Fri May 10 10:08:17 UTC 2024 I: starting to build mdanalysis/unstable/amd64 on jenkins on '2024-05-10 10:07' Fri May 10 10:08:17 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_12/20363/console.log Fri May 10 10:08:17 UTC 2024 I: Downloading source for unstable/mdanalysis=2.5.0+dfsg1-2 --2024-05-10 10:08:17-- http://deb.debian.org/debian/pool/main/m/mdanalysis/mdanalysis_2.5.0%2bdfsg1-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2912 (2.8K) [text/prs.lines.tag] Saving to: ‘mdanalysis_2.5.0+dfsg1-2.dsc’ 0K .. 100% 230M=0s 2024-05-10 10:08:17 (230 MB/s) - ‘mdanalysis_2.5.0+dfsg1-2.dsc’ saved [2912/2912] Fri May 10 10:08:17 UTC 2024 I: mdanalysis_2.5.0+dfsg1-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: mdanalysis Binary: python3-mdanalysis, python-mdanalysis-doc Architecture: any all Version: 2.5.0+dfsg1-2 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 (>= 1.21.0~), 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-tqdm (>= 4.43.0), python3-threadpoolctl, python3-packaging, python3-fasteners, python3-gsd (>= 3.0.1~), python3-netcdf4 (>= 1.0~), python3-h5py, python3-seaborn, python3-sklearn, python3-duecredit, python3-hypothesis , python3-pytest , python3-sphinx 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: 341bf0f84e2949b275b424f88fda8ac89a5ce735 46737412 mdanalysis_2.5.0+dfsg1.orig.tar.xz 1f8b6a2535663e398877c1d3f18c61ce79c18fd0 12540 mdanalysis_2.5.0+dfsg1-2.debian.tar.xz Checksums-Sha256: c78b22f689e8d61ffd04ca79a99fa8b5a2f1bf57d309d2a619b1dd0c13c498b9 46737412 mdanalysis_2.5.0+dfsg1.orig.tar.xz a4469f90f0d36a7e14f56ac19e0a02f139b96c4b9e3541dfbd2fb592fe5153b1 12540 mdanalysis_2.5.0+dfsg1-2.debian.tar.xz Files: b5302a7768aef4cead08b451794c8811 46737412 mdanalysis_2.5.0+dfsg1.orig.tar.xz d67bbd2f7f43f20fbaa0481a6891e904 12540 mdanalysis_2.5.0+dfsg1-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAmTDtQ0ACgkQVz7x5L1a AfochQ//cRm5O8YPjuyC4cMhrmUQRhlB2Ernn1VnALUdk+SfEQegCa19DPc6eBm0 h6GltJx69JU0gBSB4DsWFF+VFHJxHMRsCtyqAh0ql71UGPoF2p/A6G4xgFgYaKU9 RAeuhRiJehmPbPJ58gldOu7/0E6VPDv6VFetRZcu0UeqH9gq7iVSa/t7CgzSZ6h4 /VJ/FhxUEBpgb40H78c3+g8ZkOQ8BpGS5SKS6KiPE/TljnqIldTaWhJRnz07RWPy CEpi/wbQaUXnoBIgO1XKMTcPkEbhwop7JDYSBrc5QHNab3nF+o3JVBY7HpEuINbq 5Cb//uGMh9RtqiUfg9VkKJcmII1JR7XmH6DhbSxvnzxV16KOyg/FXTPmKD6ibHCG m+IeLsrEer1W8lt7FQTYeCWi3sowmtd/MgQqFi7WFBYEi/bRFxAja5T8gvDtL/9Q fXa0KtxyS8pOVKWhxL2adxj9UBbJwcLUHzpgqexB3TPqUQaYa+gOb/blk6NJzY5M baa1hRfCaE/rXqquMr8xqeY9w647z0AXm4fuYemKrpjR/CVqDISrYvhIZV7h2qGj aPd/DG3JYcVFLNUVW8k50CPGP7vFea2HdmlYkKv74A277IhwDFAKG67yrJsFml7W 0eZZajFXRjeufIYa8jW80HNNV7nIuAFsvIGqnm8KG7tR7C9eYS8= =vTvh -----END PGP SIGNATURE----- Fri May 10 10:08:17 UTC 2024 I: Checking whether the package is not for us Fri May 10 10:08:17 UTC 2024 I: Starting 1st build on remote node ionos15-amd64.debian.net. Fri May 10 10:08:17 UTC 2024 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Fri May 10 10:16:11 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jun 12 04:31:20 -12 2025 I: pbuilder-time-stamp: 1749745880 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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_2.5.0+dfsg1-2.dsc] I: copying [./mdanalysis_2.5.0+dfsg1.orig.tar.xz] I: copying [./mdanalysis_2.5.0+dfsg1-2.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Jul 28 12:31:09 2023 gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.5.0+dfsg1-2.dsc: no acceptable signature found dpkg-source: info: extracting mdanalysis in mdanalysis-2.5.0+dfsg1 dpkg-source: info: unpacking mdanalysis_2.5.0+dfsg1.orig.tar.xz dpkg-source: info: unpacking mdanalysis_2.5.0+dfsg1-2.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 dpkg-source: info: applying gsd3_PR4153.diff dpkg-source: info: applying gsd3_PR4174.diff I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3309321/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=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='e3a0d6c2c1d348ea93a91101c68c96ee' 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='3309321' 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.dBPIcNVR/pbuilderrc_ssdP --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dBPIcNVR/b1 --logfile b1/build.log mdanalysis_2.5.0+dfsg1-2.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://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 12 14:05 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3309321/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 (>= 1.21.0~), 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-tqdm (>= 4.43.0), python3-threadpoolctl, python3-packaging, python3-fasteners, python3-gsd (>= 3.0.1~), python3-netcdf4 (>= 1.0~), python3-h5py, python3-seaborn, python3-sklearn, python3-duecredit, python3-hypothesis, python3-pytest, python3-sphinx, 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 ... 19699 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 (>= 1.21.0~); 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-tqdm (>= 4.43.0); however: Package python3-tqdm 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-gsd (>= 3.0.1~); however: Package python3-gsd 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-h5py; however: Package python3-h5py 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-duecredit; however: Package python3-duecredit 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-sphinx; however: Package python3-sphinx 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-dejavu-mono{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} libbrotli1{a} libbsd0{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhdf5-103-1t64{a} libhdf5-hl-100t64{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblzf1{a} libmagic-mgc{a} libmagic1t64{a} libnetcdf19t64{a} libnghttp2-14{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libsub-override-perl{a} libsz2{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{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-biopython{a} python3-brotli{a} python3-build{a} python3-cairo{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-freetype{a} python3-fs{a} python3-griddataformats{a} python3-gsd{a} python3-h5py{a} python3-h5py-serial{a} python3-hypothesis{a} python3-idna{a} python3-imagesize{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-monotonic{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-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-pluggy{a} python3-pybtex{a} python3-pybtex-docutils{a} python3-pygments{a} python3-pyparsing{a} python3-pyproject-hooks{a} python3-pytest{a} python3-reportlab{a} python3-requests{a} python3-rlpycairo{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-sphinxcontrib.jquery{a} python3-sympy{a} python3-threadpoolctl{a} python3-tk{a} python3-toml{a} python3-tqdm{a} python3-tz{a} python3-ufolib2{a} python3-urllib3{a} python3-wheel{a} python3-yaml{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} 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 fonts-dejavu-extra isympy-common javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules lynx ncbi-blast+ psmisc publicsuffix python-biopython-doc python3-bottleneck python3-bs4 python3-click python3-cssselect python3-gdal python3-html5lib 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, 252 newly installed, 0 to remove and 0 not upgraded. Need to get 208 MB of archives. After unpacking 927 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.3-1 [809 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.3-1 [2139 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1 [23.0 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 48 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-1 [144 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get: 63 http://deb.debian.org/debian unstable/main amd64 cython3 amd64 3.0.10+dfsg-5 [3571 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 71 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240422 [107 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.20.1+dfsg-3 [128 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.0~RC4-1 [189 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.3-1 [23.4 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-1 [114 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-1 [105 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 99 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.7.1-5 [433 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.7.1-5 [441 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.2-1 [155 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14-20240429-1 [836 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.80.1-1 [1485 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.3-1 [7740 B] Get: 118 http://deb.debian.org/debian unstable/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.3 [1241 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-3.3 [63.3 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b1 [35.3 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.2.6-6 [150 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 liblzf1 amd64 3.6-4+b1 [10.4 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libnetcdf19t64 amd64 