Wed Nov 6 23:37:02 UTC 2024 I: starting to build mdanalysis/trixie/arm64 on jenkins on '2024-11-06 23:36' Wed Nov 6 23:37:02 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_18/65879/console.log Wed Nov 6 23:37:02 UTC 2024 I: Downloading source for trixie/mdanalysis=2.7.0-5 --2024-11-06 23:37:02-- http://deb.debian.org/debian/pool/main/m/mdanalysis/mdanalysis_2.7.0-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2889 (2.8K) [text/prs.lines.tag] Saving to: ‘mdanalysis_2.7.0-5.dsc’ 0K .. 100% 272M=0s 2024-11-06 23:37:02 (272 MB/s) - ‘mdanalysis_2.7.0-5.dsc’ saved [2889/2889] Wed Nov 6 23:37:02 UTC 2024 I: mdanalysis_2.7.0-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: mdanalysis Binary: python3-mdanalysis, python-mdanalysis-doc Architecture: any all Version: 2.7.0-5 Maintainer: Debichem Team Uploaders: Drew Parsons Homepage: https://www.mdanalysis.org/ Standards-Version: 4.7.0 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-all, python3-hypothesis, python3-pytest, python3-sklearn Build-Depends: debhelper-compat (= 13), cython3, dh-sequence-python3, pybuild-plugin-pyproject, python3-all-dev, python3-setuptools, python3-numpy, python3-biopython (>= 1.80), python3-networkx, python3-griddataformats, python3-mmtf, python3-joblib, python3-scipy, python3-matplotlib, python3-mda-xdrlib, python3-tqdm, python3-threadpoolctl, python3-packaging, python3-fasteners, python3-gsd (>= 3.0.1~) [!s390x !hppa !m68k !powerpc !ppc64 !sparc64], python3-netcdf4, 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: 850f34c7dc9e42ae992581b0ecbfa2646a6ab8bb 46994492 mdanalysis_2.7.0.orig.tar.xz 8eb619f45257026f07dc59530edc15bb96f7274b 10864 mdanalysis_2.7.0-5.debian.tar.xz Checksums-Sha256: 52021a0476fd183eaa45e14cf8cba455beaadb25801fc16bd6dddadabc4b91cf 46994492 mdanalysis_2.7.0.orig.tar.xz f1295bcc5b71d6d626e66834ca637e881f3a5c758cb5c08a4e5f2ec4484e062f 10864 mdanalysis_2.7.0-5.debian.tar.xz Files: d02b4538f3cfe26628b0ac7f5c6c8e49 46994492 mdanalysis_2.7.0.orig.tar.xz ec117204a55a900b4f6d49d5de1ed486 10864 mdanalysis_2.7.0-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAma3pXUUHGRwYXJzb25z QGRlYmlhbi5vcmcACgkQVz7x5L1aAfoUgQ/+O7ktiA/5sPMi8NKKgAwESMnWNlZ7 vSGVk1IUXEy86FzPbz7xU4OYdaYK9hlpqfCUd/5mKNYlyeQQ0pB3bwCUZ0UrhkdY aDpQC265vhqjU/41f9y+0/h5/BhkaQg2Lxxu+Ca5Si9k0IRUPHLBXzFAMvuyEMsm t5r60R5N07Bn+ndDd8fyItgz2FIgasz1DHA9VNPk4cQKub2ELiudXsdaNydKIeCv 0vpfDmqliuaUWDJOCovtvLWKKRtgONkyT57w5sWx6VOqeNrUmvX168FPw8N9vAxi cYi/HTd/eNBxsbmWqwq+NwYXoWkuchXItrKOnNANsySb0EAOBCGnzSWymIxwf3fR 3F9+c+I4MTz7Pbd4FiDEIfABr3JkW/AzKHQmyk303YbzzWlsd+/FMvqwUAG6bKqk Ow2vOCL6syTm2hFZvrffe2VwNhn+zU82PHvbErOY6UYJeNf72XoOxpvPgGVsPYzu CRiajiy0P3a+ahnKXXaSpAHuegBt7S3WH0ZYr5d2OA/eNpPGaccWPKVj/WrSqJ2I WYiZCFZK2JlIndQL9GE2sF77i8fPh4tM603L837ri4fwnjqdjDOFyUXKlVyyrVW0 Z30qbr0/fsJznwXYbWxPlwyvPrA+2QlcnPSadZHTHExf7v59+BgDOlxgk7FplhIL DjYKP1cVOYfvA8Q= =a3aH -----END PGP SIGNATURE----- Wed Nov 6 23:37:02 UTC 2024 I: Checking whether the package is not for us Wed Nov 6 23:37:02 UTC 2024 I: Starting 1st build on remote node codethink04-arm64.debian.net. Wed Nov 6 23:37:02 UTC 2024 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Thu Nov 7 17:37:06 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Nov 6 11:37:05 -12 2024 I: pbuilder-time-stamp: 1730936225 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [mdanalysis_2.7.0-5.dsc] I: copying [./mdanalysis_2.7.0.orig.tar.xz] I: copying [./mdanalysis_2.7.0-5.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Aug 10 17:37:57 2024 gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA gpgv: issuer "dparsons@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.7.0-5.dsc: no acceptable signature found dpkg-source: info: extracting mdanalysis in mdanalysis-2.7.0 dpkg-source: info: unpacking mdanalysis_2.7.0.orig.tar.xz dpkg-source: info: unpacking mdanalysis_2.7.0-5.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_sphinx_warnings_are_not_errors.patch dpkg-source: info: applying docs_local_mathjax.patch dpkg-source: info: applying xdr_type_PR4408.patch dpkg-source: info: applying doc_no_mdanalysis_sphinx.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2778107/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='bb6c056660f849bd9b508fa2fc8d5eba' 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='2778107' 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.0ABJt9tc/pbuilderrc_Bvc2 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0ABJt9tc/b1 --logfile b1/build.log mdanalysis_2.7.0-5.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2778107/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: arm64 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-sequence-python3, pybuild-plugin-pyproject, python3-all-dev, python3-setuptools, python3-numpy, python3-biopython (>= 1.80), python3-networkx, python3-griddataformats, python3-mmtf, python3-joblib, python3-scipy, python3-matplotlib, python3-mda-xdrlib, python3-tqdm, python3-threadpoolctl, python3-packaging, python3-fasteners, python3-gsd (>= 3.0.1~), python3-netcdf4, 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 ... 20089 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-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on python3-all-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; 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; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-griddataformats; however: Package python3-griddataformats is not installed. pbuilder-satisfydepends-dummy depends on python3-mmtf; however: Package python3-mmtf is not installed. pbuilder-satisfydepends-dummy depends on python3-joblib; however: Package python3-joblib is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-mda-xdrlib; however: Package python3-mda-xdrlib is not installed. pbuilder-satisfydepends-dummy depends on python3-tqdm; 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; 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} 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} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{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} libpython3.12-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} libsz2{a} libtcl8.6{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{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-autocommand{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-defusedxml{a} python3-dev{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-inflect{a} python3-iniconfig{a} python3-installer{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jinja2{a} python3-joblib{a} python3-kiwisolver{a} python3-latexcodec{a} python3-looseversion{a} python3-lxml{a} python3-lz4{a} python3-markupsafe{a} python3-matplotlib{a} python3-mda-xdrlib{a} python3-minimal{a} python3-mmtf{a} python3-monotonic{a} python3-more-itertools{a} python3-mpmath{a} python3-mrcfile{a} python3-msgpack{a} python3-msmb-theme{a} python3-netcdf4{a} python3-networkx{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-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-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-urllib3{a} python3-wheel{a} python3-yaml{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} python3.12-tk{a} python3.13-tk{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 linux-sysctl-defaults lynx ncbi-blast+ psmisc publicsuffix python-biopython-doc python3-bottleneck python3-bs4 python3-click python3-cssselect python3-gdal python3-html5lib python3-numexpr python3-odf python3-olefile python3-openpyxl python3-psutil python3-pydot python3-pygraphviz python3-simplejson python3-tables shared-mime-info wget xdg-user-dirs 0 packages upgraded, 260 newly installed, 0 to remove and 0 not upgraded. Need to get 172 MB of archives. After unpacking 758 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.6-1 [806 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.3-2 [90.1 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.6-1 [1935 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.12.6-1 [26.7 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-4 [255 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 13 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.6-1 [1898 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.6-1 [669 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.12.6-1 [9692 B] Get: 23 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.12.6-1 [27.8 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-6 [872 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.3.2-2 [1347 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-9 [96.6 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [982 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b5 [296 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libfontenc1 arm64 1:1.1.8-1+b1 [22.5 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 55 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.2-3+b2 [24.4 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b2 [27.2 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libxft2 arm64 2.3.6-1+b2 [51.6 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libxss1 arm64 1:1.2.3-1+b2 [17.1 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libtk8.6 arm64 8.6.15-1 [738 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7+b1 [538 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 blt arm64 2.5.3+dfsg-7+b1 [6344 B] Get: 69 http://deb.debian.org/debian trixie/main arm64 cython3 arm64 3.0.11+dfsg-1 [2192 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 76 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 90 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 74.1.2-2 [736 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20241024 [109 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 fonts-lyx all 2.4.2.1-1 [190 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libaec0 arm64 1.1.3-1+b1 [22.5 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-3+b1 [98.9 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.4.0-1+b1 [59.6 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.6.0-1 [112 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.6.0-1 [18.5 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.10.1-2 [328 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libcurl4t64 arm64 8.10.1-2 [322 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libexpat1-dev arm64 2.6.3-2 [142 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-6 [361 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.82.2-2 [1409 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libsz2 arm64 1.1.3-1+b1 [8044 B] Get: 126 http://deb.debian.org/debian trixie/main arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4 [1050 