/rms.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-311/MDAnalysis/auxiliary/EDR.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-311/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-311/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-311/MDAnalysis/auxiliary/base.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/auxiliary copying build/lib.linux-x86_64-cpython-311/MDAnalysis/auxiliary/core.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/auxiliary creating build/bdist.linux-x86_64/wheel/MDAnalysis/converters copying build/lib.linux-x86_64-cpython-311/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/converters copying build/lib.linux-x86_64-cpython-311/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/converters copying build/lib.linux-x86_64-cpython-311/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/converters copying build/lib.linux-x86_64-cpython-311/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/converters copying build/lib.linux-x86_64-cpython-311/MDAnalysis/converters/RDKit.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/converters copying build/lib.linux-x86_64-cpython-311/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/converters copying build/lib.linux-x86_64-cpython-311/MDAnalysis/converters/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/converters creating build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/timestep.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/timestep.pyx -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/timestep.pxd -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/timestep.cpp -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/H5MD.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/TNG.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/base.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/chain.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/core.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/memory.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates copying build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates/null.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/coordinates creating build/bdist.linux-x86_64/wheel/MDAnalysis/core copying build/lib.linux-x86_64-cpython-311/MDAnalysis/core/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/core copying build/lib.linux-x86_64-cpython-311/MDAnalysis/core/_get_readers.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/core copying build/lib.linux-x86_64-cpython-311/MDAnalysis/core/accessors.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/core copying build/lib.linux-x86_64-cpython-311/MDAnalysis/core/groups.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/core copying build/lib.linux-x86_64-cpython-311/MDAnalysis/core/selection.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/core copying build/lib.linux-x86_64-cpython-311/MDAnalysis/core/topology.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/core copying build/lib.linux-x86_64-cpython-311/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/core copying build/lib.linux-x86_64-cpython-311/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/core copying build/lib.linux-x86_64-cpython-311/MDAnalysis/core/universe.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/core creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/nsgrid.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/_augment.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/_cutil.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/_transformations.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/qcprot.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/c_distances_openmp.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/c_distances.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src/transformations copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/src/transformations/transformations.c -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src/transformations copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/src/transformations/LICENCE -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src/transformations copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/src/transformations/AUTHOR -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/src/transformations creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/libmdanalysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/libmdanalysis creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/include copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/include/calc_distances.h -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/include copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/qcprot.pyx -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/qcprot.c -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/nsgrid.pyx -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/nsgrid.cpp -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/c_distances_openmp.pyx -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/c_distances_openmp.c -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/c_distances.pyx -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/c_distances.c -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/_cutil.pyx -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/_cutil.pxd -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/_cutil.cpp -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/_augment.pyx -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/_augment.cpp -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/cython_util.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/libmdaxdr.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/libdcd.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/src/xtc_seek.c -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/src/xdrfile.c -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/src copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/src/trr_seek.c -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/src creating build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/include/xtc_seek.h -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/include/xdrfile.h -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/include/trr_seek.h -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/include/readdcd.h -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/include/fastio.h -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/include/endianswap.h -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/libmdaxdr.pyx -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/libmdaxdr.pxd -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/libmdaxdr.c -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/libdcd.pyx -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/libdcd.pxd -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/libdcd.c -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/cython_util.pyx -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/cython_util.pxd -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/cython_util.c -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/correlations.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/distances.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/log.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/mdamath.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/transformations.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/util.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib creating build/bdist.linux-x86_64/wheel/MDAnalysis/selections copying build/lib.linux-x86_64-cpython-311/MDAnalysis/selections/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/selections copying build/lib.linux-x86_64-cpython-311/MDAnalysis/selections/base.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/selections copying build/lib.linux-x86_64-cpython-311/MDAnalysis/selections/charmm.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/selections copying build/lib.linux-x86_64-cpython-311/MDAnalysis/selections/gromacs.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/selections copying build/lib.linux-x86_64-cpython-311/MDAnalysis/selections/jmol.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/selections copying build/lib.linux-x86_64-cpython-311/MDAnalysis/selections/pymol.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/selections copying build/lib.linux-x86_64-cpython-311/MDAnalysis/selections/vmd.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/selections creating build/bdist.linux-x86_64/wheel/MDAnalysis/tests copying build/lib.linux-x86_64-cpython-311/MDAnalysis/tests/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/tests copying build/lib.linux-x86_64-cpython-311/MDAnalysis/tests/datafiles.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/tests creating build/bdist.linux-x86_64/wheel/MDAnalysis/topology creating build/bdist.linux-x86_64/wheel/MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology/tpr copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/GROParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/base.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/core.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/guessers.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology copying build/lib.linux-x86_64-cpython-311/MDAnalysis/topology/tables.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/topology creating build/bdist.linux-x86_64/wheel/MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-311/MDAnalysis/transformations/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-311/MDAnalysis/transformations/base.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-311/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-311/MDAnalysis/transformations/fit.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-311/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-311/MDAnalysis/transformations/rotate.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-311/MDAnalysis/transformations/translate.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-311/MDAnalysis/transformations/wrap.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/transformations creating build/bdist.linux-x86_64/wheel/MDAnalysis/visualization copying build/lib.linux-x86_64-cpython-311/MDAnalysis/visualization/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/visualization copying build/lib.linux-x86_64-cpython-311/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/visualization copying build/lib.linux-x86_64-cpython-311/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/visualization copying build/lib.linux-x86_64-cpython-311/MDAnalysis/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/due.py -> build/bdist.linux-x86_64/wheel/MDAnalysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/exceptions.py -> build/bdist.linux-x86_64/wheel/MDAnalysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/units.py -> build/bdist.linux-x86_64/wheel/MDAnalysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/version.py -> build/bdist.linux-x86_64/wheel/MDAnalysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/authors.py -> build/bdist.linux-x86_64/wheel/MDAnalysis running install_egg_info Copying MDAnalysis.egg-info to build/bdist.linux-x86_64/wheel/MDAnalysis-2.4.2.