1:4.9.2-5+b1 [472 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.0-2+b3 [190 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libpython3.11t64 amd64 3.11.9-1 [1960 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libpython3.11-dev amd64 3.11.9-1 [4513 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.11.8-1 [9560 B] Get: 140 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.3-1 [1951 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.3-1 [2107 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.3-1 [5069 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.11.8-1 [1072 B] Get: 144 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-6+b1 [245 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.1-1+b1 [14.2 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [110 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.4.0-0.1 [123 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1+b1 [232 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 python3-pyproject-hooks all 1.0.0-2 [10.6 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 python3-toml all 0.10.2-1 [16.2 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 python3-wheel all 0.43.0-1 [52.5 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 python3-build all 1.2.1-1 [34.1 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 pybuild-plugin-pyproject all 6.20240422 [11.1 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.6.3-2 [2744 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.3-1 [659 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.11.8-1 [1056 B] Get: 165 http://deb.debian.org/debian unstable/main amd64 python3.11-dev amd64 3.11.9-1 [501 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.11.8-1 [26.1 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.3-1 [499 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.11.8-1 [1072 B] Get: 169 http://deb.debian.org/debian unstable/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.14.0-1 [111 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-8 [5466 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.12.3-1 [109 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 10.3.0-2 [79.5 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 10.3.0-2 [564 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 python3-cairo amd64 1.26.0-1 [142 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 python3-freetype all 2.4.0-1 [80.3 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 181 http://deb.debian.org/debian unstable/main amd64 python3-reportlab all 4.2.0-1 [1149 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 python3-biopython amd64 1.83+dfsg1-2 [1634 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b3 [312 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2023.11.17-1 [155 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 python3-cftime amd64 1.6.3-1+b1 [344 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer all 3.3.2-1 [51.6 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 5.2.1-1 [1995 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 python3-citeproc all 0.6.0-3 [96.7 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.0.7-3 [285 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get: 192 http://deb.debian.org/debian unstable/main amd64 python3-six all 1.16.0-6 [16.3 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 python3-roman all 3.3-3 [9880 B] Get: 196 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.20.1+dfsg-3 [389 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.6-2 [37.0 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 1.26.18-2 [116 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.31.0+dfsg-1 [68.6 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 python3-duecredit all 0.9.1-1.1 [66.7 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 python3-monotonic all 1.6-2 [5728 B] Get: 202 http://deb.debian.org/debian unstable/main amd64 python3-fasteners all 0.18-2 [14.0 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.11.4-6 [19.5 MB] Get: 204 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.12-7 [3869 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-4 [95.4 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b3 [25.5 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.46.0-1 [1623 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1021 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 python3-mrcfile all 1.4.3-3 [113 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 python3-griddataformats all 1.0.2-1 [2048 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 python3-gsd amd64 3.0.1-3+b1 [197 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 python3-h5py-serial amd64 3.10.0-1+b3 [1400 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 python3-h5py all 3.10.0-1 [14.4 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 python3-hypothesis all 6.100.4-1 [314 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 220 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 221 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1 [14.5 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 python3-joblib all 1.3.2-2 [218 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.5-1 [80.7 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 python3-latexcodec all 3.0.0-1 [17.5 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.6.3-2 [8167 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 python3-msgpack amd64 1.0.3-3+b1 [96.5 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 python3-mmtf all 1.1.3-1 [17.0 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 7.2.6-6 [702 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.17.2+dfsg-1 [818 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 7.2.6-6 [552 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 235 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-rtd-theme all 2.0.0+dfsg-1 [28.3 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 python3-msmb-theme all 1.2.0-4 [33.8 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 python3-netcdf4 amd64 1.6.5-1+b2 [916 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 python3-networkx all 3.2.1-4 [14.2 MB] Get: 239 http://deb.debian.org/debian unstable/main amd64 python3-pandas-lib amd64 2.1.4+dfsg-8 [7882 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 python3-pandas all 2.1.4+dfsg-8 [3015 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.1-2 [177 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 python3-pybtex all 0.24.0-4 [74.6 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 python3-pybtex-docutils all 1.0.2-1 [8064 B] Get: 245 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.1.2-1 [246 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 python3-seaborn all 0.13.2-3 [215 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 python3-sklearn-lib amd64 1.4.2+dfsg-1 [6606 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 python3-sklearn all 1.4.2+dfsg-1 [2247 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-sitemap all 2.2.0-2 [7252 B] Get: 251 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.bibtex all 2.6.2-1 [32.4 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 python3-tqdm all 4.66.4-1 [90.8 kB] Fetched 208 MB in 3s (75.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package fonts-lato. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21033 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:amd64. 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Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../026-libfreetype6_2.13.2+dfsg-1+b4_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../027-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../028-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package libfontenc1:amd64. Preparing to unpack .../029-libfontenc1_1%3a1.1.8-1_amd64.deb ... Unpacking libfontenc1:amd64 (1:1.1.8-1) ... Selecting previously unselected package x11-common. Preparing to unpack .../030-x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../031-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... Unpacking xfonts-encodings (1:1.0.4-2.2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../032-xfonts-utils_1%3a7.7+6_amd64.deb ... Unpacking xfonts-utils (1:7.7+6) ... Selecting previously unselected package fonts-urw-base35. Preparing to unpack .../033-fonts-urw-base35_20200910-8_all.deb ... Unpacking fonts-urw-base35 (20200910-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../034-fontconfig-config_2.15.0-1.1_amd64.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../035-libfontconfig1_2.15.0-1.1_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-1.1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../036-libxau6_1%3a1.0.9-1+b1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1+b1) ... Selecting previously unselected package libbsd0:amd64. 