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4 [60.9 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3+b1 [1812 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b2 [25.6 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-4+b2 [154 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 liblzf1 arm64 3.6-4+b2 [10.0 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libnetcdf19t64 arm64 1:4.9.2-7 [444 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 libopenjp2-7 arm64 2.5.0-2+b4 [185 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 libpython3.12t64 arm64 3.12.6-1 [1981 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 libpython3.12-dev arm64 3.12.6-1 [4782 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 libpython3-dev arm64 3.12.6-1 [9952 B] Get: 148 http://deb.debian.org/debian trixie/main arm64 libpython3-all-dev arm64 3.12.6-1 [1064 B] Get: 149 http://deb.debian.org/debian trixie/main arm64 libqhull-r8.0 arm64 2020.2-6+b2 [229 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 libraqm0 arm64 0.10.1-1+b2 [13.8 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.4.0-0.1+b1 [112 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.4.0-0.1+b1 [268 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 libwebpdemux2 arm64 1.4.0-0.1+b1 [110 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 libwebpmux3 arm64 1.4.0-0.1+b1 [122 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 libxslt1.1 arm64 1.1.35-1.1+b1 [222 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 libyaml-0-2 arm64 0.2.5-1+b2 [49.3 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.1-1 [45.8 kB] Get: 159 http://deb.debian.org/debian trixie/main arm64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 python3-toml all 0.10.2-1 [16.2 kB] Get: 161 http://deb.debian.org/debian trixie/main arm64 python3-wheel all 0.44.0-2 [53.4 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 python3-build all 1.2.2-1 [36.0 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 pybuild-plugin-pyproject all 6.20241024 [11.4 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 166 http://deb.debian.org/debian trixie/main arm64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 python3-all arm64 3.12.6-1 [1040 B] Get: 169 http://deb.debian.org/debian trixie/main arm64 python3.12-dev arm64 3.12.6-1 [506 kB] Get: 170 http://deb.debian.org/debian trixie/main arm64 python3-dev arm64 3.12.6-1 [26.1 kB] Get: 171 http://deb.debian.org/debian trixie/main arm64 python3-all-dev arm64 3.12.6-1 [1068 B] Get: 172 http://deb.debian.org/debian trixie/main arm64 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 173 http://deb.debian.org/debian trixie/main arm64 python3-attr all 23.2.0-2 [65.5 kB] Get: 174 http://deb.debian.org/debian trixie/main arm64 python3-tz all 2024.1-2 [30.9 kB] Get: 175 http://deb.debian.org/debian trixie/main arm64 python3-babel all 2.14.0-1 [111 kB] Get: 176 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.26.4+ds-11 [3351 kB] Get: 177 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 178 http://deb.debian.org/debian trixie/main arm64 python3.12-tk arm64 3.12.6-1 [110 kB] Get: 179 http://deb.debian.org/debian trixie/main arm64 python3.13-tk arm64 3.13.0-1 [101 kB] Get: 180 http://deb.debian.org/debian trixie/main arm64 python3-tk arm64 3.12.6-1 [9428 B] Get: 181 http://deb.debian.org/debian trixie/main arm64 python3-pil.imagetk arm64 10.4.0-1 [79.4 kB] Get: 182 http://deb.debian.org/debian trixie/main arm64 python3-pil arm64 10.4.0-1 [480 kB] Get: 183 http://deb.debian.org/debian trixie/main arm64 python3-cairo arm64 1.26.1-2 [113 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 185 http://deb.debian.org/debian trixie/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 186 http://deb.debian.org/debian trixie/main arm64 python3-reportlab all 4.2.5-1 [1117 kB] Get: 187 http://deb.debian.org/debian trixie/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 188 http://deb.debian.org/debian trixie/main arm64 python3-biopython arm64 1.84+dfsg-4 [1636 kB] Get: 189 http://deb.debian.org/debian trixie/main arm64 python3-brotli arm64 1.1.0-2+b5 [307 kB] Get: 190 http://deb.debian.org/debian trixie/main arm64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 191 http://deb.debian.org/debian trixie/main arm64 python3-cftime arm64 1.6.4-1+b2 [178 kB] Get: 192 http://deb.debian.org/debian trixie/main arm64 python3-charset-normalizer arm64 3.4.0-1 [112 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 python3-lxml arm64 5.3.0-1 [1096 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 python3-citeproc all 0.6.0-3 [96.7 kB] Get: 195 http://deb.debian.org/debian trixie/main arm64 python3-contourpy arm64 1.3.0-2 [191 kB] Get: 196 http://deb.debian.org/debian trixie/main arm64 python3-cycler all 0.12.1-1 [9496 B] Get: 197 http://deb.debian.org/debian trixie/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 198 http://deb.debian.org/debian trixie/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 199 http://deb.debian.org/debian trixie/main arm64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 200 http://deb.debian.org/debian trixie/main arm64 python3-roman all 4.2-1 [10.4 kB] Get: 201 http://deb.debian.org/debian trixie/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 202 http://deb.debian.org/debian trixie/main arm64 python3-looseversion all 1.3.0-3 [8964 B] Get: 203 http://deb.debian.org/debian trixie/main arm64 python3-idna all 3.8-2 [41.6 kB] Get: 204 http://deb.debian.org/debian trixie/main arm64 python3-urllib3 all 2.0.7-2 [111 kB] Get: 205 http://deb.debian.org/debian trixie/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 206 http://deb.debian.org/debian trixie/main arm64 python3-duecredit all 0.10.2-2 [70.6 kB] Get: 207 http://deb.debian.org/debian trixie/main arm64 python3-monotonic all 1.6-2 [5728 B] Get: 208 http://deb.debian.org/debian trixie/main arm64 python3-fasteners all 0.18-2 [14.0 kB] Get: 209 http://deb.debian.org/debian trixie/main arm64 python3-six all 1.16.0-7 [16.4 kB] Get: 210 http://deb.debian.org/debian trixie/main arm64 python3-fs all 2.4.16-4 [95.4 kB] Get: 211 http://deb.debian.org/debian trixie/main arm64 python3-lz4 arm64 4.0.2+dfsg-1+b5 [25.3 kB] Get: 212 http://deb.debian.org/debian trixie/main arm64 python3-scipy arm64 1.13.1-5 [15.4 MB] Get: 213 http://deb.debian.org/debian trixie/main arm64 python3-mpmath all 1.3.0-1 [419 kB] Get: 214 http://deb.debian.org/debian trixie/main arm64 python3-sympy all 1.13.3-1 [4147 kB] Get: 215 http://deb.debian.org/debian trixie/main arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get: 216 http://deb.debian.org/debian trixie/main arm64 unicode-data all 15.1.0-1 [8547 kB] Get: 217 http://deb.debian.org/debian trixie/main arm64 python3-fonttools arm64 4.54.1-4 [1356 kB] Get: 218 http://deb.debian.org/debian trixie/main arm64 sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1022 kB] Get: 219 http://deb.debian.org/debian trixie/main arm64 python3-mrcfile all 1.5.3-3 [119 kB] Get: 220 http://deb.debian.org/debian trixie/main arm64 python3-griddataformats all 1.0.2-2 [2048 kB] Get: 221 http://deb.debian.org/debian trixie/main arm64 python3-gsd arm64 3.3.0-1+b2 [192 kB] Get: 222 http://deb.debian.org/debian trixie/main arm64 python3-h5py-serial arm64 3.11.0-5 [887 kB] Get: 223 http://deb.debian.org/debian trixie/main arm64 python3-h5py all 3.11.0-5 [14.7 kB] Get: 224 http://deb.debian.org/debian trixie/main arm64 python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 225 http://deb.debian.org/debian trixie/main arm64 python3-hypothesis all 6.115.3-1 [321 kB] Get: 226 http://deb.debian.org/debian trixie/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 227 http://deb.debian.org/debian trixie/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 228 http://deb.debian.org/debian trixie/main arm64 python3-markupsafe arm64 2.1.5-1+b2 [13.8 kB] Get: 229 http://deb.debian.org/debian trixie/main arm64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 230 http://deb.debian.org/debian trixie/main arm64 python3-joblib all 1.3.2-4 [216 kB] Get: 231 http://deb.debian.org/debian trixie/main arm64 python3-kiwisolver arm64 1.4.7-2 [56.7 kB] Get: 232 http://deb.debian.org/debian trixie/main arm64 python3-latexcodec all 3.0.0-1 [17.5 kB] Get: 233 http://deb.debian.org/debian trixie/main arm64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 234 http://deb.debian.org/debian trixie/main arm64 python3-matplotlib arm64 3.8.3-3 [5509 kB] Get: 235 http://deb.debian.org/debian trixie/main arm64 python3-mda-xdrlib all 0.2.0-3 [11.6 kB] Get: 236 http://deb.debian.org/debian trixie/main arm64 python3-msgpack arm64 1.0.3-3+b3 [77.4 kB] Get: 237 http://deb.debian.org/debian trixie/main arm64 python3-mmtf all 1.1.3-1 [17.0 kB] Get: 238 http://deb.debian.org/debian trixie/main arm64 sphinx-common all 7.4.7-4 [731 kB] Get: 239 http://deb.debian.org/debian trixie/main arm64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 240 http://deb.debian.org/debian trixie/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 241 http://deb.debian.org/debian trixie/main arm64 python3-sphinx all 7.4.7-4 [588 kB] Get: 242 http://deb.debian.org/debian trixie/main arm64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 243 http://deb.debian.org/debian trixie/main arm64 python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [29.5 kB] Get: 244 http://deb.debian.org/debian trixie/main arm64 python3-msmb-theme all 1.2.0-4 [33.8 kB] Get: 245 http://deb.debian.org/debian trixie/main arm64 python3-netcdf4 arm64 1.7.2-1+b1 [525 kB] Get: 246 http://deb.debian.org/debian trixie/main arm64 python3-networkx all 3.2.1-4 [14.2 MB] Get: 247 http://deb.debian.org/debian trixie/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [3746 kB] Get: 248 http://deb.debian.org/debian trixie/main arm64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 249 http://deb.debian.org/debian trixie/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 250 http://deb.debian.org/debian trixie/main arm64 python3-yaml arm64 6.0.2-1 [119 kB] Get: 251 http://deb.debian.org/debian trixie/main arm64 python3-pybtex all 0.24.0-4 [74.6 kB] Get: 252 http://deb.debian.org/debian trixie/main arm64 python3-pybtex-docutils all 1.0.2-1 [8064 B] Get: 253 http://deb.debian.org/debian trixie/main arm64 python3-pytest all 8.3.3-1 [249 kB] Get: 254 http://deb.debian.org/debian trixie/main arm64 python3-seaborn all 0.13.2-4 [215 kB] Get: 255 http://deb.debian.org/debian trixie/main arm64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 256 http://deb.debian.org/debian trixie/main arm64 python3-sklearn-lib arm64 1.4.2+dfsg-6 [3213 kB] Get: 257 http://deb.debian.org/debian trixie/main arm64 python3-sklearn all 1.4.2+dfsg-6 [2248 kB] Get: 258 http://deb.debian.org/debian trixie/main arm64 python3-sphinx-sitemap all 2.6.0-1 [8508 B] Get: 259 http://deb.debian.org/debian trixie/main arm64 python3-sphinxcontrib.bibtex all 2.6.2-1 [32.4 kB] Get: 260 http://deb.debian.org/debian trixie/main arm64 python3-tqdm all 4.66.5-1 [90.1 kB] Fetched 172 MB in 1s (157 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 ... 