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/MDAnalysis-2.4.2.dist-info/WHEEL creating '/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/.tmp-7hinn2mo/MDAnalysis-2.4.2-cp311-cp311-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'MDAnalysis/__init__.py' adding 'MDAnalysis/authors.py' adding 'MDAnalysis/due.py' adding 'MDAnalysis/exceptions.py' adding 'MDAnalysis/units.py' adding 'MDAnalysis/version.py' adding 'MDAnalysis/analysis/__init__.py' adding 'MDAnalysis/analysis/align.py' adding 'MDAnalysis/analysis/base.py' adding 'MDAnalysis/analysis/bat.py' adding 'MDAnalysis/analysis/contacts.py' adding 'MDAnalysis/analysis/density.py' adding 'MDAnalysis/analysis/dielectric.py' adding 'MDAnalysis/analysis/diffusionmap.py' adding 'MDAnalysis/analysis/dihedrals.py' adding 'MDAnalysis/analysis/distances.py' adding 'MDAnalysis/analysis/gnm.py' adding 'MDAnalysis/analysis/helix_analysis.py' adding 'MDAnalysis/analysis/leaflet.py' adding 'MDAnalysis/analysis/lineardensity.py' adding 'MDAnalysis/analysis/msd.py' adding 'MDAnalysis/analysis/nucleicacids.py' adding 'MDAnalysis/analysis/nuclinfo.py' adding 'MDAnalysis/analysis/pca.py' adding 'MDAnalysis/analysis/polymer.py' adding 'MDAnalysis/analysis/psa.py' adding 'MDAnalysis/analysis/rdf.py' adding 'MDAnalysis/analysis/rms.py' adding 'MDAnalysis/analysis/waterdynamics.py' adding 'MDAnalysis/analysis/data/__init__.py' adding 'MDAnalysis/analysis/data/filenames.py' adding 'MDAnalysis/analysis/data/janin_ref_data.npy' adding 'MDAnalysis/analysis/data/rama_ref_data.npy' adding 'MDAnalysis/analysis/encore/__init__.py' adding 'MDAnalysis/analysis/encore/bootstrap.py' adding 'MDAnalysis/analysis/encore/confdistmatrix.py' adding 'MDAnalysis/analysis/encore/covariance.py' adding 'MDAnalysis/analysis/encore/cutils.c' adding 'MDAnalysis/analysis/encore/cutils.cpython-311-x86_64-linux-gnu.so' adding 'MDAnalysis/analysis/encore/cutils.pyx' adding 'MDAnalysis/analysis/encore/similarity.py' adding 'MDAnalysis/analysis/encore/utils.py' adding 'MDAnalysis/analysis/encore/clustering/ClusterCollection.py' adding 'MDAnalysis/analysis/encore/clustering/ClusteringMethod.py' adding 'MDAnalysis/analysis/encore/clustering/__init__.py' adding 'MDAnalysis/analysis/encore/clustering/affinityprop.c' adding 'MDAnalysis/analysis/encore/clustering/affinityprop.cpython-311-x86_64-linux-gnu.so' adding 'MDAnalysis/analysis/encore/clustering/affinityprop.pyx' adding 'MDAnalysis/analysis/encore/clustering/cluster.py' adding 'MDAnalysis/analysis/encore/clustering/include/ap.h' adding 'MDAnalysis/analysis/encore/clustering/src/ap.c' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-311-x86_64-linux-gnu.so' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h' adding 'MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c' adding 'MDAnalysis/analysis/hbonds/__init__.py' adding 'MDAnalysis/analysis/hbonds/hbond_autocorrel.py' adding 'MDAnalysis/analysis/hole2/__init__.py' adding 'MDAnalysis/analysis/hole2/hole.py' adding 'MDAnalysis/analysis/hole2/templates.py' adding 'MDAnalysis/analysis/hole2/utils.py' adding 'MDAnalysis/analysis/hydrogenbonds/__init__.py' adding 'MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py' adding 'MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py' adding 'MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py' adding 'MDAnalysis/analysis/legacy/__init__.py' adding 'MDAnalysis/analysis/legacy/x3dna.py' adding 'MDAnalysis/auxiliary/EDR.py' adding 'MDAnalysis/auxiliary/XVG.py' adding 'MDAnalysis/auxiliary/__init__.py' adding 'MDAnalysis/auxiliary/base.py' adding 'MDAnalysis/auxiliary/core.py' adding 'MDAnalysis/converters/OpenMM.py' adding 'MDAnalysis/converters/OpenMMParser.py' adding 'MDAnalysis/converters/ParmEd.py' adding 'MDAnalysis/converters/ParmEdParser.py' adding 'MDAnalysis/converters/RDKit.py' adding 'MDAnalysis/converters/RDKitParser.py' adding 'MDAnalysis/converters/__init__.py' adding 'MDAnalysis/coordinates/CRD.py' adding 'MDAnalysis/coordinates/DCD.py' adding 'MDAnalysis/coordinates/DLPoly.py' adding 'MDAnalysis/coordinates/DMS.py' adding 'MDAnalysis/coordinates/FHIAIMS.py' adding 'MDAnalysis/coordinates/GMS.py' adding 'MDAnalysis/coordinates/GRO.py' adding 'MDAnalysis/coordinates/GSD.py' adding 'MDAnalysis/coordinates/H5MD.py' adding 'MDAnalysis/coordinates/INPCRD.py' adding 'MDAnalysis/coordinates/LAMMPS.py' adding 'MDAnalysis/coordinates/MMTF.py' adding 'MDAnalysis/coordinates/MOL2.py' adding 'MDAnalysis/coordinates/NAMDBIN.py' adding 'MDAnalysis/coordinates/PDB.py' adding 'MDAnalysis/coordinates/PDBQT.py' adding 'MDAnalysis/coordinates/PQR.py' adding 'MDAnalysis/coordinates/ParmEd.py' adding 'MDAnalysis/coordinates/TNG.py' adding 'MDAnalysis/coordinates/TRJ.py' adding 'MDAnalysis/coordinates/TRR.py' adding 'MDAnalysis/coordinates/TRZ.py' adding 'MDAnalysis/coordinates/TXYZ.py' adding 'MDAnalysis/coordinates/XDR.py' adding 'MDAnalysis/coordinates/XTC.py' adding 'MDAnalysis/coordinates/XYZ.py' adding 'MDAnalysis/coordinates/__init__.py' adding 'MDAnalysis/coordinates/base.py' adding 'MDAnalysis/coordinates/chain.py' adding 'MDAnalysis/coordinates/chemfiles.py' adding 'MDAnalysis/coordinates/core.py' adding 'MDAnalysis/coordinates/memory.py' adding 'MDAnalysis/coordinates/null.py' adding 'MDAnalysis/coordinates/timestep.cpp' adding 'MDAnalysis/coordinates/timestep.cpython-311-x86_64-linux-gnu.so' adding 'MDAnalysis/coordinates/timestep.pxd' adding 'MDAnalysis/coordinates/timestep.pyx' adding 'MDAnalysis/core/__init__.py' adding 'MDAnalysis/core/_get_readers.py' adding 'MDAnalysis/core/accessors.py' adding 'MDAnalysis/core/groups.py' adding 'MDAnalysis/core/selection.py' adding 'MDAnalysis/core/topology.py' adding 'MDAnalysis/core/topologyattrs.py' adding 'MDAnalysis/core/topologyobjects.py' adding 'MDAnalysis/core/universe.py' adding 'MDAnalysis/lib/NeighborSearch.py' adding 'MDAnalysis/lib/__init__.py' adding 'MDAnalysis/lib/_augment.cpp' adding 'MDAnalysis/lib/_augment.cpython-311-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/_augment.pyx' adding 'MDAnalysis/lib/_cutil.cpp' adding 'MDAnalysis/lib/_cutil.cpython-311-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/_cutil.pxd' adding 'MDAnalysis/lib/_cutil.pyx' adding 'MDAnalysis/lib/_transformations.cpython-311-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/c_distances.c' adding 'MDAnalysis/lib/c_distances.cpython-311-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/c_distances.pyx' adding 'MDAnalysis/lib/c_distances_openmp.c' adding 'MDAnalysis/lib/c_distances_openmp.cpython-311-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/c_distances_openmp.pyx' adding 'MDAnalysis/lib/correlations.py' adding 'MDAnalysis/lib/distances.py' adding 'MDAnalysis/lib/log.py' adding 'MDAnalysis/lib/mdamath.py' adding 'MDAnalysis/lib/nsgrid.cpp' adding 'MDAnalysis/lib/nsgrid.cpython-311-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/nsgrid.pyx' adding 'MDAnalysis/lib/picklable_file_io.py' adding 'MDAnalysis/lib/pkdtree.py' adding 'MDAnalysis/lib/qcprot.c' adding 'MDAnalysis/lib/qcprot.cpython-311-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/qcprot.pyx' adding 'MDAnalysis/lib/transformations.py' adding 'MDAnalysis/lib/util.py' adding 'MDAnalysis/lib/formats/__init__.py' adding 'MDAnalysis/lib/formats/cython_util.c' adding 'MDAnalysis/lib/formats/cython_util.cpython-311-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/formats/cython_util.pxd' adding 'MDAnalysis/lib/formats/cython_util.pyx' adding 'MDAnalysis/lib/formats/libdcd.c' adding 'MDAnalysis/lib/formats/libdcd.cpython-311-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/formats/libdcd.pxd' adding 'MDAnalysis/lib/formats/libdcd.pyx' adding 'MDAnalysis/lib/formats/libmdaxdr.c' adding 'MDAnalysis/lib/formats/libmdaxdr.cpython-311-x86_64-linux-gnu.so' adding 'MDAnalysis/lib/formats/libmdaxdr.pxd' adding 'MDAnalysis/lib/formats/libmdaxdr.pyx' adding 'MDAnalysis/lib/formats/include/endianswap.h' adding 'MDAnalysis/lib/formats/include/fastio.h' adding 'MDAnalysis/lib/formats/include/readdcd.h' adding 'MDAnalysis/lib/formats/include/trr_seek.h' adding 'MDAnalysis/lib/formats/include/xdrfile.h' adding 'MDAnalysis/lib/formats/include/xdrfile_trr.h' adding 'MDAnalysis/lib/formats/include/xdrfile_xtc.h' adding 'MDAnalysis/lib/formats/include/xtc_seek.h' adding 'MDAnalysis/lib/formats/src/trr_seek.c' adding 'MDAnalysis/lib/formats/src/xdrfile.c' adding 'MDAnalysis/lib/formats/src/xdrfile_trr.c' adding 'MDAnalysis/lib/formats/src/xdrfile_xtc.c' adding 'MDAnalysis/lib/formats/src/xtc_seek.c' adding 'MDAnalysis/lib/include/calc_distances.h' adding 'MDAnalysis/lib/libmdanalysis/__init__.pxd' adding 'MDAnalysis/lib/src/transformations/AUTHOR' adding 'MDAnalysis/lib/src/transformations/LICENCE' adding 'MDAnalysis/lib/src/transformations/transformations.c' adding 'MDAnalysis/selections/__init__.py' adding 'MDAnalysis/selections/base.py' adding 'MDAnalysis/selections/charmm.py' adding 'MDAnalysis/selections/gromacs.py' adding 'MDAnalysis/selections/jmol.py' adding 'MDAnalysis/selections/pymol.py' adding 'MDAnalysis/selections/vmd.py' adding 'MDAnalysis/tests/__init__.py' adding 'MDAnalysis/tests/datafiles.py' adding 'MDAnalysis/topology/CRDParser.py' adding 'MDAnalysis/topology/DLPolyParser.py' adding 'MDAnalysis/topology/DMSParser.py' adding 'MDAnalysis/topology/ExtendedPDBParser.py' adding 'MDAnalysis/topology/FHIAIMSParser.py' adding 'MDAnalysis/topology/GMSParser.py' adding 'MDAnalysis/topology/GROParser.py' adding 'MDAnalysis/topology/GSDParser.py' adding 'MDAnalysis/topology/HoomdXMLParser.py' adding 'MDAnalysis/topology/ITPParser.py' adding 'MDAnalysis/topology/LAMMPSParser.py' adding 'MDAnalysis/topology/MMTFParser.py' adding 'MDAnalysis/topology/MOL2Parser.py' adding 'MDAnalysis/topology/MinimalParser.py' adding 'MDAnalysis/topology/PDBParser.py' adding 'MDAnalysis/topology/PDBQTParser.py' adding 'MDAnalysis/topology/PQRParser.py' adding 'MDAnalysis/topology/PSFParser.py' adding 'MDAnalysis/topology/ParmEdParser.py' adding 'MDAnalysis/topology/TOPParser.py' adding 'MDAnalysis/topology/TPRParser.py' adding 'MDAnalysis/topology/TXYZParser.py' adding 'MDAnalysis/topology/XYZParser.py' adding 'MDAnalysis/topology/__init__.py' adding 'MDAnalysis/topology/base.py' adding 'MDAnalysis/topology/core.py' adding 'MDAnalysis/topology/guessers.py' adding 'MDAnalysis/topology/tables.py' adding 'MDAnalysis/topology/tpr/__init__.py' adding 'MDAnalysis/topology/tpr/obj.py' adding 'MDAnalysis/topology/tpr/setting.py' adding 'MDAnalysis/topology/tpr/utils.py' adding 'MDAnalysis/transformations/__init__.py' adding 'MDAnalysis/transformations/base.py' adding 'MDAnalysis/transformations/boxdimensions.py' adding 'MDAnalysis/transformations/fit.py' adding 'MDAnalysis/transformations/positionaveraging.py' adding 'MDAnalysis/transformations/rotate.py' adding 'MDAnalysis/transformations/translate.py' adding 'MDAnalysis/transformations/wrap.py' adding 'MDAnalysis/visualization/__init__.py' adding 'MDAnalysis/visualization/streamlines.py' adding 'MDAnalysis/visualization/streamlines_3D.py' adding 'MDAnalysis-2.4.2.dist-info/AUTHORS' adding 'MDAnalysis-2.4.2.dist-info/LICENSE' adding 'MDAnalysis-2.4.2.dist-info/METADATA' adding 'MDAnalysis-2.4.2.dist-info/WHEEL' adding 'MDAnalysis-2.4.2.dist-info/top_level.txt' adding 'MDAnalysis-2.4.2.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Successfully built MDAnalysis-2.4.2-cp311-cp311-linux_x86_64.whl I: pybuild plugin_pyproject:119: Unpacking wheel built for python3.11 with "installer" module debian/rules execute_after_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.4.2+dfsg1' PYTHONPATH=/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build make html -C package/doc/sphinx/ BUILDDIR=/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild # HTML generator make[2]: Entering directory '/build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/doc/sphinx' sphinx-build -v -b html source /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/html Running Sphinx v5.3.0 /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/topology/TPRParser.py:160: DeprecationWarning: 'xdrlib' is deprecated and slated for removal in Python 3.13 import xdrlib making output directory... done checking bibtex cache... out of date parsing bibtex file /build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/doc/sphinx/source/references.bib... parsed 64 entries locale_dir /build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exists loading intersphinx inventory from https://docs.h5py.org/en/stable/objects.inv... WARNING: failed to reach any of the inventories with the following issues: 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'))) 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... 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... 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'))) 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'))) 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'))) 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'))) 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'))) 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 updating environment: locale_dir /build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exists [new config] 164 added, 0 changed, 0 removed reading sources... [ 0%] documentation_pages/analysis/align Didn't find AlignTraj.reference_atoms in MDAnalysis.analysis.align Didn't find AlignTraj.mobile_atoms in MDAnalysis.analysis.align Didn't find AlignTraj.results.rmsd in MDAnalysis.analysis.align Didn't find AlignTraj.filename in MDAnalysis.analysis.align Didn't find AverageStructure.reference_atoms in MDAnalysis.analysis.align Didn't find AverageStructure.mobile_atoms in MDAnalysis.analysis.align Didn't find AverageStructure.results.universe in MDAnalysis.analysis.align Didn't find AverageStructure.results.positions in MDAnalysis.analysis.align Didn't find AverageStructure.results.rmsd in MDAnalysis.analysis.align Didn't find AverageStructure.filename in MDAnalysis.analysis.align reading sources... [ 1%] documentation_pages/analysis/base Didn't find AnalysisBase.times in MDAnalysis.analysis.base Didn't find AnalysisBase.frames in MDAnalysis.analysis.base Didn't find AnalysisBase.results in MDAnalysis.analysis.base Didn't find AnalysisFromFunction.results.frames in MDAnalysis.analysis.base Didn't find AnalysisFromFunction.results.times in MDAnalysis.analysis.base Didn't find AnalysisFromFunction.results.timeseries in MDAnalysis.analysis.base Didn't find results.frames in MDAnalysis.analysis.base Didn't find results.times in MDAnalysis.analysis.base Didn't find results.timeseries in MDAnalysis.analysis.base reading sources... [ 1%] documentation_pages/analysis/bat Didn't find BAT.results.bat in MDAnalysis.analysis.bat reading sources... [ 2%] documentation_pages/analysis/contacts Didn't find Contacts.results.timeseries in MDAnalysis.analysis.contacts reading sources... [ 3%] documentation_pages/analysis/data reading sources... [ 3%] documentation_pages/analysis/density Didn't find DensityAnalysis.results.density in MDAnalysis.analysis.density Didn't find Density.grid in MDAnalysis.analysis.density Didn't find Density.edges in MDAnalysis.analysis.density Didn't find Density.delta in MDAnalysis.analysis.density Didn't find Density.origin in MDAnalysis.analysis.density Didn't find Density.units in MDAnalysis.analysis.density reading sources... [ 4%] documentation_pages/analysis/dielectric Didn't find DielectricConstant.results.M in MDAnalysis.analysis.dielectric Didn't find DielectricConstant.results.M2 in MDAnalysis.analysis.dielectric Didn't find DielectricConstant.results.fluct in MDAnalysis.analysis.dielectric Didn't find DielectricConstant.results.eps in MDAnalysis.analysis.dielectric Didn't find DielectricConstant.results.eps_mean in MDAnalysis.analysis.dielectric reading sources... [ 4%] documentation_pages/analysis/diffusionmap Didn't find DiffusionMap.eigenvalues in MDAnalysis.analysis.diffusionmap 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. 