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Preparing to unpack .../043-libxft2_2.3.6-1+b1_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b1) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../044-libxext6_2%3a1.3.4-1+b1_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../045-libxss1_1%3a1.2.3-1+b1_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1+b1) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../046-libtk8.6_8.6.14-1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.14-1) ... Selecting previously unselected package tk8.6-blt2.5. Preparing to unpack .../047-tk8.6-blt2.5_2.5.3+dfsg-7_amd64.deb ... Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7) ... Selecting previously unselected package blt. Preparing to unpack .../048-blt_2.5.3+dfsg-7_amd64.deb ... Unpacking blt (2.5.3+dfsg-7) ... Selecting previously unselected package cython3. 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Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.61.0-1+b1) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libqhull-r8.0:amd64 (2020.2-6+b1) ... Setting up libcom-err2:amd64 (1.47.1~rc2-1) ... Setting up file (1:5.45-3) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up libaec0:amd64 (1.1.3-1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up python-babel-localedata (2.14.0-1) ... Setting up libkrb5support0:amd64 (1.20.1-6+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Jun 12 16:32:22 UTC 2025. Universal Time is now: Thu Jun 12 16:32:22 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... Setting up libfontenc1:amd64 (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:amd64 (2.80.1-1) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libexpat1-dev:amd64 (2.6.2-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up liblzf1:amd64 (3.6-4+b1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... Setting up libimagequant0:amd64 (2.18.0-1+b1) ... Setting up libproc2-0:amd64 (2:4.0.4-4) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up libtcl8.6:amd64 (8.6.14+dfsg-1) ... 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Setting up libwebpmux3:amd64 (1.4.0-0.1) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... Setting up libsz2:amd64 (1.1.3-1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.12-minimal (3.12.3-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.17.0-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:amd64 (1.17.0-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... Setting up libxcb-shm0:amd64 (1.17.0-1) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libjs-sphinxdoc (7.2.6-6) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1+b1) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Setting up libpython3.12-stdlib:amd64 (3.12.3-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up libcurl4t64:amd64 (8.7.1-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libpython3.11t64:amd64 (3.11.9-1) ... Setting up libcurl3t64-gnutls:amd64 (8.7.1-5) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up libpython3.12t64:amd64 (3.12.3-1) ... Setting up libpython3.11-dev:amd64 (3.11.9-1) ... Setting up libraqm0:amd64 (0.10.1-1+b1) ... Setting up sphinx-common (7.2.6-6) ... Setting up libxss1:amd64 (1:1.2.3-1+b1) ... Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-3.3) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-3.3) ... Setting up python3.11 (3.11.9-1) ... Setting up libnetcdf19t64:amd64 (1:4.9.2-5+b1) ... Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libpython3-dev:amd64 (3.11.8-1) ... Setting up python3.11-dev (3.11.9-1) ... Setting up libtk8.6:amd64 (8.6.14-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up libpython3.12-dev:amd64 (3.12.3-1) ... Setting up python3-sortedcontainers (2.4.0-2) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-freetype (2.4.0-1) ... Setting up python3-markupsafe (2.1.5-1) ... Setting up python3-wheel (0.43.0-1) ... Setting up python3-tz (2024.1-2) ... Setting up python3-monotonic (1.6-2) ... Setting up python3-six (1.16.0-6) ... Setting up python3-pil:amd64 (10.3.0-2) ... Setting up python3-roman (3.3-3) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-jinja2 (3.1.3-1) ... 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Setting up python3-appdirs (1.4.4-4) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sympy (1.12-7) ... Setting up python3-attr (23.2.0-2) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up python3-cairo (1.26.0-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-joblib (1.3.2-2) ... Setting up python3-babel (2.14.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-lz4 (4.0.2+dfsg-1+b3) ... Setting up python3-citeproc (0.6.0-3) ... Setting up python3-charset-normalizer (3.3.2-1) ... Setting up python3-pytest (8.1.2-1) ... Setting up python3-alabaster (0.7.12-1) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3-hypothesis (6.100.4-1) ... Setting up python3-tqdm (4.66.4-1) ... Setting up python3-threadpoolctl (3.1.0-1) ... Setting up python3-latexcodec (3.0.0-1) ... Setting up python3-all (3.11.8-1) ... Setting up python3-yaml (6.0.1-2) ... Setting up python3-tk:amd64 (3.12.3-1) ... Setting up python3-networkx (3.2.1-4) ... Setting up python3-fs (2.4.16-4) ... Setting up python3-pygments (2.17.2+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-pil.imagetk:amd64 (10.3.0-2) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-dev (3.11.8-1) ... Setting up python3-requests (2.31.0+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-8) ... Setting up python3-reportlab (4.2.0-1) ... Setting up python3-pybtex (0.24.0-4) ... Setting up python3-contourpy (1.0.7-3) ... Setting up python3-mrcfile (1.4.3-3) ... Setting up dh-python (6.20240422) ... Setting up python3-all-dev (3.11.8-1) ... Setting up python3-scipy (1.11.4-6) ... Setting up python3-duecredit (0.9.1-1.1) ... Setting up pybuild-plugin-pyproject (6.20240422) ... Setting up python3-pandas-lib:amd64 (2.1.4+dfsg-8) ... Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-1) ... Setting up python3-h5py-serial (3.10.0-1+b3) ... Setting up python3-gsd (3.0.1-3+b1) ... Setting up python3-mmtf (1.1.3-1) ... Setting up python3-griddataformats (1.0.2-1) ... Setting up python3-pandas (2.1.4+dfsg-8) ... Setting up python3-h5py (3.10.0-1) ... Setting up python3-sklearn (1.4.2+dfsg-1) ... Setting up python3-cftime (1.6.3-1+b1) ... Setting up python3-netcdf4 (1.6.5-1+b2) ... Setting up python3-fonttools (4.46.0-1) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up python3-matplotlib (3.6.3-2) ... Setting up python3-seaborn (0.13.2-3) ... Processing triggers for libc-bin (2.38-8) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.20.1+dfsg-3) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.83+dfsg1-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.20.1+dfsg-3) ... Setting up python3-pybtex-docutils (1.0.2-1) ... Setting up python3-sphinx (7.2.6-6) ... Setting up python3-sphinxcontrib.bibtex (2.6.2-1) ... Setting up python3-sphinx-sitemap (2.2.0-2) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-sphinx-rtd-theme (2.0.0+dfsg-1) ... Setting up python3-msmb-theme (1.2.0-4) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.34-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/mdanalysis-2.5.0+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_2.5.0+dfsg1-2_source.changes dpkg-buildpackage: info: source package mdanalysis dpkg-buildpackage: info: source version 2.5.0+dfsg1-2 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-2.5.0+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-2.5.0+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-2.5.0+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:129: Building wheel for python3.12 with "build" module I: pybuild base:311: python3.12 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/mdanalysis-2.5.0+dfsg1/.pybuild/cpython3_3.12_mdanalysis * Building wheel... performance hint: MDAnalysis/lib/c_distances.pyx:301:5: Exception check on '_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:328:5: Exception check on '_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:416:37: Exception check after calling '__pyx_fuse_0_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_0_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_0_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:416:37: Exception check after calling '__pyx_fuse_1_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_1_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_1_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:440:36: Exception check after calling '__pyx_fuse_0_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_0_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_0_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:440:36: Exception check after calling '__pyx_fuse_1_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_1_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_1_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:417:37: Exception check after calling 'coord2cellid' will always require the GIL to be acquired. Declare 'coord2cellid' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:431:26: Exception check after calling 'coord2cellxyz' will always require the GIL to be acquired. Possible solutions: 1. Declare 'coord2cellxyz' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'coord2cellxyz' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:559:34: Exception check after calling 'coord2cellxyz' will always require the GIL to be acquired. Possible solutions: 1. Declare 'coord2cellxyz' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'coord2cellxyz' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:567:56: Exception check after calling 'cellxyz2cellid' will always require the GIL to be acquired. Declare 'cellxyz2cellid' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:574:53: Exception check after calling 'calc_distsq' will always require the GIL to be acquired. Declare 'calc_distsq' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:578:57: Exception check after calling 'add_neighbors' will always require the GIL to be acquired. Possible solutions: 1. Declare 'add_neighbors' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'add_neighbors' to allow an error code to be returned. 