20089 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 libpython3.12-minimal:arm64. Preparing to unpack .../libpython3.12-minimal_3.12.6-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.6-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.3-2_arm64.deb ... Unpacking libexpat1:arm64 (2.6.3-2) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_arm64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:arm64 (3.12.6-1) ... Setting up libexpat1:arm64 (2.6.3-2) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20435 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_arm64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-5_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_arm64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21509 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_arm64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-6_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-6_arm64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.3.2-2_arm64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../008-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../011-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.40.2-9_arm64.deb ... Unpacking bsdextrautils (2.40.2-9) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../014-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../016-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../017-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../018-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../019-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../020-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libtcl8.6:arm64. Preparing to unpack .../021-libtcl8.6_8.6.15+dfsg-2_arm64.deb ... Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../022-libbrotli1_1.1.0-2+b5_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b5) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../023-libpng16-16t64_1.6.44-2_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.44-2) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../024-libfreetype6_2.13.3+dfsg-1_arm64.deb ... Unpacking libfreetype6:arm64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../025-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 .../026-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package libfontenc1:arm64. Preparing to unpack .../027-libfontenc1_1%3a1.1.8-1+b1_arm64.deb ... Unpacking libfontenc1:arm64 (1:1.1.8-1+b1) ... Selecting previously unselected package x11-common. Preparing to unpack .../028-x11-common_1%3a7.7+23.1_all.deb ... Unpacking x11-common (1:7.7+23.1) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../029-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 .../030-xfonts-utils_1%3a7.7+7_arm64.deb ... Unpacking xfonts-utils (1:7.7+7) ... Selecting previously unselected package fonts-urw-base35. Preparing to unpack .../031-fonts-urw-base35_20200910-8_all.deb ... Unpacking fonts-urw-base35 (20200910-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../032-fontconfig-config_2.15.0-1.1+b1_arm64.deb ... Unpacking fontconfig-config (2.15.0-1.1+b1) ... Selecting previously unselected package libfontconfig1:arm64. 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Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.82.2-2) ... No schema files found: doing nothing. Setting up libblas3:arm64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libexpat1-dev:arm64 (2.6.3-2) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up liblzf1:arm64 (3.6-4+b2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:arm64 (1.0.15-1) ... Setting up libimagequant0:arm64 (2.18.0-1+b2) ... Setting up libproc2-0:arm64 (2:4.0.4-6) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.44-2) ... Setting up libtcl8.6:arm64 (8.6.15+dfsg-2) ... Setting up autopoint (0.22.5-2) ... Setting up fonts-dejavu-core (2.37-8) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/mdanalysis-2.7.0/ && 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_2.7.0-5_source.changes dpkg-buildpackage: info: source package mdanalysis dpkg-buildpackage: info: source version 2.7.0-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Drew Parsons dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 dpkg-source: info: using options from mdanalysis-2.7.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.7.0' 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/coordinates/timestep.cpp \ 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-2.7.0' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with 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-2.7.0/.pybuild/cpython3_3.12_mdanalysis * Building wheel... performance hint: MDAnalysis/lib/c_distances.pyx:275:5: 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:302:5: 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:390:37: 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:390:37: 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:414:36: 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:414:36: 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/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:78: 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-aarch64-cpython-312 creating build/lib.linux-aarch64-cpython-312/MDAnalysis copying MDAnalysis/authors.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis copying MDAnalysis/version.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis copying MDAnalysis/units.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis copying MDAnalysis/exceptions.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis copying MDAnalysis/due.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis copying MDAnalysis/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis creating build/lib.linux-aarch64-cpython-312/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/visualization copying MDAnalysis/visualization/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/visualization creating build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/wrap.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/translate.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/rotate.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/nojump.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/fit.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/base.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations creating build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/tables.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/guessers.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/core.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/base.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/GROParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology creating build/lib.linux-aarch64-cpython-312/MDAnalysis/tests copying MDAnalysis/tests/datafiles.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/tests copying MDAnalysis/tests/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/tests creating build/lib.linux-aarch64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/vmd.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/pymol.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/jmol.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/gromacs.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/charmm.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/base.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/selections creating build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/util.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/transformations.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/mdamath.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/log.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/distances.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/correlations.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/_distopia.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib creating build/lib.linux-aarch64-cpython-312/MDAnalysis/core copying MDAnalysis/core/universe.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/core copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/core copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/core copying MDAnalysis/core/topology.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/core copying MDAnalysis/core/selection.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/core copying MDAnalysis/core/groups.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/core copying MDAnalysis/core/accessors.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/core copying MDAnalysis/core/_get_readers.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/core copying MDAnalysis/core/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/core creating build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/null.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/memory.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/core.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/chain.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/base.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRC.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TNG.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates creating build/lib.linux-aarch64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/base.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/RDKit.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/converters creating build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/core.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/base.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/rms.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/rdf.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/psa.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/polymer.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/pca.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/msd.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/gnm.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/distances.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/dielectric.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/density.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/contacts.