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 reading sources... [ 6%] documentation_pages/analysis/distances reading sources... [ 6%] documentation_pages/analysis/encore reading sources... [ 7%] documentation_pages/analysis/encore/bootstrap reading sources... [ 7%] documentation_pages/analysis/encore/clustering Didn't find Cluster.id in MDAnalysis.analysis.encore.clustering.ClusterCollection Didn't find Cluster.metadata in MDAnalysis.analysis.encore.clustering.ClusterCollection Didn't find Cluster.size in MDAnalysis.analysis.encore.clustering.ClusterCollection Didn't find Cluster.centroid in MDAnalysis.analysis.encore.clustering.ClusterCollection Didn't find Cluster.elements in MDAnalysis.analysis.encore.clustering.ClusterCollection Didn't find ClusterCollection.clusters in MDAnalysis.analysis.encore.clustering.ClusterCollection reading sources... [ 8%] documentation_pages/analysis/encore/confdistmatrix reading sources... [ 9%] documentation_pages/analysis/encore/covariance reading sources... [ 9%] documentation_pages/analysis/encore/dimensionality_reduction reading sources... [ 10%] documentation_pages/analysis/encore/similarity reading sources... [ 10%] documentation_pages/analysis/encore/utils Didn't find ParallelCalculation.n_jobs in MDAnalysis.analysis.encore.utils Didn't find ParallelCalculation.function in MDAnalysis.analysis.encore.utils Didn't find ParallelCalculation.args in MDAnalysis.analysis.encore.utils Didn't find ParallelCalculation.kwargs in MDAnalysis.analysis.encore.utils Didn't find ParallelCalculation.nruns in MDAnalysis.analysis.encore.utils reading sources... [ 11%] documentation_pages/analysis/gnm Didn't find GNMAnalysis.results.times in MDAnalysis.analysis.gnm Didn't find GNMAnalysis.results.eigenvalues in MDAnalysis.analysis.gnm Didn't find GNMAnalysis.results.eigenvectors in MDAnalysis.analysis.gnm Didn't find closeContactGNMAnalysis.results.times in MDAnalysis.analysis.gnm Didn't find closeContactGNMAnalysis.results.eigenvalues in MDAnalysis.analysis.gnm Didn't find closeContactGNMAnalysis.results.eigenvectors in MDAnalysis.analysis.gnm reading sources... [ 12%] documentation_pages/analysis/hbond_autocorrel reading sources... [ 12%] documentation_pages/analysis/hbond_autocorrel_deprecated /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52: DeprecationWarning: This module was moved to MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel; hbonds.hbond_autocorrel will be removed in 3.0.0. warnings.warn(wmsg, category=DeprecationWarning) reading sources... [ 13%] documentation_pages/analysis/helix_analysis reading sources... [ 14%] documentation_pages/analysis/hole2 Didn't find HoleAnalysis.results.sphpdbs in MDAnalysis.analysis.hole2 Didn't find HoleAnalysis.results.outfiles in MDAnalysis.analysis.hole2 Didn't find HoleAnalysis.results.profiles in MDAnalysis.analysis.hole2 reading sources... [ 14%] documentation_pages/analysis/hydrogenbonds Didn't find HydrogenBondAnalysis.results.hbonds in MDAnalysis.analysis.hydrogenbonds.hbond_analysis reading sources... [ 15%] documentation_pages/analysis/leaflet reading sources... [ 15%] documentation_pages/analysis/legacy/x3dna Didn't find X3DNA.profiles in MDAnalysis.analysis.legacy.x3dna Didn't find X3DNAtraj.profiles in MDAnalysis.analysis.legacy.x3dna reading sources... [ 16%] documentation_pages/analysis/legacy_modules reading sources... [ 17%] documentation_pages/analysis/lineardensity Didn't find LinearDensity.results.x.dim in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.mass_density in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.mass_density_stddev in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.charge_density in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.charge_density_stddev in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.pos in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.pos_std in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.char in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.char_std in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.slice_volume in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.hist_bin_edges in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.Note in MDAnalysis.analysis.lineardensity reading sources... [ 17%] documentation_pages/analysis/msd Didn't find EinsteinMSD.dim_fac in MDAnalysis.analysis.msd Didn't find EinsteinMSD.results.timeseries in MDAnalysis.analysis.msd Didn't find EinsteinMSD.results.msds_by_particle in MDAnalysis.analysis.msd Didn't find EinsteinMSD.ag in MDAnalysis.analysis.msd Didn't find EinsteinMSD.n_frames in MDAnalysis.analysis.msd Didn't find EinsteinMSD.n_particles in MDAnalysis.analysis.msd reading sources... [ 18%] documentation_pages/analysis/nucleicacids Didn't find NucPairDist.times in MDAnalysis.analysis.nucleicacids Didn't find NucPairDist.results in MDAnalysis.analysis.nucleicacids Didn't find NucPairDist.results.times in MDAnalysis.analysis.nucleicacids Didn't find NucPairDist.results.pair_distances in MDAnalysis.analysis.nucleicacids Didn't find WatsonCrickDist.times in MDAnalysis.analysis.nucleicacids Didn't find WatsonCrickDist.results in MDAnalysis.analysis.nucleicacids Didn't find WatsonCrickDist.results.times in MDAnalysis.analysis.nucleicacids Didn't find WatsonCrickDist.results.pair_distances in MDAnalysis.analysis.nucleicacids reading sources... [ 18%] documentation_pages/analysis/nuclinfo reading sources... [ 19%] documentation_pages/analysis/pca Didn't find PCA.results.p_components in MDAnalysis.analysis.pca Didn't find PCA.results.variance in MDAnalysis.analysis.pca Didn't find PCA.results.cumulated_variance in MDAnalysis.analysis.pca reading sources... [ 20%] documentation_pages/analysis/polymer Didn't find PersistenceLength.results.bond_autocorrelation in MDAnalysis.analysis.polymer Didn't find PersistenceLength.results.lb in MDAnalysis.analysis.polymer Didn't find PersistenceLength.results.x in MDAnalysis.analysis.polymer Didn't find PersistenceLength.results.lp in MDAnalysis.analysis.polymer Didn't find PersistenceLength.results.fit in MDAnalysis.analysis.polymer reading sources... [ 20%] documentation_pages/analysis/psa Didn't find Path.u_original in MDAnalysis.analysis.psa Didn't find Path.u_reference in MDAnalysis.analysis.psa Didn't find Path.select in MDAnalysis.analysis.psa Didn't find Path.path_select in MDAnalysis.analysis.psa Didn't find Path.ref_frame in MDAnalysis.analysis.psa Didn't find Path.u_fitted in MDAnalysis.analysis.psa Didn't find Path.path in MDAnalysis.analysis.psa Didn't find PSAPair.npaths in MDAnalysis.analysis.psa Didn't find PSAPair.matrix_id in MDAnalysis.analysis.psa Didn't find PSAPair.pair_id in MDAnalysis.analysis.psa Didn't find PSAPair.nearest_neighbors in MDAnalysis.analysis.psa Didn't find PSAPair.hausdorff_pair in MDAnalysis.analysis.psa Didn't find PSAnalysis.universes in MDAnalysis.analysis.psa Didn't find PSAnalysis.u_reference in MDAnalysis.analysis.psa Didn't find PSAnalysis.select in MDAnalysis.analysis.psa Didn't find PSAnalysis.path_select in MDAnalysis.analysis.psa Didn't find PSAnalysis.ref_frame in MDAnalysis.analysis.psa Didn't find PSAnalysis.paths in MDAnalysis.analysis.psa Didn't find PSAnalysis.D in MDAnalysis.analysis.psa reading sources... [ 21%] documentation_pages/analysis/rdf Didn't find InterRDF.results.bins in MDAnalysis.analysis.rdf Didn't find InterRDF.results.edges in MDAnalysis.analysis.rdf Didn't find InterRDF.results.rdf in MDAnalysis.analysis.rdf Didn't find InterRDF.results.count in MDAnalysis.analysis.rdf Didn't find InterRDF_s.results.bins in MDAnalysis.analysis.rdf Didn't find InterRDF_s.results.edges in MDAnalysis.analysis.rdf Didn't find InterRDF_s.results.rdf in MDAnalysis.analysis.rdf Didn't find InterRDF_s.results.count in MDAnalysis.analysis.rdf Didn't find InterRDF_s.results.cdf in MDAnalysis.analysis.rdf reading sources... [ 21%] documentation_pages/analysis/rms Didn't find RMSD.results.rmsd in MDAnalysis.analysis.rms Didn't find RMSF.results.rmsf in MDAnalysis.analysis.rms reading sources... [ 22%] documentation_pages/analysis/waterdynamics reading sources... [ 23%] documentation_pages/analysis/wbridge_analysis Didn't find WaterBridgeAnalysis.timesteps in MDAnalysis.analysis.hydrogenbonds.wbridge_analysis Didn't find WaterBridgeAnalysis.results.network in MDAnalysis.analysis.hydrogenbonds.wbridge_analysis Didn't find WaterBridgeAnalysis.table in MDAnalysis.analysis.hydrogenbonds.wbridge_analysis Didn't find WaterBridgeAnalysis.results.timeseries in MDAnalysis.analysis.hydrogenbonds.wbridge_analysis reading sources... [ 23%] documentation_pages/analysis_modules reading sources... [ 24%] documentation_pages/auxiliary/EDR Didn't find EDRReader._auxdata in MDAnalysis.auxiliary.EDR Didn't find EDRReader.data_dict in MDAnalysis.auxiliary.EDR Didn't find EDRReader.unit_dict in MDAnalysis.auxiliary.EDR Didn't find EDRReader._n_steps in MDAnalysis.auxiliary.EDR Didn't find EDRReader.terms in MDAnalysis.auxiliary.EDR reading sources... [ 25%] documentation_pages/auxiliary/XVG reading sources... [ 25%] documentation_pages/auxiliary/base Didn't find AuxStep.step in MDAnalysis.auxiliary.base Didn't find AuxReader.auxstep in MDAnalysis.auxiliary.base Didn't find AuxReader.frame_data in MDAnalysis.auxiliary.base Didn't find AuxReader.frame_rep in MDAnalysis.auxiliary.base Didn't find AuxFileReader.auxfile in MDAnalysis.auxiliary.base reading sources... [ 26%] documentation_pages/auxiliary/core reading sources... [ 26%] documentation_pages/auxiliary/init reading sources... [ 27%] documentation_pages/auxiliary_modules reading sources... [ 28%] documentation_pages/converters reading sources... [ 28%] documentation_pages/converters/OpenMM reading sources... [ 29%] documentation_pages/converters/ParmEd reading sources... [ 29%] documentation_pages/converters/RDKit reading sources... [ 30%] documentation_pages/coordinates/CRD reading sources... [ 31%] documentation_pages/coordinates/DCD reading sources... [ 31%] documentation_pages/coordinates/DLPoly reading sources... [ 32%] documentation_pages/coordinates/DMS reading sources... [ 32%] documentation_pages/coordinates/FHIAIMS reading sources... [ 33%] documentation_pages/coordinates/GMS reading sources... [ 34%] documentation_pages/coordinates/GRO reading sources... [ 34%] documentation_pages/coordinates/GSD reading sources... [ 35%] documentation_pages/coordinates/H5MD reading sources... [ 35%] documentation_pages/coordinates/INPCRD reading sources... [ 36%] documentation_pages/coordinates/LAMMPS reading sources... [ 37%] documentation_pages/coordinates/MMTF reading sources... [ 37%] documentation_pages/coordinates/MOL2 reading sources... [ 38%] documentation_pages/coordinates/NAMDBIN reading sources... [ 39%] documentation_pages/coordinates/PDB reading sources... [ 39%] documentation_pages/coordinates/PDBQT reading sources... [ 40%] documentation_pages/coordinates/PQR reading sources... [ 40%] documentation_pages/coordinates/TNG reading sources... [ 41%] documentation_pages/coordinates/TRJ reading sources... [ 42%] documentation_pages/coordinates/TRR reading sources... [ 42%] documentation_pages/coordinates/TRZ Didn't find TRZReader.ts in MDAnalysis.coordinates.TRZ reading sources... [ 43%] documentation_pages/coordinates/TXYZ reading sources... [ 43%] documentation_pages/coordinates/XDR reading sources... [ 44%] documentation_pages/coordinates/XTC reading sources... [ 45%] documentation_pages/coordinates/XYZ reading sources... [ 45%] documentation_pages/coordinates/base reading sources... [ 46%] documentation_pages/coordinates/chain reading sources... [ 46%] documentation_pages/coordinates/chemfiles reading sources... [ 47%] documentation_pages/coordinates/core reading sources... [ 48%] documentation_pages/coordinates/init reading sources... [ 48%] documentation_pages/coordinates/memory reading sources... [ 49%] documentation_pages/coordinates/null reading sources... [ 50%] documentation_pages/coordinates/pickle_readers reading sources... [ 50%] documentation_pages/coordinates/timestep reading sources... [ 51%] documentation_pages/coordinates_modules reading sources... [ 51%] documentation_pages/core/accessors reading sources... [ 52%] documentation_pages/core/groups reading sources... [ 53%] documentation_pages/core/init reading sources... [ 53%] documentation_pages/core/selection reading sources... [ 54%] documentation_pages/core/topology Didn't find TransTable.n_atoms in MDAnalysis.core.topology Didn't find TransTable.n_residues in MDAnalysis.core.topology Didn't find TransTable.n_segments in MDAnalysis.core.topology reading sources... [ 54%] documentation_pages/core/topologyattrs reading sources... [ 55%] documentation_pages/core/topologyobjects reading sources... [ 56%] documentation_pages/core/universe Didn't find Universe.atoms in MDAnalysis.core.universe Didn't find Universe.residues in MDAnalysis.core.universe Didn't find Universe.segments in MDAnalysis.core.universe reading sources... [ 56%] documentation_pages/core_modules reading sources... [ 57%] documentation_pages/exceptions reading sources... [ 57%] documentation_pages/lib/NeighborSearch reading sources... [ 58%] documentation_pages/lib/c_distances reading sources... [ 59%] documentation_pages/lib/c_distances_openmp reading sources... [ 59%] documentation_pages/lib/correlations reading sources... [ 60%] documentation_pages/lib/distances reading sources... [ 60%] documentation_pages/lib/formats/libdcd reading sources... [ 61%] documentation_pages/lib/formats/libmdaxdr reading sources... [ 62%] documentation_pages/lib/log reading sources... [ 62%] documentation_pages/lib/mdamath reading sources... [ 63%] documentation_pages/lib/nsgrid reading sources... 