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:80: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) corresp(dist, value, root_dir) running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-cpython-312 creating build/lib.linux-x86_64-cpython-312/MDAnalysis copying MDAnalysis/version.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis copying MDAnalysis/authors.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis copying MDAnalysis/units.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis copying MDAnalysis/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis copying MDAnalysis/due.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis copying MDAnalysis/exceptions.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis creating build/lib.linux-x86_64-cpython-312/MDAnalysis/tests copying MDAnalysis/tests/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/tests copying MDAnalysis/tests/datafiles.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/tests creating build/lib.linux-x86_64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/base.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/pymol.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/gromacs.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/vmd.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/jmol.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/charmm.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/selections creating build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/base.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/chain.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/null.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/core.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/memory.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TNG.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates creating build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/base.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/tables.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/core.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/GROParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/guessers.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology creating build/lib.linux-x86_64-cpython-312/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/visualization copying MDAnalysis/visualization/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/visualization creating build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/base.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/core.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/auxiliary creating build/lib.linux-x86_64-cpython-312/MDAnalysis/core copying MDAnalysis/core/_get_readers.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core copying MDAnalysis/core/topology.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core copying MDAnalysis/core/groups.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core copying MDAnalysis/core/universe.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core copying MDAnalysis/core/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core copying MDAnalysis/core/selection.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core copying MDAnalysis/core/accessors.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/core creating build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/base.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/wrap.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/fit.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/nojump.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/rotate.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/translate.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/transformations creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/base.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/polymer.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/psa.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/rdf.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/dielectric.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/density.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/contacts.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/rms.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/msd.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/align.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/pca.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/gnm.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/atomicdistances.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/distances.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/bat.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis creating build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/correlations.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/mdamath.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/_distopia.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/transformations.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/distances.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/util.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/log.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib creating build/lib.linux-x86_64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/RDKit.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/converters creating build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/topology/tpr creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/data creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/legacy creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hbonds creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hydrogenbonds creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/hole.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/utils.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/templates.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/hole2 creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering creating build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats 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' dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/analysis/encore/clustering/include/ap.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative reading manifest file '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:204: _Warning: Package 'MDAnalysis.analysis.encore.clustering.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.clustering.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.analysis.encore.clustering.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.analysis.encore.clustering.include' to be distributed and are already explicitly excluding 'MDAnalysis.analysis.encore.clustering.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.analysis.encore.clustering.src' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.clustering.src' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.analysis.encore.clustering.src' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.analysis.encore.clustering.src' to be distributed and are already explicitly excluding 'MDAnalysis.analysis.encore.clustering.src' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.analysis.encore.dimensionality_reduction.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.analysis.encore.dimensionality_reduction.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.analysis.encore.dimensionality_reduction.include' to be distributed and are already explicitly excluding 'MDAnalysis.analysis.encore.dimensionality_reduction.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.analysis.encore.dimensionality_reduction.src' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.src' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.analysis.encore.dimensionality_reduction.src' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.analysis.encore.dimensionality_reduction.src' to be distributed and are already explicitly excluding 'MDAnalysis.analysis.encore.dimensionality_reduction.src' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.lib.formats.