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/bat.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/base.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/atomicdistances.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/align.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis creating build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/tpr creating build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/legacy creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hydrogenbonds creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/utils.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/templates.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/hole.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hole2 creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hbonds creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/data creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering running egg_info creating MDAnalysis.egg-info writing MDAnalysis.egg-info/PKG-INFO writing dependency_links to MDAnalysis.egg-info/dependency_links.txt writing requirements to MDAnalysis.egg-info/requires.txt writing top-level names to MDAnalysis.egg-info/top_level.txt writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' 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-2.7.0/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-2.7.0/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-2.7.0/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-2.7.0/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-2.7.0/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-2.7.0/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:218: _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:218: _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:218: _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:218: _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:218: _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:218: _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:218: _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:218: _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:218: _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-aarch64-cpython-312/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/data copying MDAnalysis/lib/_augment.cpp -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/_augment.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/_cutil.cpp -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pxd -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/c_distances.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pxd -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.cpp -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/qcprot.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/qcprot.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib creating build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/include copying MDAnalysis/lib/include/calc_distances.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/include creating build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/libmdanalysis copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/libmdanalysis creating build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/src creating build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/src/transformations copying MDAnalysis/coordinates/timestep.cpp -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pxd -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/lib/formats/cython_util.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats creating build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include creating build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/include copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/include creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/include copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/include creating build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/src copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/src running build_ext building 'MDAnalysis.lib.formats.libdcd' extension creating build/temp.linux-aarch64-cpython-312 creating build/temp.linux-aarch64-cpython-312/MDAnalysis creating build/temp.linux-aarch64-cpython-312/MDAnalysis/lib creating build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats aarch64-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-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats/include -I/usr/include/python3.12 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libdcd.o -std=c99 -O3 -funroll-loops -fsigned-zeros 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:1261: /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:1268: 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:1267: 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) { | ^~~~~~~~~~~~~~ aarch64-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-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libdcd.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libdcd.cpython-312-aarch64-linux-gnu.so building 'MDAnalysis.lib.c_distances' extension aarch64-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-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/include -I/usr/include/python3.12 -c MDAnalysis/lib/c_distances.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances.o -std=c99 -O3 -funroll-loops -fsigned-zeros 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:1263: /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 " \ | ^~~~~~~ aarch64-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-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances.o -L/usr/lib/aarch64-linux-gnu -lm -o build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances.cpython-312-aarch64-linux-gnu.so building 'MDAnalysis.lib.c_distances_openmp' extension aarch64-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-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPARALLEL -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/include -I/usr/include/python3.12 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -O3 -funroll-loops -fsigned-zeros 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:1272: /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 " \ | ^~~~~~~ aarch64-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-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances_openmp.o -L/usr/lib/aarch64-linux-gnu -lm -lgomp -o build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances_openmp.cpython-312-aarch64-linux-gnu.so -fopenmp building 'MDAnalysis.lib.qcprot' extension aarch64-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-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-aarch64-cpython-312/MDAnalysis/lib/qcprot.o -std=c99 -O3 -funroll-loops -fsigned-zeros 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:1255: /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_fuse_0__pyx_f_10MDAnalysis_3lib_6qcprot_InnerProduct': MDAnalysis/lib/qcprot.c:21123:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 21123 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ^ MDAnalysis/lib/qcprot.c:21331:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 21331 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ^ MDAnalysis/lib/qcprot.c: In function '__pyx_fuse_1__pyx_f_10MDAnalysis_3lib_6qcprot_InnerProduct': MDAnalysis/lib/qcprot.c:21801:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 21801 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ^ MDAnalysis/lib/qcprot.c:22009:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 22009 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { | ^ aarch64-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-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/qcprot.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/qcprot.cpython-312-aarch64-linux-gnu.so building 'MDAnalysis.lib._transformations' extension creating build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/src creating build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/src/transformations aarch64-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-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-aarch64-cpython-312/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -O3 -funroll-loops -fsigned-zeros 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:1837: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 1837 | #pragma vector always MDAnalysis/lib/src/transformations/transformations.c:1954: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 1954 | #pragma vector always MDAnalysis/lib/src/transformations/transformations.c:1978: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 1978 | #pragma vector always MDAnalysis/lib/src/transformations/transformations.c: In function 'py_vector_norm': MDAnalysis/lib/src/transformations/transformations.c:3414: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 3414 | #pragma vector always MDAnalysis/lib/src/transformations/transformations.c:3495: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 3495 | #pragma vector always MDAnalysis/lib/src/transformations/transformations.c: In function 'py_unit_vector': MDAnalysis/lib/src/transformations/transformations.c:3597: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 3597 | #pragma vector always MDAnalysis/lib/src/transformations/transformations.c:3602: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 3602 | #pragma vector always MDAnalysis/lib/src/transformations/transformations.c:3666: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 3666 | #pragma vector always MDAnalysis/lib/src/transformations/transformations.c:3671: warning: ignoring '#pragma vector always' [-Wunknown-pragmas] 3671 | #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( | ^~~~~~~~~~~~~~~~~~~~~~~ aarch64-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-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/src/transformations/transformations.o -L/usr/lib/aarch64-linux-gnu -lm -o build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_transformations.cpython-312-aarch64-linux-gnu.so building 'MDAnalysis.lib.formats.libmdaxdr' extension creating build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src aarch64-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-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats -I/usr/include/python3.12 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -O3 -funroll-loops -fsigned-zeros 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:1282: /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:1288: 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:1289: 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:1290: 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 -*- aarch64-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-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats -I/usr/include/python3.12 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -O3 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/formats/src/trr_seek.c:30: /build/reproducible-path/mdanalysis-2.7.0/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-2.7.0/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-2.7.0/package/MDAnalysis/lib/formats/include/xdrfile_trr.h:42: /build/reproducible-path/mdanalysis-2.7.0/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; | ^~~~ aarch64-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-2.7.