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The HTML pages are in /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/html. make[2]: Leaving directory '/build/reproducible-path/mdanalysis-2.4.2+dfsg1/package/doc/sphinx' make[1]: Leaving directory '/build/reproducible-path/mdanalysis-2.4.2+dfsg1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.4.2+dfsg1' py3versions: no X-Python3-Version in control file, using supported versions for py in 3.11; do \ echo "=== testing with python$py ==="; \ pydir=`pybuild -p $py --system=distutils --print {build_dir}`; \ MPLBACKEND=agg PYTHONPATH=$pydir python$py -mpytest testsuite; \ rm -rf $pydir/MDAnalysis/.hypothesis; \ done === testing with python3.11 === ============================= test session starts ============================== platform linux -- Python 3.11.2, pytest-7.2.1, pluggy-1.0.0+repack rootdir: /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite, configfile: setup.cfg plugins: hypothesis-6.67.1 collected 18847 items / 6 skipped testsuite/MDAnalysisTests/test_api.py ............................ 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[100%] =============================== warnings summary =============================== .pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/topology/TPRParser.py:160 /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/topology/TPRParser.py:160: DeprecationWarning: 'xdrlib' is deprecated and slated for removal in Python 3.13 import xdrlib ../../../usr/lib/python3/dist-packages/duecredit/versions.py:78 ../../../usr/lib/python3/dist-packages/duecredit/versions.py:78 ../../../usr/lib/python3/dist-packages/duecredit/versions.py:78 ../../../usr/lib/python3/dist-packages/duecredit/versions.py:78 ../../../usr/lib/python3/dist-packages/duecredit/versions.py:78 MDAnalysisTests/analysis/test_leaflet.py::test_leaflet_finder /usr/lib/python3/dist-packages/duecredit/versions.py:78: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. return StrictVersion(version) .pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/DCD.py:165: 2 warnings MDAnalysisTests/analysis/test_align.py: 77 warnings MDAnalysisTests/analysis/test_base.py: 3 warnings MDAnalysisTests/analysis/test_bat.py: 2 warnings MDAnalysisTests/analysis/test_contacts.py: 21 warnings MDAnalysisTests/analysis/test_dielectric.py: 6 warnings MDAnalysisTests/analysis/test_encore.py: 10 warnings MDAnalysisTests/analysis/test_helix_analysis.py: 7 warnings MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 6 warnings MDAnalysisTests/analysis/test_lineardensity.py: 6 warnings MDAnalysisTests/analysis/test_msd.py: 2 warnings MDAnalysisTests/analysis/test_pca.py: 12 warnings MDAnalysisTests/analysis/test_psa.py: 123 warnings MDAnalysisTests/analysis/test_rms.py: 37 warnings MDAnalysisTests/analysis/test_waterdynamics.py: 1 warning MDAnalysisTests/coordinates/test_chainreader.py: 72 warnings MDAnalysisTests/coordinates/test_copying.py: 18 warnings MDAnalysisTests/coordinates/test_dcd.py: 104 warnings MDAnalysisTests/coordinates/test_lammps.py: 5 warnings MDAnalysisTests/coordinates/test_memory.py: 83 warnings MDAnalysisTests/coordinates/test_pdb.py: 7 warnings MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings MDAnalysisTests/core/test_accumulate.py: 48 warnings MDAnalysisTests/core/test_atom.py: 13 warnings MDAnalysisTests/core/test_atomgroup.py: 168 warnings MDAnalysisTests/core/test_atomselections.py: 4 warnings MDAnalysisTests/core/test_copying.py: 6 warnings MDAnalysisTests/core/test_groups.py: 11 warnings MDAnalysisTests/core/test_residue.py: 3 warnings MDAnalysisTests/core/test_residuegroup.py: 21 warnings MDAnalysisTests/core/test_segmentgroup.py: 9 warnings MDAnalysisTests/core/test_topologyattrs.py: 8 warnings MDAnalysisTests/core/test_topologyobjects.py: 4 warnings MDAnalysisTests/core/test_universe.py: 31 warnings MDAnalysisTests/lib/test_distances.py: 46 warnings MDAnalysisTests/lib/test_neighborsearch.py: 2 warnings MDAnalysisTests/lib/test_util.py: 67 warnings MDAnalysisTests/parallelism/test_multiprocessing.py: 3 warnings MDAnalysisTests/parallelism/test_pickle_transformation.py: 8 warnings MDAnalysisTests/topology/test_guessers.py: 1 warning MDAnalysisTests/topology/test_minimal.py: 2 warnings MDAnalysisTests/transformations/test_base.py: 1 warning MDAnalysisTests/utils/test_modelling.py: 3 warnings MDAnalysisTests/utils/test_selections.py: 20 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/DCD.py:165: DeprecationWarning: DCDReader currently makes independent timesteps by copying self.ts while other readers update self.ts inplace. This behavior will be changed in 3.0 to be the same as other readers. Read more at https://github.com/MDAnalysis/mdanalysis/issues/3889 to learn if this change in behavior might affect you. warnings.warn("DCDReader currently makes independent timesteps" .pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52 /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52: DeprecationWarning: This module was moved to MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel; hbonds.hbond_autocorrel will be removed in 3.0.0. warnings.warn(wmsg, category=DeprecationWarning) .pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/chemfiles.py:122 .pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/chemfiles.py:122 .pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/chemfiles.py:122 MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[ChemfilesWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[ChemfilesWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[ChemfilesWriter] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/chemfiles.py:122: UserWarning: chemfiles package not found, try installing it with 'pip install chemfiles' warnings.warn( MDAnalysisTests/analysis/test_align.py: 699 warnings MDAnalysisTests/analysis/test_psa.py: 5960 warnings MDAnalysisTests/coordinates/test_chainreader.py: 298 warnings MDAnalysisTests/coordinates/test_dcd.py: 687 warnings MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 318 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/DCD.py:448: UserWarning: No dimensions set for current frame, zeroed unitcell will be written warnings.warn(wmsg) 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. warnings.warn("Unknown elements found for some " MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_shape MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_type MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_missing MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_type MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_nanvalue /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/density.py:423: UserWarning: Box padding (currently set at 2.0) is not used in user defined grids. warnings.warn(msg) MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/density.py:556: UserWarning: Atom selection does not fit grid --- you may want to define a larger box warnings.warn(msg) MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_single_frame MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_residue_selections MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_attr_warning /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/dihedrals.py:407: UserWarning: Cannot determine phi and psi angles for the first or last residues warnings.warn("Cannot determine phi and psi angles for the first " MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_tpr MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_single_frame MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_plot MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_attr_warning /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/dihedrals.py:589: UserWarning: All residues selected with 'resname ALA CYS* GLY PRO SER THR VAL' have been removed from the selection. warnings.warn(f"All residues selected with '{select_remove}' " MDAnalysisTests/analysis/test_encore.py::TestEncore::test_rmsd_matrix_with_superimposition /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/rms.py:718: DeprecationWarning: The `rmsd` attribute was deprecated in MDAnalysis 2.0.0 and will be removed in MDAnalysis 3.0.0. Please use `results.rmsd` instead. warnings.warn(wmsg, DeprecationWarning) MDAnalysisTests/analysis/test_encore.py::TestEncore::test_ensemble_superimposition MDAnalysisTests/analysis/test_encore.py::TestEncore::test_ensemble_superimposition MDAnalysisTests/analysis/test_encore.py::TestEncore::test_ensemble_superimposition_to_reference_non_weighted MDAnalysisTests/analysis/test_encore.py::TestEncore::test_ensemble_superimposition_to_reference_non_weighted /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/rms.py:887: DeprecationWarning: The `rmsf` attribute was deprecated in MDAnalysis 2.0.0 and will be removed in MDAnalysis 3.0.0. Please use `results.rmsd` instead. warnings.warn(wmsg, DeprecationWarning) MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_plane_circle MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_ortho_circle MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_parallel_axes /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/helix_analysis.py:164: RuntimeWarning: invalid value encountered in divide cos = cos_perp, cos_ortho = np.matmul(refs, proj_plane.T)/norms MDAnalysisTests/analysis/test_helix_analysis.py: 30 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/helix_analysis.py:245: RuntimeWarning: invalid value encountered in divide local_axes = (cross_bi.T / mdamath.pnorm(cross_bi)).T # (n_res-3, 3) MDAnalysisTests/analysis/test_helix_analysis.py: 176 warnings /usr/lib/python3/dist-packages/numpy/core/_methods.py:269: RuntimeWarning: Degrees of freedom <= 0 for slice ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof, MDAnalysisTests/analysis/test_helix_analysis.py: 160 warnings /usr/lib/python3/dist-packages/numpy/core/_methods.py:258: RuntimeWarning: invalid value encountered in divide ret = um.true_divide( MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings /usr/lib/python3/dist-packages/numpy/core/_methods.py:261: RuntimeWarning: invalid value encountered in scalar divide ret = ret.dtype.type(ret / rcount) MDAnalysisTests/analysis/test_hole2.py: 1 warning MDAnalysisTests/coordinates/test_pdb.py: 16 warnings MDAnalysisTests/core/test_atomgroup.py: 26 warnings MDAnalysisTests/core/test_atomselections.py: 1 warning MDAnalysisTests/core/test_topologyattrs.py: 1 warning MDAnalysisTests/topology/test_pdb.py: 1 warning MDAnalysisTests/utils/test_modelling.py: 1 warning /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/PDB.py:432: UserWarning: 1 A^3 CRYST1 record, this is usually a placeholder. Unit cell dimensions will be set to None. warnings.warn("1 A^3 CRYST1 record," MDAnalysisTests/analysis/test_hole2.py: 1 warning MDAnalysisTests/coordinates/test_pdb.py: 22 warnings MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 15 warnings MDAnalysisTests/utils/test_modelling.py: 1 warning /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/PDB.py:753: UserWarning: Unit cell dimensions not found. CRYST1 record set to unitary