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.formats.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.lib.formats.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.lib.formats.include' to be distributed and are already explicitly excluding 'MDAnalysis.lib.formats.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.lib.formats.src' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.formats.src' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.lib.formats.src' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.lib.formats.src' to be distributed and are already explicitly excluding 'MDAnalysis.lib.formats.src' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.lib.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.lib.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.lib.include' to be distributed and are already explicitly excluding 'MDAnalysis.lib.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.lib.libmdanalysis' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.libmdanalysis' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.lib.libmdanalysis' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.lib.libmdanalysis' to be distributed and are already explicitly excluding 'MDAnalysis.lib.libmdanalysis' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.lib.src.transformations' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.src.transformations' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.lib.src.transformations' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.lib.src.transformations' to be distributed and are already explicitly excluding 'MDAnalysis.lib.src.transformations' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/data copying MDAnalysis/coordinates/timestep.cpp -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pxd -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pyx -> build/lib.linux-x86_64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/lib/_augment.cpp -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/_augment.pyx -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/_cutil.cpp -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pxd -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pyx -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/c_distances.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pyx -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.cpp -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.pyx -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/qcprot.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/qcprot.pyx -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib creating build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/include copying MDAnalysis/lib/include/calc_distances.h -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/include creating build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/libmdanalysis copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/libmdanalysis creating build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/src creating build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/src/transformations copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/include copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/include creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/include copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/include creating build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/src copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/analysis/encore/clustering/src copying MDAnalysis/lib/formats/cython_util.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats creating build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/include creating build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/src running build_ext building 'MDAnalysis.lib.formats.libdcd' extension creating build/temp.linux-x86_64-cpython-312 creating build/temp.linux-x86_64-cpython-312/MDAnalysis creating build/temp.linux-x86_64-cpython-312/MDAnalysis/lib creating build/temp.linux-x86_64-cpython-312/MDAnalysis/lib/formats x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/formats/include -I/usr/include/python3.12 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.linux-x86_64-cpython-312/MDAnalysis/lib/formats/libdcd.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: '-fassociative-math' disabled; other options take precedence In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/formats/libdcd.c:1262: /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:1269: 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:1268: 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) { | ^~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/MDAnalysis/lib/formats/libdcd.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/formats/libdcd.cpython-312-x86_64-linux-gnu.so building 'MDAnalysis.lib.c_distances' extension x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/include -I/usr/include/python3.12 -c MDAnalysis/lib/c_distances.c -o build/temp.linux-x86_64-cpython-312/MDAnalysis/lib/c_distances.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: '-fassociative-math' disabled; other options take precedence In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/c_distances.c:1262: /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 " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/MDAnalysis/lib/c_distances.o -L/usr/lib/x86_64-linux-gnu -lm -o build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/c_distances.cpython-312-x86_64-linux-gnu.so building 'MDAnalysis.lib.c_distances_openmp' extension x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPARALLEL -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/include -I/usr/include/python3.12 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.linux-x86_64-cpython-312/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: '-fassociative-math' disabled; other options take precedence In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/c_distances_openmp.c:1273: /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 " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/MDAnalysis/lib/c_distances_openmp.o -L/usr/lib/x86_64-linux-gnu -lm -lgomp -o build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/c_distances_openmp.cpython-312-x86_64-linux-gnu.so -fopenmp building 'MDAnalysis.lib.qcprot' extension x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c MDAnalysis/lib/qcprot.c -o build/temp.linux-x86_64-cpython-312/MDAnalysis/lib/qcprot.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: '-fassociative-math' disabled; other options take precedence In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/qcprot.c:1256: /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:5156:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 5156 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ^ MDAnalysis/lib/qcprot.c:5364:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 5364 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ^ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/MDAnalysis/lib/qcprot.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/MDAnalysis/lib/qcprot.cpython-312-x86_64-linux-gnu.so building 'MDAnalysis.lib._transformations' extension creating build/temp.linux-x86_64-cpython-312/MDAnalysis/lib/src creating build/temp.linux-x86_64-cpython-312/MDAnalysis/lib/src/transformations x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.linux-x86_64-cpython-312/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: '-fassociative-math' disabled; other options take precedence In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from 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:2122:35: error: implicit declaration of function 'PyUnicode_GetSize'; did you mean 'PyUnicode_Resize'? [-Werror=implicit-function-declaration] 2122 | if (PyUnicode_Check(axes) && (PyUnicode_GetSize(axes) == 4)) { | ^~~~~~~~~~~~~~~~~ | PyUnicode_Resize 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( | ^~~~~~~~~~~~~~~~~~~~~~~ cc1: some warnings being treated as errors error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1 ERROR Backend subprocess exited when trying to invoke build_wheel E: pybuild pybuild:389: build: plugin pyproject failed with: exit code=1: python3.12 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/mdanalysis-2.5.0+dfsg1/.pybuild/cpython3_3.12_mdanalysis I: pybuild plugin_pyproject:129: Building wheel for python3.11 with "build" module I: pybuild base:311: python3.11 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/mdanalysis-2.5.0+dfsg1/.pybuild/cpython3_3.11_mdanalysis * Building wheel... Attempting to autodetect OpenMP support... Compiler supports OpenMP Will attempt to use Cython. /usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:80: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) corresp(dist, value, root_dir) running bdist_wheel running build running build_py creating build/lib.linux-x86_64-cpython-311 creating build/lib.linux-x86_64-cpython-311/MDAnalysis copying MDAnalysis/version.