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.7.0/package/MDAnalysis/lib/formats -I/usr/include/python3.12 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -O3 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/formats/src/xdrfile.c:62: /build/reproducible-path/mdanalysis-2.7.0/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-aarch64/wheel/./MDAnalysis/analysis/data copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/data copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/data copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/data creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/cutils.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/cutils.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/cutils.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/clustering copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/clustering/src copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/src/ap.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering/src creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/clustering/include copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/include/ap.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering/include copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction/src creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction/include copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/hbonds copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hbonds copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hbonds creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/hole2 copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hole2 copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hole2/hole.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hole2 copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hole2/templates.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hole2 copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hole2/utils.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hole2 creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hydrogenbonds creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/legacy copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/legacy copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/legacy copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/align.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/atomicdistances.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/bat.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/contacts.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/density.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/dielectric.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/distances.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/gnm.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/msd.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/nucleicacids.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/pca.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/polymer.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/psa.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/rdf.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/rms.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis creating build/bdist.linux-aarch64/wheel/MDAnalysis/auxiliary copying build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary/EDR.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-aarch64-cpython-312/MDAnalysis/auxiliary/core.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/auxiliary creating build/bdist.linux-aarch64/wheel/MDAnalysis/converters copying build/lib.linux-aarch64-cpython-312/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters copying build/lib.linux-aarch64-cpython-312/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters copying build/lib.linux-aarch64-cpython-312/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters copying build/lib.linux-aarch64-cpython-312/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters copying build/lib.linux-aarch64-cpython-312/MDAnalysis/converters/RDKit.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters copying build/lib.linux-aarch64-cpython-312/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters copying build/lib.linux-aarch64-cpython-312/MDAnalysis/converters/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters copying build/lib.linux-aarch64-cpython-312/MDAnalysis/converters/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters creating build/bdist.linux-aarch64/wheel/MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/timestep.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/timestep.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/timestep.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/timestep.cpp -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/H5MD.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/TNG.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/TRC.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/chain.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/core.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/memory.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-312/MDAnalysis/coordinates/null.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates creating build/bdist.linux-aarch64/wheel/MDAnalysis/core copying build/lib.linux-aarch64-cpython-312/MDAnalysis/core/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core copying build/lib.linux-aarch64-cpython-312/MDAnalysis/core/_get_readers.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core copying build/lib.linux-aarch64-cpython-312/MDAnalysis/core/accessors.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core copying build/lib.linux-aarch64-cpython-312/MDAnalysis/core/groups.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core copying build/lib.linux-aarch64-cpython-312/MDAnalysis/core/selection.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core copying build/lib.linux-aarch64-cpython-312/MDAnalysis/core/topology.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core copying build/lib.linux-aarch64-cpython-312/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core copying build/lib.linux-aarch64-cpython-312/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core copying build/lib.linux-aarch64-cpython-312/MDAnalysis/core/universe.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/nsgrid.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_augment.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_cutil.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_transformations.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/qcprot.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances_openmp.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/src creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/src/transformations copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/src/transformations/transformations.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/src/transformations copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/src/transformations/LICENCE -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/src/transformations copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/src/transformations/AUTHOR -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/src/transformations creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/libmdanalysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/libmdanalysis creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/include copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/include/calc_distances.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/include copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/qcprot.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/qcprot.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/nsgrid.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/nsgrid.cpp -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances_openmp.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances_openmp.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/c_distances.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_cutil.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_cutil.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_cutil.cpp -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_augment.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_augment.cpp -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/cython_util.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libmdaxdr.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libdcd.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/formats/src copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/xtc_seek.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/xdrfile.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/src/trr_seek.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include/xtc_seek.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include/xdrfile.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include/trr_seek.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include/readdcd.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include/fastio.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/include/endianswap.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libmdaxdr.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libmdaxdr.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libmdaxdr.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libdcd.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libdcd.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/libdcd.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/cython_util.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/cython_util.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/cython_util.