values. warnings.warn("Unit cell dimensions not found. " MDAnalysisTests/analysis/test_hole2.py: 1 warning MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings MDAnalysisTests/coordinates/test_pdb.py: 21 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 15 warnings MDAnalysisTests/utils/test_modelling.py: 2 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1129: UserWarning: Found no information for attr: 'elements' Using default value of ' ' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/analysis/test_hole2.py: 1 warning MDAnalysisTests/coordinates/test_h5md.py: 3 warnings MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings MDAnalysisTests/coordinates/test_pdb.py: 28 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 15 warnings MDAnalysisTests/topology/test_altloc.py: 1 warning MDAnalysisTests/utils/test_modelling.py: 3 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1129: UserWarning: Found no information for attr: 'formalcharges' Using default value of '0' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 9 warnings MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 9 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py:375: RuntimeWarning: Desired number of sample points too high, using 6 warnings.warn("Desired number of sample points too high, using {0}" MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:62: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. hbond = HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous_excl /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:79: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. hbond = HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:99: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. hbond = HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_timecut /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:117: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. hbond = HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_excl /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:135: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. hbond = HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_continuous /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:156: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. hbond = HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_intermittent /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:181: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. hbond = HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_wronglength_DA /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:210: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_exclusions /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:225: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_bond_type_VE /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:236: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_before_run_VE /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:247: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. hbond = HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_unslicable_traj_VE /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:262: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. HBAC( MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_repr /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:272: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! `HydrogenBondAutoCorrel` will be removed in release 3.0.0. The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. hbond = HBAC(u, MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_find_donors /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:300: DeprecationWarning: `find_hydrogen_donors` is deprecated! `find_hydrogen_donors` will be removed in release 3.0.0. The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. D = hbonds.find_hydrogen_donors(H) MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_donors_nobonds /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:312: DeprecationWarning: `find_hydrogen_donors` is deprecated! `find_hydrogen_donors` will be removed in release 3.0.0. The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. hbonds.find_hydrogen_donors(u.atoms) MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:722: UserWarning: No hydrogen bonds were found given d-a cutoff of 3.0 between Donor, name O, and Acceptor, name O. warnings.warn( MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:751: UserWarning: No hydrogen bonds were found given angle of 120.0 between Donor, name O, and Acceptor, name O. warnings.warn( MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:3464: RuntimeWarning: Mean of empty slice. return _methods._mean(a, axis=axis, dtype=dtype, MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules /usr/lib/python3/dist-packages/numpy/core/_methods.py:192: RuntimeWarning: invalid value encountered in scalar divide ret = ret.dtype.type(ret / rcount) MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:722: UserWarning: No hydrogen bonds were found given d-a cutoff of 3.0 between Donor, type O, and Acceptor, type O. warnings.warn( MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:751: UserWarning: No hydrogen bonds were found given angle of 120.0 between Donor, type O, and Acceptor, type O. warnings.warn( MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 10 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:722: UserWarning: No hydrogen bonds were found given d-a cutoff of 3.0 between Donor, None, and Acceptor, name OH2. warnings.warn( MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 10 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:751: UserWarning: No hydrogen bonds were found given angle of 120.0 between Donor, None, and Acceptor, name OH2. warnings.warn( MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:351: UserWarning: donors_sel is an empty selection string - no hydrogen bonds will be found. This may be intended, but please check your selection. warnings.warn(msg.format(sel)) MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:351: UserWarning: hydrogens_sel is an empty selection string - no hydrogen bonds will be found. This may be intended, but please check your selection. warnings.warn(msg.format(sel)) MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:351: UserWarning: acceptors_sel is an empty selection string - no hydrogen bonds will be found. This may be intended, but please check your selection. warnings.warn(msg.format(sel)) MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 23 warnings MDAnalysisTests/coordinates/test_dcd.py: 1 warning MDAnalysisTests/coordinates/test_gro.py: 4 warnings MDAnalysisTests/coordinates/test_h5md.py: 1 warning MDAnalysisTests/coordinates/test_memory.py: 1 warning MDAnalysisTests/coordinates/test_xdr.py: 2 warnings MDAnalysisTests/coordinates/test_xyz.py: 2 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/core/groups.py:3207: UserWarning: Empty string to select atoms, empty group returned. warnings.warn("Empty string to select atoms, empty group returned.", MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 10 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:722: UserWarning: No hydrogen bonds were found given d-a cutoff of 3.0 between Donor, , and Acceptor, . warnings.warn( MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 10 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:751: UserWarning: No hydrogen bonds were found given angle of 150 between Donor, , and Acceptor, . warnings.warn( MDAnalysisTests/analysis/test_leaflet.py::test_sparse_on_off_none[True] /usr/lib/python3/dist-packages/networkx/convert.py:158: DeprecationWarning: The scipy.sparse array containers will be used instead of matrices in Networkx 3.0. Use `from_scipy_sparse_array` instead. return nx.from_scipy_sparse_matrix(data, create_using=create_using) MDAnalysisTests/analysis/test_leaflet.py::test_write_selection /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/analysis/test_leaflet.py:170: ResourceWarning: unclosed file <_io.TextIOWrapper name='leaflet.vmd' mode='r' encoding='utf-8'> assert lines2one(open('leaflet.vmd').readlines()) == expected_output 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/analysis/test_msd.py: 100 warnings MDAnalysisTests/analysis/test_pca.py: 100 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/topology/PDBParser.py:345: UserWarning: Unknown element X found for some atoms. These have been given an empty element record. If needed they can be guessed using MDAnalysis.topology.guessers. warnings.warn(wmsg) MDAnalysisTests/analysis/test_msd.py: 103 warnings MDAnalysisTests/analysis/test_pca.py: 306 warnings MDAnalysisTests/coordinates/test_copying.py: 16 warnings MDAnalysisTests/coordinates/test_dcd.py: 201 warnings MDAnalysisTests/coordinates/test_dms.py: 9 warnings MDAnalysisTests/coordinates/test_timestep_api.py: 3 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_xdr.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 12 warnings MDAnalysisTests/lib/test_util.py: 654 warnings MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning MDAnalysisTests/topology/test_dms.py: 4 warnings MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/lib/mdamath.py:300: RuntimeWarning: invalid value encountered in scalar divide alpha = np.rad2deg(np.arccos(np.dot(y, z) / (ly * lz))) MDAnalysisTests/analysis/test_msd.py: 103 warnings MDAnalysisTests/analysis/test_pca.py: 306 warnings MDAnalysisTests/coordinates/test_copying.py: 16 warnings MDAnalysisTests/coordinates/test_dcd.py: 201 warnings MDAnalysisTests/coordinates/test_dms.py: 9 warnings MDAnalysisTests/coordinates/test_timestep_api.py: 3 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_xdr.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 12 warnings MDAnalysisTests/lib/test_util.py: 678 warnings MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning MDAnalysisTests/topology/test_dms.py: 4 warnings MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/lib/mdamath.py:301: RuntimeWarning: invalid value encountered in scalar divide beta = np.rad2deg(np.arccos(np.dot(x, z) / (lx * lz))) MDAnalysisTests/analysis/test_msd.py: 103 warnings MDAnalysisTests/analysis/test_pca.py: 306 warnings MDAnalysisTests/coordinates/test_copying.py: 16 warnings MDAnalysisTests/coordinates/test_dcd.py: 201 warnings MDAnalysisTests/coordinates/test_dms.py: 9 warnings MDAnalysisTests/coordinates/test_timestep_api.py: 3 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_xdr.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 12 warnings MDAnalysisTests/lib/test_util.py: 1071 warnings MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning MDAnalysisTests/topology/test_dms.py: 4 warnings MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/lib/mdamath.py:302: RuntimeWarning: invalid value encountered in scalar divide gamma = np.rad2deg(np.arccos(np.dot(x, y) / (lx * ly))) MDAnalysisTests/analysis/test_psa.py::TestPSAnalysis::test_dist_mat_to_vec_i_greater_j /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/psa.py:749: UserWarning: Column index entered (j = 3 is smaller than row index (i = 4). Using symmetric element in upper triangle of distance matrix instead: i --> j, j --> i warnings.warn("Column index entered (j = {:d} is smaller than row " MDAnalysisTests/analysis/test_rdf_s.py: 13 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/rdf.py:531: DeprecationWarning: The `u` attribute is superflous and will be removed in MDAnalysis 3.0.0. warnings.warn("The `u` attribute is superflous and will be removed " MDAnalysisTests/analysis/test_rdf_s.py::test_density[True-0.021915460340071267] MDAnalysisTests/analysis/test_rdf_s.py::test_overwrite_norm /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/rdf.py:544: DeprecationWarning: The `density` attribute was deprecated in MDAnalysis 2.3.0 and will be removed in MDAnalysis 3.0.0. Please use `norm=density` instead. warnings.warn("The `density` attribute was deprecated in " MDAnalysisTests/analysis/test_wbridge.py::TestWaterBridgeAnalysis::test_nodata /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1779: MissingDataWarning: No data computed, do run() first. warnings.warn(msg, category=MissingDataWarning) MDAnalysisTests/auxiliary/test_core.py: 1 warning MDAnalysisTests/auxiliary/test_xvg.py: 30 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/auxiliary/base.py:174: UserWarning: AuxStep does not support time selection. Reverting to default warnings.warn("{} does not support time selection. Reverting to " MDAnalysisTests/auxiliary/test_xvg.py: 50 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/auxiliary/base.py:210: UserWarning: AuxStep does not support data selection. Reverting to default warnings.warn("{} does not support data selection. Reverting to " MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_missing /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/chain.py:344: UserWarning: Missing frame in continuous chain warnings.warn("Missing frame in continuous