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis copying MDAnalysis/authors.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis copying MDAnalysis/units.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis copying MDAnalysis/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis copying MDAnalysis/due.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis copying MDAnalysis/exceptions.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis creating build/lib.linux-x86_64-cpython-311/MDAnalysis/tests copying MDAnalysis/tests/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/tests copying MDAnalysis/tests/datafiles.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/tests creating 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/pymol.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/vmd.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/selections copying MDAnalysis/selections/__init__.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/charmm.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/selections creating 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/PQR.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/FHIAIMS.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/DLPoly.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/LAMMPS.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/GSD.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/chain.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/PDB.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/TXYZ.py -> 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/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/ParmEd.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/H5MD.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/CRD.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/GMS.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/TNG.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/NAMDBIN.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/XYZ.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/coordinates creating 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/base.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/TXYZParser.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/CRDParser.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/ParmEdParser.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/tables.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/HoomdXMLParser.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/TPRParser.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/PSFParser.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/MMTFParser.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/__init__.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/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/PQRParser.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/PDBQTParser.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/guessers.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/topology 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/__init__.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/visualization creating 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/core.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/core copying MDAnalysis/core/_get_readers.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/groups.py -> 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/__init__.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/selection.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/core copying MDAnalysis/core/accessors.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/core creating 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/wrap.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/nojump.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/rotate.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/transformations copying MDAnalysis/transformations/__init__.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/translate.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/transformations creating 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/polymer.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/rdf.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/lineardensity.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/rms.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/align.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/helix_analysis.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/__init__.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/gnm.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis copying MDAnalysis/analysis/atomicdistances.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/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/leaflet.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/waterdynamics.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis creating 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/picklable_file_io.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/NeighborSearch.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/mdamath.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib copying MDAnalysis/lib/_distopia.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/distances.py -> 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/log.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/lib creating 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/OpenMMParser.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/__init__.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/OpenMM.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/converters copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/converters creating 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/utils.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/analysis/encore copying MDAnalysis/analysis/encore/similarity.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/utils.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 copying MDAnalysis/analysis/encore/bootstrap.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 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/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/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/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.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/hbond_autocorrel.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/hole.py -> 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/__init__.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 creating 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 copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.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/ClusteringMethod.py -> 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/ClusterCollection.py -> build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/encore/clustering 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 running 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 dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/analysis/encore/clustering/include/ap.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative reading manifest file '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:204: _Warning: Package 'MDAnalysis.analysis.encore.clustering.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.clustering.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.analysis.encore.clustering.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.analysis.encore.clustering.include' to be distributed and are already explicitly excluding 'MDAnalysis.analysis.encore.clustering.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.analysis.encore.clustering.src' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.clustering.src' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.analysis.encore.clustering.src' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.analysis.encore.clustering.src' to be distributed and are already explicitly excluding 'MDAnalysis.analysis.encore.clustering.src' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.analysis.encore.dimensionality_reduction.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.analysis.encore.dimensionality_reduction.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.analysis.encore.dimensionality_reduction.include' to be distributed and are already explicitly excluding 'MDAnalysis.analysis.encore.dimensionality_reduction.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.analysis.encore.dimensionality_reduction.src' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.src' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.analysis.encore.dimensionality_reduction.src' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.analysis.encore.dimensionality_reduction.src' to be distributed and are already explicitly excluding 'MDAnalysis.analysis.encore.dimensionality_reduction.src' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.lib.formats.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.formats.