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/_distopia.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/correlations.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/distances.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/log.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/mdamath.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/transformations.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-312/MDAnalysis/lib/util.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib creating build/bdist.linux-aarch64/wheel/MDAnalysis/selections copying build/lib.linux-aarch64-cpython-312/MDAnalysis/selections/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections copying build/lib.linux-aarch64-cpython-312/MDAnalysis/selections/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections copying build/lib.linux-aarch64-cpython-312/MDAnalysis/selections/charmm.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections copying build/lib.linux-aarch64-cpython-312/MDAnalysis/selections/gromacs.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections copying build/lib.linux-aarch64-cpython-312/MDAnalysis/selections/jmol.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections copying build/lib.linux-aarch64-cpython-312/MDAnalysis/selections/pymol.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections copying build/lib.linux-aarch64-cpython-312/MDAnalysis/selections/vmd.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections creating build/bdist.linux-aarch64/wheel/MDAnalysis/tests copying build/lib.linux-aarch64-cpython-312/MDAnalysis/tests/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/tests copying build/lib.linux-aarch64-cpython-312/MDAnalysis/tests/datafiles.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/tests creating build/bdist.linux-aarch64/wheel/MDAnalysis/topology creating build/bdist.linux-aarch64/wheel/MDAnalysis/topology/tpr copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/GROParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/core.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/guessers.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-312/MDAnalysis/topology/tables.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology creating build/bdist.linux-aarch64/wheel/MDAnalysis/transformations copying build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations copying build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations copying build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations copying build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations/fit.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations copying build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations/nojump.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations copying build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations copying build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations/rotate.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations copying build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations/translate.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations copying build/lib.linux-aarch64-cpython-312/MDAnalysis/transformations/wrap.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations creating build/bdist.linux-aarch64/wheel/MDAnalysis/visualization copying build/lib.linux-aarch64-cpython-312/MDAnalysis/visualization/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/visualization copying build/lib.linux-aarch64-cpython-312/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/visualization copying build/lib.linux-aarch64-cpython-312/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/visualization copying build/lib.linux-aarch64-cpython-312/MDAnalysis/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/due.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/exceptions.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/units.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/version.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis copying build/lib.linux-aarch64-cpython-312/MDAnalysis/authors.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis running install_egg_info Copying MDAnalysis.egg-info to build/bdist.linux-aarch64/wheel/./MDAnalysis-2.7.0.egg-info running install_scripts creating build/bdist.linux-aarch64/wheel/MDAnalysis-2.7.0.dist-info/WHEEL creating '/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/.tmp-5xzndsa0/MDAnalysis-2.7.0-cp312-cp312-linux_aarch64.whl' and adding 'build/bdist.linux-aarch64/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-312-aarch64-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-312-aarch64-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-312-aarch64-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/converters/base.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/TRC.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-312-aarch64-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-312-aarch64-linux-gnu.so' adding 'MDAnalysis/lib/_augment.pyx' adding 'MDAnalysis/lib/_cutil.cpp' adding 'MDAnalysis/lib/_cutil.cpython-312-aarch64-linux-gnu.so' adding 'MDAnalysis/lib/_cutil.pxd' adding 'MDAnalysis/lib/_cutil.pyx' adding 'MDAnalysis/lib/_distopia.py' adding 'MDAnalysis/lib/_transformations.cpython-312-aarch64-linux-gnu.so' adding 'MDAnalysis/lib/c_distances.c' adding 'MDAnalysis/lib/c_distances.cpython-312-aarch64-linux-gnu.so' adding 'MDAnalysis/lib/c_distances.pxd' adding 'MDAnalysis/lib/c_distances.pyx' adding 'MDAnalysis/lib/c_distances_openmp.c' adding 'MDAnalysis/lib/c_distances_openmp.cpython-312-aarch64-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-312-aarch64-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-312-aarch64-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-312-aarch64-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-312-aarch64-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-312-aarch64-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-2.7.0.dist-info/AUTHORS' adding 'MDAnalysis-2.7.0.dist-info/LICENSE' adding 'MDAnalysis-2.7.0.dist-info/METADATA' adding 'MDAnalysis-2.7.0.dist-info/WHEEL' adding 'MDAnalysis-2.7.0.dist-info/top_level.txt' adding 'MDAnalysis-2.7.0.dist-info/RECORD' removing build/bdist.linux-aarch64/wheel Successfully built MDAnalysis-2.7.0-cp312-cp312-linux_aarch64.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.12 with "installer" module debian/rules execute_after_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.7.0' PYTHONPATH=/build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build make html -C package/doc/sphinx/ BUILDDIR=/build/reproducible-path/mdanalysis-2.7.0/.pybuild # HTML generator make[2]: Entering directory '/build/reproducible-path/mdanalysis-2.7.0/package/doc/sphinx' sphinx-build -v -b html source /build/reproducible-path/mdanalysis-2.7.0/.pybuild/html Running Sphinx v7.4.7 loading translations [en]... locale_dir /build/reproducible-path/mdanalysis-2.7.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist locale_dir /build/reproducible-path/mdanalysis-2.7.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. checking bibtex cache... out of date parsing bibtex file /build/reproducible-path/mdanalysis-2.7.0/package/doc/sphinx/source/references.bib... parsed 66 entries locale_dir /build/reproducible-path/mdanalysis-2.7.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist loading intersphinx inventory 'h5py' from https://docs.h5py.org/en/stable/objects.inv... loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv... loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy/objects.inv... loading intersphinx inventory 'gsd' from https://gsd.readthedocs.io/en/stable/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'maplotlib' from https://matplotlib.org/stable/objects.inv... loading intersphinx inventory 'griddataformats' from https://mdanalysis.org/GridDataFormats/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.h5py.org/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.h5py.org', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'pmda' from https://mdanalysis.org/pmda/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mdanalysis.org/GridDataFormats/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /GridDataFormats/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mdanalysis.org/pmda/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mdanalysis.org', port=443): Max retries exceeded with url: /pmda/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://gsd.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='gsd.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://matplotlib.org/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='matplotlib.org', port=443): Max retries exceeded with url: /stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'networkx' from https://networkx.org/documentation/stable/objects.inv... loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.scipy.org/doc/scipy/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.scipy.org', port=443): Max retries exceeded with url: /doc/scipy/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'parmed' from https://parmed.github.io/ParmEd/html/objects.inv... loading intersphinx inventory 'rdkit' from https://rdkit.org/docs/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://numpy.org/doc/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='numpy.org', port=443): Max retries exceeded with url: /doc/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://rdkit.org/docs/objects.inv' not fetchable due to : HTTPSConnectionPool(host='rdkit.org', port=443): Max retries exceeded with url: /docs/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://networkx.org/documentation/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='networkx.org', port=443): Max retries exceeded with url: /documentation/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://parmed.github.io/ParmEd/html/objects.inv' not fetchable due to : HTTPSConnectionPool(host='parmed.github.io', port=443): Max retries exceeded with url: /ParmEd/html/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) locale_dir /build/reproducible-path/mdanalysis-2.7.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 168 source files that are out of date updating environment: locale_dir /build/reproducible-path/mdanalysis-2.7.