chain", UserWarning) MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resnames] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/CRD.py:245: UserWarning: Supplied AtomGroup was missing the following attributes: resnames, tempfactors. These will be written with default values. warnings.warn( MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resids] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/CRD.py:245: UserWarning: Supplied AtomGroup was missing the following attributes: resids, tempfactors. These will be written with default values. warnings.warn( MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[names] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/CRD.py:245: UserWarning: Supplied AtomGroup was missing the following attributes: names, tempfactors. These will be written with default values. warnings.warn( MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[tempfactors] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/CRD.py:245: UserWarning: Supplied AtomGroup was missing the following attributes: tempfactors, tempfactors. These will be written with default values. warnings.warn( MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_empty_dcd /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: 'MDAnalysis.lib.formats.libdcd.DCDFile._setup_buffers' 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 144, in __init__ self._file = DCDFile(self.filename) ^^^^^^^^^^^^^^^^^^^^^^ IndexError: index 0 is out of bounds for axis 1 with size 0 warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_dcd.py::TestDCDWriter::test_no_container 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: 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__ self.close() File "/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/DCD.py", line 464, in close self._file.close() ^^^^^^^^^^ AttributeError: 'DCDWriter' object has no attribute '_file' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_dcd.py: 2 warnings MDAnalysisTests/coordinates/test_netcdf.py: 108 warnings MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings MDAnalysisTests/coordinates/test_trj.py: 3 warnings MDAnalysisTests/coordinates/test_windows.py: 2 warnings MDAnalysisTests/coordinates/test_xdr.py: 4 warnings MDAnalysisTests/core/test_atomselections.py: 3 warnings MDAnalysisTests/topology/test_top.py: 63 warnings MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/topology/TOPParser.py:288: UserWarning: ATOMIC_NUMBER record not found, elements attribute will not be populated. If needed these can be guessed using MDAnalysis.topology.guessers. warnings.warn(msg) MDAnalysisTests/coordinates/test_fhiaims.py::TestFHIAIMSWriter::test_writer_no_atom_names MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[FHIAIMSWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[FHIAIMSWriter] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/FHIAIMS.py:281: UserWarning: Supplied AtomGroup was missing the following attributes: names, ids. These will be written with default values. warnings.warn( MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resnames /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: resnames. These will be written with default values. Alternatively these can be supplied as keyword arguments. warnings.warn( MDAnalysisTests/coordinates/test_gro.py: 4 warnings MDAnalysisTests/coordinates/test_writer_api.py: 2 warnings MDAnalysisTests/core/test_atomgroup.py: 8 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/GRO.py:479: UserWarning: missing dimension - setting unit cell to zeroed box [0., 0., 0.] warnings.warn(wmsg) MDAnalysisTests/coordinates/test_gro.py: 3 warnings MDAnalysisTests/core/test_atomgroup.py: 8 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/GRO.py:228: UserWarning: Empty box [0., 0., 0.] found - treating as missing unit cell. Dimensions set to `None`. warnings.warn(wmsg) MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resids /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: resids. These will be written with default values. Alternatively these can be supplied as keyword arguments. warnings.warn( MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_writer_no_atom_names /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: names. These will be written with default values. Alternatively these can be supplied as keyword arguments. warnings.warn( MDAnalysisTests/coordinates/test_gro.py: 85 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/GRO.py:216: UserWarning: Not all velocities were present. Unset velocities set to zero. warnings.warn("Not all velocities were present. " MDAnalysisTests/coordinates/test_gro.py::test_growriter_resid_truncation /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: names, resnames. These will be written with default values. Alternatively these can be supplied as keyword arguments. warnings.warn( MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderWithRealTrajectory::test_wrong_driver /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__ self.close() File "/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/H5MD.py", line 728, in close self._file.close() ^^^^^^^^^^ AttributeError: 'H5MDReader' object has no attribute '_file' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_h5md.py: 3 warnings MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings MDAnalysisTests/coordinates/test_pdb.py: 16 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 15 warnings MDAnalysisTests/utils/test_modelling.py: 2 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1129: UserWarning: Found no information for attr: 'altLocs' Using default value of ' ' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_h5md.py: 3 warnings MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings MDAnalysisTests/coordinates/test_pdb.py: 16 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 15 warnings MDAnalysisTests/utils/test_modelling.py: 2 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1129: UserWarning: Found no information for attr: 'icodes' Using default value of ' ' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_h5md.py: 3 warnings MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings MDAnalysisTests/coordinates/test_pdb.py: 17 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 15 warnings MDAnalysisTests/utils/test_modelling.py: 2 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1129: UserWarning: Found no information for attr: 'chainIDs' Using default value of '' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_h5md.py: 3 warnings MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings MDAnalysisTests/coordinates/test_pdb.py: 16 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 15 warnings MDAnalysisTests/utils/test_modelling.py: 2 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1129: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_h5md.py: 3 warnings MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings MDAnalysisTests/coordinates/test_pdb.py: 16 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 15 warnings MDAnalysisTests/utils/test_modelling.py: 2 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1129: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_h5md.py: 3 warnings MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings MDAnalysisTests/coordinates/test_pdb.py: 15 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 15 warnings MDAnalysisTests/utils/test_modelling.py: 2 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1129: UserWarning: Found no information for attr: 'record_types' Using default value of 'ATOM' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_h5md.py: 3 warnings MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings MDAnalysisTests/coordinates/test_pdb.py: 54 warnings MDAnalysisTests/coordinates/test_trz.py: 1 warning MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings MDAnalysisTests/core/test_atomgroup.py: 15 warnings MDAnalysisTests/utils/test_modelling.py: 2 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1176: UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X' 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: 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__ for aux in self.aux_list: ^^^^^^^^^^^^^ File "/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1150, in aux_list return self._auxs.keys() ^^^^^^^^^^ AttributeError: 'H5MDReader' object has no attribute '_auxs' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_lammps.py: 57 warnings MDAnalysisTests/coordinates/test_windows.py: 20 warnings MDAnalysisTests/topology/test_lammpsdata.py: 18 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/topology/LAMMPSParser.py:631: UserWarning: Guessed all Masses to 1.0 warnings.warn('Guessed all Masses to 1.0') 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: 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__ for aux in self.aux_list: ^^^^^^^^^^^^^ File "/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1150, in aux_list return self._auxs.keys() ^^^^^^^^^^ AttributeError: 'DCDReader' object has no attribute '_auxs' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_timeseries_subarray_view /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/memory.py:529: DeprecationWarning: MemoryReader.timeseries inclusive `stop` indexing will be removed in 3.0 in favour of exclusive indexing warnings.warn("MemoryReader.timeseries inclusive `stop` " MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netCDF4 MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netCDF4 MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf /usr/lib/python3/dist-packages/scipy/io/_netcdf.py:305: RuntimeWarning: Cannot close a netcdf_file opened with mmap=True, when netcdf_variables or arrays referring to its data still exist. All data arrays obtained from such files refer directly to data on disk, and must be copied before the file can be cleanly closed. (See netcdf_file docstring for more information on mmap.) warnings.warn(( MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_factors_default MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[-2.0--2.0--2.0--2.0--2.0--2.0] MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[-2.0--2.0--2.0--2.0--2.0--2.0] MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[1.0-1.0-1.0-1.0-1.0-1.0] MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[1.0-1.0-1.0-1.0-1.0-1.0] MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[2.0-4.0-8.0-16.0-32.0-64.0] MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[2.0-4.0-8.0-16.0-32.0-64.0] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/TRJ.py:958: UserWarning: Could not find netCDF4 module. Falling back to MUCH slower scipy.io.netcdf implementation for writing. 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: 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__ self.close() File "/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/TRJ.py", line 1173, in close if self.trjfile is not None: ^^^^^^^^^^^^ AttributeError: 'NCDFWriter' object has no attribute 'trjfile' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resnames MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1129: UserWarning: Found no information for attr: 'resnames' Using default value of 'UNK' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_pdb.py: 8 warnings MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1129: UserWarning: Found no information for attr: 'segids' Using default value of ' ' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resids MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1129: UserWarning: Found no information for attr: 'resids' Using default value of '1' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_pdb.py: 6 warnings MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1129: UserWarning: Found no information for attr: 'names' Using default value of 'X' warnings.warn("Found no information for attr: '{}'" MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[@] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1172: UserWarning: Found chainIDs using unnaccepted character. Corresponding atoms will use value of 'X' warnings.warn("Found chainIDs using unnaccepted character." MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[AA] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/PDB.py:1168: UserWarning: Found chainIDs with invalid length. Corresponding atoms will use value of 'X' warnings.warn("Found chainIDs with invalid length." MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/topology/PDBParser.py:301: UserWarning: Serial numbers went over 100,000. Higher serials have been guessed warnings.warn("Serial numbers went over 100,000. " MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/topology/PDBParser.py:419: UserWarning: Invalid atom serials were present, bonds will not be parsed warnings.warn("Invalid atom serials were present, bonds will not" MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/topology/PDBParser.py:212: UserWarning: Invalid atom serials were present, bonds will not be parsed warnings.warn("Invalid atom serials were present, " MDAnalysisTests/coordinates/test_pdb.py::TestWriterAlignments::test_atomname_alignment MDAnalysisTests/coordinates/test_pdb.py::TestWriterAlignments::test_atomname_alignment /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/topology/PDBParser.py:345: UserWarning: Unknown element found for some atoms. These have been given an empty element record. If needed they can be guessed using MDAnalysis.topology.guessers. warnings.warn(wmsg) MDAnalysisTests/coordinates/test_pdb.py::test_partially_missing_cryst /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/coordinates/test_pdb.py:1208: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/data/incomplete.pdb' mode='r' encoding='utf-8'> raw = open(INC_PDB, 'r').readlines() 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/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/PDBQT.py:290: UserWarning: Supplied AtomGroup was missing the following attributes: altLocs, charges, icodes, occupancies, tempfactors. These will be written with default values. 