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.lib.formats.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.lib.formats.include' to be distributed and are already explicitly excluding 'MDAnalysis.lib.formats.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.lib.formats.src' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.formats.src' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.lib.formats.src' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.lib.formats.src' to be distributed and are already explicitly excluding 'MDAnalysis.lib.formats.src' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.lib.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.lib.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.lib.include' to be distributed and are already explicitly excluding 'MDAnalysis.lib.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.lib.libmdanalysis' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.libmdanalysis' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.lib.libmdanalysis' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.lib.libmdanalysis' to be distributed and are already explicitly excluding 'MDAnalysis.lib.libmdanalysis' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.lib.src.transformations' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'MDAnalysis.lib.src.transformations' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'MDAnalysis.lib.src.transformations' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'MDAnalysis.lib.src.transformations' to be distributed and are already explicitly excluding 'MDAnalysis.lib.src.transformations' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying 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/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/_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/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 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 running build_ext building 'MDAnalysis.lib.formats.libdcd' extension 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 x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/formats/include -I/usr/include/python3.11 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.linux-x86_64-cpython-311/MDAnalysis/lib/formats/libdcd.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: '-fassociative-math' disabled; other options take precedence In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/formats/libdcd.c:1262: /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:1269: 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:1268: 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) { | ^~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/include -I/usr/include/python3.11 -c MDAnalysis/lib/c_distances.c -o build/temp.linux-x86_64-cpython-311/MDAnalysis/lib/c_distances.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: '-fassociative-math' disabled; other options take precedence In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/c_distances.c:1262: /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 " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPARALLEL -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/include -I/usr/include/python3.11 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.linux-x86_64-cpython-311/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: '-fassociative-math' disabled; other options take precedence In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/c_distances_openmp.c:1273: /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 " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c MDAnalysis/lib/qcprot.c -o build/temp.linux-x86_64-cpython-311/MDAnalysis/lib/qcprot.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: '-fassociative-math' disabled; other options take precedence In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/qcprot.c:1256: /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:5156:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 5156 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ^ MDAnalysis/lib/qcprot.c:5364:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 5364 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ^ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 creating build/temp.linux-x86_64-cpython-311/MDAnalysis/lib/src creating build/temp.linux-x86_64-cpython-311/MDAnalysis/lib/src/transformations x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.linux-x86_64-cpython-311/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: '-fassociative-math' disabled; other options take precedence In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from 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( | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 creating build/temp.linux-x86_64-cpython-311/MDAnalysis/lib/formats/src x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/formats -I/usr/include/python3.11 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.linux-x86_64-cpython-311/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: '-fassociative-math' disabled; other options take precedence In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/formats/libmdaxdr.c:1283: /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/libmdaxdr.c:1289: 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/libmdaxdr.c:1290: 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/include/xdrfile_xtc.h:43: 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/libmdaxdr.c:1291: 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 -*- | x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/formats -I/usr/include/python3.11 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.linux-x86_64-cpython-311/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 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-2.5.0+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-2.5.0+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 /build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:42: /build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | MDAnalysis/lib/formats/src/trr_seek.c: In function 'read_trr_n_frames': MDAnalysis/lib/formats/src/trr_seek.c:39:27: warning: unused variable 'totalframebytes' [-Wunused-variable] 39 | int result, framebytes, totalframebytes; | ^~~~~~~~~~~~~~~ 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; | ^~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.5.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.5.0+dfsg1/package/MDAnalysis/lib/formats -I/usr/include/python3.11 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.linux-x86_64-cpython-311/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros cc1: warning: '-fassociative-math' disabled; other options take precedence In file included from MDAnalysis/lib/formats/src/xdrfile.c:62: /build/reproducible-path/mdanalysis-2.5.0+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 copying build/lib.linux-x86_64-cpython-311/MDAnalysis/authors.py -> build/bdist.linux-x86_64/wheel/MDAnalysis 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/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/pymol.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/vmd.py -> 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/jmol.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 creating 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/PQR.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/FHIAIMS.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/DLPoly.py -> 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/PDBQT.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/DMS.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/XDR.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/TRJ.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/MOL2.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/timestep.pyx -> 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 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/chemfiles.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/__init__.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/MMTF.py -> 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/memory.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/XTC.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/GRO.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/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/TRZ.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/INPCRD.py -> 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/units.py -> build/bdist.linux-x86_64/wheel/MDAnalysis creating 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/base.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/TXYZParser.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/CRDParser.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/ParmEdParser.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/tables.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/HoomdXMLParser.