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist [new config] 168 added, 0 changed, 0 removed reading sources... [ 1%] documentation_pages/analysis/align /usr/lib/python3/dist-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated. Due to the on going maintenance burden of keeping command line application wrappers up to date, we have decided to deprecate and eventually remove these modules. We instead now recommend building your command line and invoking it directly with the subprocess module. warnings.warn( Didn't find AlignTraj.reference_atoms in MDAnalysis.analysis.align Didn't find AlignTraj.mobile_atoms in MDAnalysis.analysis.align Didn't find AlignTraj.results.rmsd in MDAnalysis.analysis.align Didn't find AlignTraj.filename in MDAnalysis.analysis.align Didn't find AverageStructure.reference_atoms in MDAnalysis.analysis.align Didn't find AverageStructure.mobile_atoms in MDAnalysis.analysis.align Didn't find AverageStructure.results.universe in MDAnalysis.analysis.align Didn't find AverageStructure.results.positions in MDAnalysis.analysis.align Didn't find AverageStructure.results.rmsd in MDAnalysis.analysis.align Didn't find AverageStructure.filename in MDAnalysis.analysis.align reading sources... [ 1%] documentation_pages/analysis/atomicdistances Didn't find AtomicDistances.results in MDAnalysis.analysis.atomicdistances Didn't find AtomicDistances.n_frames in MDAnalysis.analysis.atomicdistances Didn't find AtomicDistances.n_atoms in MDAnalysis.analysis.atomicdistances reading sources... [ 2%] documentation_pages/analysis/base Didn't find AnalysisBase.times in MDAnalysis.analysis.base Didn't find AnalysisBase.frames in MDAnalysis.analysis.base Didn't find AnalysisBase.results in MDAnalysis.analysis.base Didn't find AnalysisFromFunction.results.frames in MDAnalysis.analysis.base Didn't find AnalysisFromFunction.results.times in MDAnalysis.analysis.base Didn't find AnalysisFromFunction.results.timeseries in MDAnalysis.analysis.base Didn't find results.frames in MDAnalysis.analysis.base Didn't find results.times in MDAnalysis.analysis.base Didn't find results.timeseries in MDAnalysis.analysis.base reading sources... [ 2%] documentation_pages/analysis/bat Didn't find BAT.results.bat in MDAnalysis.analysis.bat reading sources... [ 3%] documentation_pages/analysis/contacts Didn't find Contacts.results.timeseries in MDAnalysis.analysis.contacts reading sources... [ 4%] documentation_pages/analysis/data reading sources... [ 4%] documentation_pages/analysis/density Didn't find DensityAnalysis.results.density in MDAnalysis.analysis.density Didn't find Density.grid in MDAnalysis.analysis.density Didn't find Density.edges in MDAnalysis.analysis.density Didn't find Density.delta in MDAnalysis.analysis.density Didn't find Density.origin in MDAnalysis.analysis.density Didn't find Density.units in MDAnalysis.analysis.density reading sources... [ 5%] documentation_pages/analysis/dielectric Didn't find DielectricConstant.results.M in MDAnalysis.analysis.dielectric Didn't find DielectricConstant.results.M2 in MDAnalysis.analysis.dielectric Didn't find DielectricConstant.results.fluct in MDAnalysis.analysis.dielectric Didn't find DielectricConstant.results.eps in MDAnalysis.analysis.dielectric Didn't find DielectricConstant.results.eps_mean in MDAnalysis.analysis.dielectric reading sources... [ 5%] documentation_pages/analysis/diffusionmap Didn't find DiffusionMap.eigenvalues in MDAnalysis.analysis.diffusionmap Didn't find DistanceMatrix.atoms in MDAnalysis.analysis.diffusionmap Didn't find DistanceMatrix.results.dist_matrix in MDAnalysis.analysis.diffusionmap reading sources... [ 6%] documentation_pages/analysis/dihedrals Matplotlib created a temporary cache directory at /tmp/matplotlib-_lz0tm8b because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Didn't find Dihedral.results.angles in MDAnalysis.analysis.dihedrals Didn't find Ramachandran.results.angles in MDAnalysis.analysis.dihedrals Didn't find Janin.results.angles in MDAnalysis.analysis.dihedrals reading sources... [ 7%] documentation_pages/analysis/distances reading sources... [ 7%] documentation_pages/analysis/encore reading sources... [ 8%] documentation_pages/analysis/encore/bootstrap reading sources... [ 8%] documentation_pages/analysis/encore/clustering Didn't find Cluster.id in MDAnalysis.analysis.encore.clustering.ClusterCollection Didn't find Cluster.metadata in MDAnalysis.analysis.encore.clustering.ClusterCollection Didn't find Cluster.size in MDAnalysis.analysis.encore.clustering.ClusterCollection Didn't find Cluster.centroid in MDAnalysis.analysis.encore.clustering.ClusterCollection Didn't find Cluster.elements in MDAnalysis.analysis.encore.clustering.ClusterCollection Didn't find ClusterCollection.clusters in MDAnalysis.analysis.encore.clustering.ClusterCollection reading sources... [ 9%] documentation_pages/analysis/encore/confdistmatrix reading sources... [ 10%] documentation_pages/analysis/encore/covariance reading sources... [ 10%] documentation_pages/analysis/encore/dimensionality_reduction reading sources... [ 11%] documentation_pages/analysis/encore/similarity reading sources... [ 11%] documentation_pages/analysis/encore/utils Didn't find ParallelCalculation.n_jobs in MDAnalysis.analysis.encore.utils Didn't find ParallelCalculation.function in MDAnalysis.analysis.encore.utils Didn't find ParallelCalculation.args in MDAnalysis.analysis.encore.utils Didn't find ParallelCalculation.kwargs in MDAnalysis.analysis.encore.utils Didn't find ParallelCalculation.nruns in MDAnalysis.analysis.encore.utils reading sources... [ 12%] documentation_pages/analysis/gnm Didn't find GNMAnalysis.results.times in MDAnalysis.analysis.gnm Didn't find GNMAnalysis.results.eigenvalues in MDAnalysis.analysis.gnm Didn't find GNMAnalysis.results.eigenvectors in MDAnalysis.analysis.gnm Didn't find closeContactGNMAnalysis.results.times in MDAnalysis.analysis.gnm Didn't find closeContactGNMAnalysis.results.eigenvalues in MDAnalysis.analysis.gnm Didn't find closeContactGNMAnalysis.results.eigenvectors in MDAnalysis.analysis.gnm reading sources... [ 12%] documentation_pages/analysis/hbond_autocorrel reading sources... [ 13%] documentation_pages/analysis/hbond_autocorrel_deprecated /build/reproducible-path/mdanalysis-2.7.0/.pybuild/cpython3_3.12_mdanalysis/build/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52: DeprecationWarning: This module was moved to MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel; hbonds.hbond_autocorrel will be removed in 3.0.0. warnings.warn(wmsg, category=DeprecationWarning) reading sources... [ 14%] documentation_pages/analysis/helix_analysis Didn't find HELANAL.results.local_twists in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_nres_per_turn in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_axes in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_heights in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_helix_directions in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_origins in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_screw_angles in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.local_bends in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.all_bends in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.global_axis in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.global_tilts in MDAnalysis.analysis.helix_analysis Didn't find HELANAL.results.summary in MDAnalysis.analysis.helix_analysis reading sources... [ 14%] documentation_pages/analysis/hole2 Didn't find HoleAnalysis.results.sphpdbs in MDAnalysis.analysis.hole2 Didn't find HoleAnalysis.results.outfiles in MDAnalysis.analysis.hole2 Didn't find HoleAnalysis.results.profiles in MDAnalysis.analysis.hole2 reading sources... [ 15%] documentation_pages/analysis/hydrogenbonds Didn't find HydrogenBondAnalysis.results.hbonds in MDAnalysis.analysis.hydrogenbonds.hbond_analysis reading sources... [ 15%] documentation_pages/analysis/leaflet reading sources... [ 16%] documentation_pages/analysis/legacy/x3dna Didn't find X3DNA.profiles in MDAnalysis.analysis.legacy.x3dna Didn't find X3DNAtraj.profiles in MDAnalysis.analysis.legacy.x3dna reading sources... [ 17%] documentation_pages/analysis/legacy_modules reading sources... [ 17%] documentation_pages/analysis/lineardensity Didn't find LinearDensity.results.x.dim in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.mass_density in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.mass_density_stddev in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.charge_density in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.charge_density_stddev in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.pos in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.pos_std in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.char in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.char_std in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.slice_volume in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.results.x.hist_bin_edges in MDAnalysis.analysis.lineardensity Didn't find LinearDensity.Note in MDAnalysis.analysis.lineardensity reading sources... [ 18%] documentation_pages/analysis/msd Didn't find EinsteinMSD.dim_fac in MDAnalysis.analysis.msd Didn't find EinsteinMSD.results.timeseries in MDAnalysis.analysis.msd Didn't find EinsteinMSD.results.msds_by_particle in MDAnalysis.analysis.msd Didn't find EinsteinMSD.ag in MDAnalysis.analysis.msd Didn't find EinsteinMSD.n_frames in MDAnalysis.analysis.msd Didn't find EinsteinMSD.n_particles in MDAnalysis.analysis.msd reading sources... [ 18%] documentation_pages/analysis/nucleicacids Didn't find NucPairDist.results.pair_distances in MDAnalysis.analysis.nucleicacids Didn't find NucPairDist.results.distances in MDAnalysis.analysis.nucleicacids Didn't find NucPairDist.times in MDAnalysis.analysis.nucleicacids Didn't find WatsonCrickDist.results.distances in MDAnalysis.analysis.nucleicacids Didn't find WatsonCrickDist.results.pair_distances in MDAnalysis.analysis.nucleicacids Didn't find WatsonCrickDist.times in MDAnalysis.analysis.nucleicacids Didn't find MinorPairDist.results.distances in MDAnalysis.analysis.nucleicacids Didn't find MinorPairDist.times in MDAnalysis.analysis.nucleicacids Didn't find MajorPairDist.results.distances in MDAnalysis.analysis.nucleicacids Didn't find MajorPairDist.times in MDAnalysis.analysis.nucleicacids reading sources... [ 19%] documentation_pages/analysis/nuclinfo reading sources... [ 20%] documentation_pages/analysis/pca Didn't find PCA.results.p_components in MDAnalysis.analysis.pca Didn't find PCA.results.variance in MDAnalysis.analysis.pca Didn't find PCA.results.cumulated_variance in MDAnalysis.analysis.pca reading sources... [ 20%] documentation_pages/analysis/polymer Didn't find PersistenceLength.results.bond_autocorrelation in MDAnalysis.analysis.polymer Didn't find PersistenceLength.results.lb in MDAnalysis.analysis.polymer Didn't find PersistenceLength.results.x in MDAnalysis.analysis.polymer