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: 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__ for aux in self.aux_list: ^^^^^^^^^^^^^ File "/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/base.py", line 1150, in aux_list return self._auxs.keys() ^^^^^^^^^^ AttributeError: 'TNGReader' object has no attribute '_auxs' 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: 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__ self.close() File "/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/TRJ.py", line 352, in close if self.trjfile is None: ^^^^^^^^^^^^ AttributeError: 'TRJReader' object has no attribute 'trjfile' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/TRZ.py:536: UserWarning: Timestep didn't have the following attributes: 'pressure, pressure_tensor, total_energy, potential_energy, kinetic_energy, temperature, step', these will be set to 0 in the output trajectory warnings.warn("Timestep didn't have the following attributes: '{0}', " MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/TRZ.py:544: UserWarning: Timestep didn't have dimensions information, box will be written as all zero values warnings.warn("Timestep didn't have dimensions information, " MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/TRZ.py:552: UserWarning: Timestep didn't have velocity information, this will be set to zero in output trajectory. 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: 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__ self.close() File "/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/TRZ.py", line 590, in close if self.trzfile is None: ^^^^^^^^^^^^ AttributeError: 'TRZWriter' object has no attribute 'trzfile' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[CRDWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[CRDWriter] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/CRD.py:245: UserWarning: Supplied AtomGroup was missing the following attributes: resnames, resids, names, tempfactors, tempfactors. These will be written with default values. warnings.warn( MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[GROWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[GROWriter] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: names, resnames, resids. These will be written with default values. Alternatively these can be supplied as keyword arguments. warnings.warn( MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBQTWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBQTWriter] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/PDBQT.py:290: UserWarning: Supplied AtomGroup was missing the following attributes: altLocs, charges, icodes, names, occupancies, resids, resnames, tempfactors, types, chainids. These will be written with default values. warnings.warn( MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PQRWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PQRWriter] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/PQR.py:297: UserWarning: Supplied AtomGroup was missing the following attributes: names, resnames, resids, charges, radii. These will be written with default values. warnings.warn( MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[XYZWriter] MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[XYZWriter] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/XYZ.py:193: UserWarning: Input AtomGroup or Universe does not have atom elements or names attributes, writer will default atom names to 'X' 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: 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__ self.close() File "/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/XDR.py", line 322, in close self._xdr.close() ^^^^^^^^^ AttributeError: 'XTCWriter' object has no attribute '_xdr' 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: 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__ self.close() File "/build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/XDR.py", line 322, in close self._xdr.close() ^^^^^^^^^ AttributeError: 'TRRWriter' object has no attribute '_xdr' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 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 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. Consider setting 'refresh_offsets=True' when loading your Universe. warnings.warn("Reading offsets from {} failed, " MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_unsupported_format MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_unsupported_format /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/coordinates/XDR.py:241: UserWarning: Reload offsets from trajectory ctime or size or n_atoms did not match warnings.warn("Reload offsets from trajectory\n " 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 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. Consider setting 'refresh_offsets=True' when loading your Universe. warnings.warn("Reading offsets from {} failed, " MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms] MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms] MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[residues] MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[residues] MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[segments] MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[segments] /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:86: RuntimeWarning: overflow encountered in reduce return ufunc.reduce(obj, axis, dtype, out, **passkwargs) MDAnalysisTests/core/test_atomgroup.py: 17 warnings MDAnalysisTests/core/test_universe.py: 2 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/core/universe.py:817: DeprecationWarning: The bfactor topology attribute is only provided as an alias to the tempfactor attribute. It will be removed in 3.0. Please use the tempfactor attribute instead. warnings.warn(BFACTOR_WARNING, DeprecationWarning) MDAnalysisTests/core/test_atomgroup.py: 20 warnings MDAnalysisTests/core/test_universe.py: 4 warnings MDAnalysisTests/topology/test_mmtf.py: 3 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/core/topologyattrs.py:282: DeprecationWarning: The bfactor topology attribute is only provided as an alias to the tempfactor attribute. It will be removed in 3.0. Please use the tempfactor attribute instead. warnings.warn(BFACTOR_WARNING, DeprecationWarning) MDAnalysisTests/core/test_atomgroup.py: 13840 warnings MDAnalysisTests/core/test_wrap.py: 3 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/core/groups.py:1069: RuntimeWarning: invalid value encountered in divide return (coords * weights[:, None]).sum(axis=0) / weights.sum() MDAnalysisTests/core/test_atomgroup.py: 59 warnings MDAnalysisTests/core/test_wrap.py: 12 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/core/groups.py:1099: RuntimeWarning: invalid value encountered in divide _centers /= _weights.sum(axis=1)[:, None] MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/core/selection.py:988: SelectionWarning: Using float equality to select atoms is not recommended because of inherent limitations in representing numbers on computers (see https://docs.python.org/3.8/tutorial/floatingpoint.html for more). Instead, we recommend using a range to select, e.g. 'mass -11.0 to -9.0'. If you still want to compare floats, use the `atol` and `rtol` keywords to modify the tolerance for `np.isclose`. warnings.warn(msg, category=SelectionWarning) MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/core/selection.py:988: SelectionWarning: Using float equality to select atoms is not recommended because of inherent limitations in representing numbers on computers (see https://docs.python.org/3.8/tutorial/floatingpoint.html for more). Instead, we recommend using a range to select, e.g. 'mass -4.0 to -2.0'. If you still want to compare floats, use the `atol` and `rtol` keywords to modify the tolerance for `np.isclose`. warnings.warn(msg, category=SelectionWarning) MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs12] MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs13] MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-5-selkwargs15] MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-5-selkwargs16] MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-5-selkwargs16] MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-10-selkwargs17] MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-10-selkwargs18] MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-10-selkwargs19] MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-10-selkwargs19] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/core/selection.py:988: SelectionWarning: Using float equality to select atoms is not recommended because of inherent limitations in representing numbers on computers (see https://docs.python.org/3.8/tutorial/floatingpoint.html for more). Instead, we recommend using a range to select, e.g. 'mass -0.7 to 1.3'. If you still want to compare floats, use the `atol` and `rtol` keywords to modify the tolerance for `np.isclose`. warnings.warn(msg, category=SelectionWarning) MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-fragments] MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-molecules] MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-residues] MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-group] MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-segments] MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_cog_pbc MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_com_pbc MDAnalysisTests/transformations/test_translate.py::test_center_in_box_coords_all_options /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/core/groups.py:440: DeprecationWarning: The 'pbc' kwarg has been deprecated and will be removed in version 3.0., please use 'wrap' instead warnings.warn("The 'pbc' kwarg has been deprecated and will be " MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance[serial] MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance[serial] MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance[serial] MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance[openmp] MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance[openmp] MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance[openmp] MDAnalysisTests/lib/test_util.py::TestGeometryFunctions::test_vectors[x_axis5-y_axis5-nan] /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/lib/mdamath.py:158: RuntimeWarning: invalid value encountered in scalar divide x = np.dot(a, b) / (norm(a) * norm(b)) MDAnalysisTests/lib/test_util.py: 48 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/lib/test_util.py:292: RuntimeWarning: invalid value encountered in sqrt ref[2, 2] = np.sqrt(z * z - ref[2, 0] ** 2 - ref[2, 1] ** 2) MDAnalysisTests/lib/test_util.py: 353 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/lib/mdamath.py:394: RuntimeWarning: invalid value encountered in sqrt box_matrix[2, 2] = np.sqrt(lz * lz - box_matrix[2, 0] ** 2 - MDAnalysisTests/lib/test_util.py: 339 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/lib/test_util.py:322: RuntimeWarning: invalid value encountered in scalar divide a = np.rad2deg(np.arccos(np.dot(tri_vecs[1], tri_vecs[2]) / (y * z))) MDAnalysisTests/lib/test_util.py: 363 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/lib/test_util.py:323: RuntimeWarning: invalid value encountered in scalar divide b = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[2]) / (x * z))) MDAnalysisTests/lib/test_util.py: 756 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/lib/test_util.py:324: RuntimeWarning: invalid value encountered in scalar divide c = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[1]) / (x * y))) MDAnalysisTests/lib/test_util.py: 43 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/lib/test_util.py:314: RuntimeWarning: invalid value encountered in scalar divide ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c MDAnalysisTests/lib/test_util.py: 986 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: invalid value encountered in sqrt ref[2, 2] = np.sqrt(z * z - ref[2, 0] ** 2 - ref[2, 1] ** 2) MDAnalysisTests/lib/test_util.py: 17 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/lib/test_util.py:314: RuntimeWarning: divide by zero encountered in scalar divide ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c MDAnalysisTests/parallelism/test_pickle_transformation.py::test_add_PositionAverager_pickle[u0] MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_fwd MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_bwd MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_reset MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_specific /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/transformations/positionaveraging.py:193: Warning: Cannot average position for non sequentialiterations. Averager will be reset. warnings.warn('Cannot average position for non sequential' MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/topology/PDBParser.py:287: UserWarning: PDB file is missing resid information. Defaulted to '1' warnings.warn("PDB file is missing resid information. " MDAnalysisTests/topology/test_top.py: 42 warnings /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/topology/TOPParser.py:295: UserWarning: Unknown ATOMIC_NUMBER value found for some atoms, these have been given an empty element record. If needed these can be guessed using MDAnalysis.topology.guessers. warnings.warn(msg) MDAnalysisTests/transformations/test_fit.py::test_fit_translation_no_masses /build/reproducible-path/mdanalysis-2.4.2+dfsg1/.pybuild/cpython3_3.11_mdanalysis/build/MDAnalysis/analysis/align.py:1466: SelectionWarning: Atoms could not be matched since they don't contain masses. warnings.warn(msg, category=SelectionWarning) MDAnalysisTests/utils/test_pickleio.py::test_get_right_open_handler_text[f_text0] MDAnalysisTests/utils/test_pickleio.py::test_get_right_open_handler_text[f_text1] MDAnalysisTests/utils/test_pickleio.py::test_iopickle_text[f_text0] MDAnalysisTests/utils/test_pickleio.py::test_iopickle_text[f_text1] MDAnalysisTests/utils/test_pickleio.py::test_offset_text_to_0[f_text0] MDAnalysisTests/utils/test_pickleio.py::test_offset_text_to_0[f_text1] /usr/lib/python3/dist-packages/_pytest/runner.py:137: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/data/adk_oplsaa.pdb' encoding='utf-8'> item.funcargs = None # type: ignore[attr-defined] 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_iopickle_text[f_text0] MDAnalysisTests/utils/test_pickleio.py::test_iopickle_text[f_text1] MDAnalysisTests/utils/test_pickleio.py::test_offset_text_to_0[f_text0] MDAnalysisTests/utils/test_pickleio.py::test_offset_text_to_0[f_text1] MDAnalysisTests/utils/test_pickleio.py::test_context_manager_pickle /usr/lib/python3/dist-packages/_pytest/python.py:195: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/data/adk_oplsaa.pdb' encoding='utf-8'> 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_get_right_open_handler_byte[f_byte0] MDAnalysisTests/utils/test_pickleio.py::test_iopickle_byte[f_byte0] MDAnalysisTests/utils/test_pickleio.py::test_offset_byte_to_tell[f_byte0] /usr/lib/python3/dist-packages/_pytest/runner.py:137: ResourceWarning: unclosed file item.funcargs = None # type: ignore[attr-defined] 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_iopickle_byte[f_byte0] MDAnalysisTests/utils/test_pickleio.py::test_offset_byte_to_tell[f_byte0] /usr/lib/python3/dist-packages/_pytest/python.py:195: ResourceWarning: unclosed file 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_fileio_pickle MDAnalysisTests/utils/test_pickleio.py::test_fileio_pickle /usr/lib/python3/dist-packages/_pytest/python.py:195: ResourceWarning: unclosed file <_io.FileIO name='/build/reproducible-path/mdanalysis-2.4.2+dfsg1/testsuite/MDAnalysisTests/data/adk_oplsaa.pdb' mode='rb' 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_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> 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> 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> 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/visualization/test_streamlines.py::test_streamplot_2D MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_2D /usr/lib/python3/dist-packages/numpy/ma/core.py:858: RuntimeWarning: underflow encountered in multiply 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) = --- Logging error --- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/duecredit/utils.py", line 190, in wrapped_func return f(*args, **kwargs) ^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/duecredit/dueswitch.py", line 87, in dump due_summary.dump() File "/usr/lib/python3/dist-packages/duecredit/collector.py", line 470, in dump output.dump() File "/usr/lib/python3/dist-packages/duecredit/io.py", line 224, in dump self.fd.write(get_text_rendering(cit, ^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/duecredit/io.py", line 234, in get_text_rendering bibtex_rendering = get_bibtex_rendering(entry) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/duecredit/io.py", line 250, in get_bibtex_rendering return BibTeX(import_doi(entry.doi)) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/duecredit/io.py", line 47, in import_doi cached = get_doi_cache_file(doi) ^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/duecredit/io.py", line 41, in get_doi_cache_file os.makedirs(CACHE_DIR) File "", line 215, in makedirs File "", line 215, in makedirs File "", line 215, in makedirs [Previous line repeated 1 more time] File "", line 225, in makedirs PermissionError: [Errno 13] Permission denied: '/nonexistent' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3.11/logging/__init__.py", line 1113, in emit stream.write(msg + self.terminator) ValueError: I/O operation on closed file. 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" Arguments: () DueCredit Report: - Molecular simulation analysis library / MDAnalysis (v 2.4.2) [1, 2] - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.4.2) [3] - 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 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] - 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] - 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] - MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.4.2) [17] - Scientific tools library / numpy (v 1.24.2) [21] 2 packages cited 15 modules cited 0 functions cited References ---------- [1] make[1]: Leaving directory '/build/reproducible-path/mdanalysis-2.4.2+dfsg1' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3,sphinxdoc --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild plugin_pyproject:161: Copying package built for python3.11 to destdir dh_installdocs -O--buildsystem=pybuild dh_installdocs: warning: Cannot auto-detect main package for python-mdanalysis-doc. If the default is wrong, please use --doc-main-package dh_sphinxdoc -O--buildsystem=pybuild dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-mdanalysis-doc/usr/share/doc/python-mdanalysis-doc/html/_static/js/versions.js dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.4.2+dfsg1' dh_numpy3 make[1]: Leaving directory '/build/reproducible-path/mdanalysis-2.4.2+dfsg1' 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_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package python-mdanalysis-doc: substitution variable ${python3:Depends} unused, but is defined 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 '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 dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from mdanalysis-2.4.2+dfsg1/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: 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 Sun Jan 14 04:00:59 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Sun Jan 14 04:00:59 UTC 2024 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Sun Jan 14 06:19:39 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Sun Jan 14 06:19:40 UTC 2024 I: mdanalysis_2.4.2+dfsg1-1_amd64.changes: Format: 1.8 Date: Mon, 09 Jan 2023 17:54:02 +0100 Source: mdanalysis Binary: python-mdanalysis-doc python3-mdanalysis python3-mdanalysis-dbgsym Architecture: all amd64 Version: 2.4.2+dfsg1-1 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Drew Parsons Description: python-mdanalysis-doc - analyse molecular dynamics files and trajectories ( documentation python3-mdanalysis - analyse molecular dynamics files and trajectories Closes: 1027227 Changes: mdanalysis (2.4.2+dfsg1-1) unstable; urgency=medium . * New upstream release. - fixes DensityAnalysis for numpy 1.24. Closes: #1027227, Checksums-Sha1: 80240de6cd2b1cb55e434ebda518002b06e3b102 12805 mdanalysis_2.4.2+dfsg1-1_amd64.buildinfo 3cfaa7956b0d2cedd1e1f9e3421a74bc69c0e548 2372308 python-mdanalysis-doc_2.4.2+dfsg1-1_all.deb c8269f2024176a1e424e3855e65a54f4103af12f 4324564 python3-mdanalysis-dbgsym_2.4.2+dfsg1-1_amd64.deb 7820bfedef9a01db229c236b4432adb3e666372f 1627676 python3-mdanalysis_2.4.2+dfsg1-1_amd64.deb Checksums-Sha256: b39f394555b9d9de8bffc24f8d77bbefa9db5e9d6fb2c4407904dd90ee5638f9 12805 mdanalysis_2.4.2+dfsg1-1_amd64.buildinfo 6374d1cd122f4a4cf60ebce9406a13dd9a132ff65a704e67080a414ddb5d956f 2372308 python-mdanalysis-doc_2.4.2+dfsg1-1_all.deb 8ad0e997842878bbc136eec4df06069bcb67561ed56d5ab7e4f4ba87e2a46efd 4324564 python3-mdanalysis-dbgsym_2.4.2+dfsg1-1_amd64.deb 5a5d9f0eecbe810522ada6abc3a91aa654968943738b7a077efab86b204b977d 1627676 python3-mdanalysis_2.4.2+dfsg1-1_amd64.deb Files: e478eb7e23af2dae3fa5270db92ba7b6 12805 python optional mdanalysis_2.4.2+dfsg1-1_amd64.buildinfo 0795980a0426b4717f836075da9fd1ac 2372308 doc optional python-mdanalysis-doc_2.4.2+dfsg1-1_all.deb e34f8194f73f1e4fed537e614a7deac1 4324564 debug optional python3-mdanalysis-dbgsym_2.4.2+dfsg1-1_amd64.deb 61d354769a6778711ed7064d2a70c207 1627676 python optional python3-mdanalysis_2.4.2+dfsg1-1_amd64.deb Sun Jan 14 06:19:41 UTC 2024 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.jGQjWCYd/mdanalysis_2.4.2+dfsg1-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.jGQjWCYd/mdanalysis_2.4.2+dfsg1-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.jGQjWCYd/mdanalysis_2.4.2+dfsg1-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.jGQjWCYd/b1/mdanalysis_2.4.2+dfsg1-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.jGQjWCYd/b2/mdanalysis_2.4.2+dfsg1-1_amd64.changes ## close_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer ## command (total time: 0.765s) 0.406s 6 calls xz 0.251s 7 calls diff 0.037s 4 calls cmp 0.037s 4 calls cmp (external) 0.033s 11 calls html2text 0.002s 36 calls cmp (internal) ## compare_files (cumulative) (total time: 5.831s) 1.555s 1 call abc.DotChangesFile 1.519s 1 call abc.DebFile 1.488s 2 calls abc.XzFile 1.003s 1 call abc.DebDataTarFile 0.201s 1 call abc.HtmlFile 0.046s 1 call abc.TarFile 0.020s 1 call abc.Md5sumsFile ## container_extract (total time: 0.667s) 0.406s 6 calls diffoscope.comparators.xz.XzContainer 0.246s 994 calls diffoscope.comparators.deb.DebTarContainer 0.011s 8 calls diffoscope.comparators.deb.DebContainer 0.004s 6 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 0.579s) 0.579s 9 calls linediff ## has_same_content_as (total time: 0.041s) 0.023s 1 call abc.DebDataTarFile 0.012s 3 calls abc.DebFile 0.002s 1 call abc.HtmlFile 0.002s 25 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 2 calls abc.Md5sumsFile 0.000s 2 calls abc.TextFile 0.000s 2 calls abc.XzFile 0.000s 1 call abc.TarFile 0.000s 1 call abc.DotChangesFile ## main (total time: 2.927s) 2.926s 2 calls outputs 0.001s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer ## output (total time: 0.627s) 0.626s 1 call html 0.001s 1 call text 0.000s 1 call json ## recognizes (total time: 0.566s) 0.481s 12 calls diffoscope.comparators.binary.FilesystemFile 0.045s 538 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.024s 256 calls diffoscope.comparators.utils.archive.ArchiveMember 0.014s 162 calls diffoscope.comparators.debian.DebControlMember 0.000s 100 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 10 calls abc.DotChangesFile 0.000s 16 calls abc.Md5sumsFile ## specialize (total time: 0.066s) 0.066s 38 calls specialize Sun Jan 14 06:19:44 UTC 2024 E: mdanalysis failed to build reproducibly in bookworm on amd64. Sun Jan 14 06:19:45 UTC 2024 E: diffoscope 240 found issues, please check https://tests.reproducible-builds.org/debian/dbd/bookworm/amd64/mdanalysis_2.4.2+dfsg1-1.diffoscope.html Sun Jan 14 06:19:46 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Jan 14 06:19:46 UTC 2024 I: Submitting 16K b1/mdanalysis_2.4.2+dfsg1-1_amd64.buildinfo.asc Sun Jan 14 06:19:46 UTC 2024 I: Submitting 16K b2/mdanalysis_2.4.2+dfsg1-1_amd64.buildinfo.asc Sun Jan 14 06:19:47 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Jan 14 06:19:47 UTC 2024 I: Done submitting .buildinfo files. Sun Jan 14 06:19:47 UTC 2024 I: Removing signed mdanalysis_2.4.2+dfsg1-1_amd64.buildinfo.asc files: removed './b1/mdanalysis_2.4.2+dfsg1-1_amd64.buildinfo.asc' removed './b2/mdanalysis_2.4.2+dfsg1-1_amd64.buildinfo.asc'