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/TPRParser.py -> 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/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/tpr/obj.py -> 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/GMSParser.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/core.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/GSDParser.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/GROParser.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/MinimalParser.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/ExtendedPDBParser.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/LAMMPSParser.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 creating 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/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 creating 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 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/XVG.py -> 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 creating 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/topologyattrs.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/groups.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 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/topologyobjects.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/accessors.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/core 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 creating 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/wrap.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/nojump.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/__init__.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/translate.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/transformations copying build/lib.linux-x86_64-cpython-311/MDAnalysis/exceptions.py -> build/bdist.linux-x86_64/wheel/MDAnalysis creating 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/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/dielectric.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis creating 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 creating 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.cpython-311-x86_64-linux-gnu.so -> 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/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/__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/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/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/cutils.c -> 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/utils.py -> 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 creating 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/ClusteringMethod.py -> 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/affinityprop.cpython-311-x86_64-linux-gnu.so -> 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 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/__init__.py -> 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/__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/covariance.py -> 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/density.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/lineardensity.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 creating 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 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/janin_ref_data.npy -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/data 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/msd.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis creating 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/legacy/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/legacy copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/align.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis creating 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 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/dihedrals.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis creating 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 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/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hydrogenbonds 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/__init__.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis creating 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/utils.py -> 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/templates.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis/hole2 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/gnm.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis copying build/lib.linux-x86_64-cpython-311/MDAnalysis/analysis/atomicdistances.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/nuclinfo.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/leaflet.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/waterdynamics.py -> build/bdist.linux-x86_64/wheel/MDAnalysis/analysis creating 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/AUTHOR -> 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/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/_cutil.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib creating 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/trr_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_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_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.c -> 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/libdcd.pyx -> 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/libmdaxdr.c -> 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/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 copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/formats/libmdaxdr.pyx -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib/formats creating 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/xdrfile.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/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/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/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/endianswap.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/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.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/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.pxd -> 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/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/correlations.py -> 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.c -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib 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/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/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/c_distances.c -> 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 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 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/_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/c_distances.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/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/_augment.cpp -> 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/_cutil.cpp -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib copying build/lib.linux-x86_64-cpython-311/MDAnalysis/lib/_distopia.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/c_distances_openmp.c -> 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/c_distances.pyx -> 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/util.py -> 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/_cutil.pyx -> 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/_augment.pyx -> build/bdist.linux-x86_64/wheel/MDAnalysis/lib creating 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/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/__init__.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/OpenMM.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 running install_egg_info Copying MDAnalysis.egg-info to build/bdist.linux-x86_64/wheel/MDAnalysis-2.5.0.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/MDAnalysis-2.5.0.dist-info/WHEEL creating '/build/reproducible-path/mdanalysis-2.5.0+dfsg1/.pybuild/cpython3_3.11_mdanalysis/.tmp-y7vkoj5y/MDAnalysis-2.5.0-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/atomicdistances.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/_distopia.py' 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/nojump.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-2.5.0.dist-info/AUTHORS' adding 'MDAnalysis-2.5.0.dist-info/LICENSE' adding 'MDAnalysis-2.5.0.dist-info/METADATA' adding 'MDAnalysis-2.5.0.dist-info/WHEEL' adding 'MDAnalysis-2.5.0.dist-info/top_level.txt' adding 'MDAnalysis-2.5.0.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Successfully built MDAnalysis-2.5.0-cp311-cp311-linux_x86_64.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.11 with "installer" module dh_auto_build: error: pybuild --build -i python{version} -p "3.12 3.11" returned exit code 13 make: *** [debian/rules:14: build] Error 25 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3309321 and its subdirectories Fri May 10 10:16:12 UTC 2024 W: No second build log, what happened?