Didn't find PersistenceLength.results.lp in MDAnalysis.analysis.polymer Didn't find PersistenceLength.results.fit in MDAnalysis.analysis.polymer reading sources... [ 21%] documentation_pages/analysis/psa Didn't find Path.u_original in MDAnalysis.analysis.psa Didn't find Path.u_reference in MDAnalysis.analysis.psa Didn't find Path.select in MDAnalysis.analysis.psa Didn't find Path.path_select in MDAnalysis.analysis.psa Didn't find Path.ref_frame in MDAnalysis.analysis.psa Didn't find Path.u_fitted in MDAnalysis.analysis.psa Didn't find Path.path in MDAnalysis.analysis.psa Didn't find PSAPair.npaths in MDAnalysis.analysis.psa Didn't find PSAPair.matrix_id in MDAnalysis.analysis.psa Didn't find PSAPair.pair_id in MDAnalysis.analysis.psa Didn't find PSAPair.nearest_neighbors in MDAnalysis.analysis.psa Didn't find PSAPair.hausdorff_pair in MDAnalysis.analysis.psa Didn't find PSAnalysis.universes in MDAnalysis.analysis.psa Didn't find PSAnalysis.u_reference in MDAnalysis.analysis.psa Didn't find PSAnalysis.select in MDAnalysis.analysis.psa Didn't find PSAnalysis.path_select in MDAnalysis.analysis.psa Didn't find PSAnalysis.ref_frame in MDAnalysis.analysis.psa Didn't find PSAnalysis.paths in MDAnalysis.analysis.psa Didn't find PSAnalysis.D in MDAnalysis.analysis.psa reading sources... [ 21%] documentation_pages/analysis/rdf Didn't find InterRDF.results.bins in MDAnalysis.analysis.rdf Didn't find InterRDF.results.edges in MDAnalysis.analysis.rdf Didn't find InterRDF.results.rdf in MDAnalysis.analysis.rdf Didn't find InterRDF.results.count in MDAnalysis.analysis.rdf Didn't find InterRDF_s.results.bins in MDAnalysis.analysis.rdf Didn't find InterRDF_s.results.edges in MDAnalysis.analysis.rdf Didn't find InterRDF_s.results.rdf in MDAnalysis.analysis.rdf Didn't find InterRDF_s.results.count in MDAnalysis.analysis.rdf Didn't find InterRDF_s.results.cdf in MDAnalysis.analysis.rdf reading sources... [ 22%] documentation_pages/analysis/rms Didn't find RMSD.results.rmsd in MDAnalysis.analysis.rms Didn't find RMSF.results.rmsf in MDAnalysis.analysis.rms reading sources... [ 23%] documentation_pages/analysis/waterdynamics reading sources... [ 23%] documentation_pages/analysis/wbridge_analysis Didn't find WaterBridgeAnalysis.timesteps in MDAnalysis.analysis.hydrogenbonds.wbridge_analysis Didn't find WaterBridgeAnalysis.results.network in MDAnalysis.analysis.hydrogenbonds.wbridge_analysis Didn't find WaterBridgeAnalysis.table in MDAnalysis.analysis.hydrogenbonds.wbridge_analysis Didn't find WaterBridgeAnalysis.results.timeseries in MDAnalysis.analysis.hydrogenbonds.wbridge_analysis reading sources... [ 24%] documentation_pages/analysis_modules reading sources... [ 24%] documentation_pages/auxiliary/EDR Didn't find EDRReader._auxdata in MDAnalysis.auxiliary.EDR Didn't find EDRReader.data_dict in MDAnalysis.auxiliary.EDR Didn't find EDRReader.unit_dict in MDAnalysis.auxiliary.EDR Didn't find EDRReader._n_steps in MDAnalysis.auxiliary.EDR Didn't find EDRReader.terms in MDAnalysis.auxiliary.EDR reading sources... [ 25%] documentation_pages/auxiliary/XVG reading sources... [ 26%] documentation_pages/auxiliary/base Didn't find AuxStep.step in MDAnalysis.auxiliary.base Didn't find AuxReader.auxstep in MDAnalysis.auxiliary.base Didn't find AuxReader.frame_data in MDAnalysis.auxiliary.base Didn't find AuxReader.frame_rep in MDAnalysis.auxiliary.base Didn't find AuxFileReader.auxfile in MDAnalysis.auxiliary.base reading sources... [ 26%] documentation_pages/auxiliary/core reading sources... [ 27%] documentation_pages/auxiliary/init reading sources... [ 27%] documentation_pages/auxiliary_modules reading sources... [ 28%] documentation_pages/converters reading sources... [ 29%] documentation_pages/converters/OpenMM reading sources... [ 29%] documentation_pages/converters/ParmEd reading sources... [ 30%] documentation_pages/converters/RDKit reading sources... [ 30%] documentation_pages/converters/base reading sources... [ 31%] documentation_pages/coordinates/CRD reading sources... [ 32%] documentation_pages/coordinates/DCD reading sources... [ 32%] documentation_pages/coordinates/DLPoly reading sources... [ 33%] documentation_pages/coordinates/DMS reading sources... [ 33%] documentation_pages/coordinates/FHIAIMS reading sources... [ 34%] documentation_pages/coordinates/GMS reading sources... [ 35%] documentation_pages/coordinates/GRO reading sources... [ 35%] documentation_pages/coordinates/GSD reading sources... [ 36%] documentation_pages/coordinates/H5MD reading sources... [ 36%] documentation_pages/coordinates/INPCRD reading sources... [ 37%] documentation_pages/coordinates/LAMMPS reading sources... [ 38%] documentation_pages/coordinates/MMTF reading sources... [ 38%] documentation_pages/coordinates/MOL2 reading sources... [ 39%] documentation_pages/coordinates/NAMDBIN reading sources... [ 39%] documentation_pages/coordinates/PDB reading sources... [ 40%] documentation_pages/coordinates/PDBQT reading sources... [ 40%] documentation_pages/coordinates/PQR reading sources... [ 41%] documentation_pages/coordinates/TNG reading sources... [ 42%] documentation_pages/coordinates/TRC reading sources... [ 42%] documentation_pages/coordinates/TRJ reading sources... [ 43%] documentation_pages/coordinates/TRR reading sources... [ 43%] documentation_pages/coordinates/TRZ Didn't find TRZReader.ts in MDAnalysis.coordinates.TRZ reading sources... [ 44%] documentation_pages/coordinates/TXYZ reading sources... [ 45%] documentation_pages/coordinates/XDR reading sources... [ 45%] documentation_pages/coordinates/XTC reading sources... [ 46%] documentation_pages/coordinates/XYZ reading sources... [ 46%] documentation_pages/coordinates/base reading sources... [ 47%] documentation_pages/coordinates/chain reading sources... [ 48%] documentation_pages/coordinates/chemfiles reading sources... [ 48%] documentation_pages/coordinates/core reading sources... [ 49%] documentation_pages/coordinates/init reading sources... [ 49%] documentation_pages/coordinates/memory reading sources... [ 50%] documentation_pages/coordinates/null reading sources... [ 51%] documentation_pages/coordinates/pickle_readers reading sources... [ 51%] documentation_pages/coordinates/timestep reading sources... [ 52%] documentation_pages/coordinates_modules reading sources... [ 52%] documentation_pages/core/accessors reading sources... [ 53%] documentation_pages/core/groups reading sources... [ 54%] documentation_pages/core/init reading sources... [ 54%] documentation_pages/core/selection reading sources... [ 55%] documentation_pages/core/topology Didn't find TransTable.n_atoms in MDAnalysis.core.topology Didn't find TransTable.n_residues in MDAnalysis.core.topology Didn't find TransTable.n_segments in MDAnalysis.core.topology reading sources... [ 55%] documentation_pages/core/topologyattrs reading sources... [ 56%] documentation_pages/core/topologyobjects reading sources... [ 57%] documentation_pages/core/universe Didn't find Universe.atoms in MDAnalysis.core.universe Didn't find Universe.residues in MDAnalysis.core.universe Didn't find Universe.segments in MDAnalysis.core.universe reading sources... [ 57%] documentation_pages/core_modules reading sources... [ 58%] documentation_pages/exceptions reading sources... [ 58%] documentation_pages/lib/NeighborSearch reading sources... [ 59%] documentation_pages/lib/c_distances reading sources... [ 60%] documentation_pages/lib/c_distances_openmp reading sources... [ 60%] documentation_pages/lib/correlations reading sources... [ 61%] documentation_pages/lib/distances reading sources... [ 61%] documentation_pages/lib/formats/libdcd reading sources... [ 62%] documentation_pages/lib/formats/libmdaxdr reading sources... [ 62%] documentation_pages/lib/log reading sources... [ 63%] documentation_pages/lib/mdamath reading sources... [ 64%] documentation_pages/lib/nsgrid reading sources... [ 64%] documentation_pages/lib/picklable_file_io reading sources... [ 65%] documentation_pages/lib/pkdtree reading sources... [ 65%] documentation_pages/lib/qcprot reading sources... [ 66%] documentation_pages/lib/transformations reading sources... [ 67%] documentation_pages/lib/util reading sources... [ 67%] documentation_pages/lib_modules reading sources... [ 68%] documentation_pages/overview reading sources... [ 68%] documentation_pages/references reading sources... [ 69%] documentation_pages/selections reading sources... [ 70%] documentation_pages/selections/base reading sources... [ 70%] documentation_pages/selections/charmm reading sources... [ 71%] documentation_pages/selections/gromacs reading sources... [ 71%] documentation_pages/selections/jmol reading sources... [ 72%] documentation_pages/selections/pymol reading sources... [ 73%] documentation_pages/selections/vmd reading sources... [ 73%] documentation_pages/selections_modules reading sources... [ 74%] documentation_pages/topology reading sources... [ 74%] documentation_pages/topology/CRDParser reading sources... [ 75%] documentation_pages/topology/DLPolyParser reading sources... [ 76%] documentation_pages/topology/DMSParser reading sources... [ 76%] documentation_pages/topology/ExtendedPDBParser reading sources... [ 77%] documentation_pages/topology/FHIAIMSParser reading sources... [ 77%] documentation_pages/topology/GMSParser reading sources... [ 78%] documentation_pages/topology/GROParser reading sources... [ 79%] documentation_pages/topology/GSDParser reading sources... [ 79%] documentation_pages/topology/HoomdXMLParser reading sources... [ 80%] documentation_pages/topology/ITPParser reading sources... [ 80%] documentation_pages/topology/LAMMPSParser reading sources... [ 81%] documentation_pages/topology/MMTFParser reading sources... [ 82%] documentation_pages/topology/MOL2Parser reading sources... [ 82%] documentation_pages/topology/MinimalParser reading sources... 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[100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... WARNING: unsupported theme option 'mda_official' given done copying assets... copying static files... done copying extra files... done copying assets: done writing output... [ 1%] documentation_pages/analysis/align writing output... [ 1%] documentation_pages/analysis/atomicdistances writing output... [ 2%] documentation_pages/analysis/base writing output... [ 2%] documentation_pages/analysis/bat writing output... [ 3%] documentation_pages/analysis/contacts writing output... [ 4%] documentation_pages/analysis/data writing output... [ 4%] documentation_pages/analysis/density writing output... [ 5%] documentation_pages/analysis/dielectric writing output... [ 5%] documentation_pages/analysis/diffusionmap writing output... [ 6%] documentation_pages/analysis/dihedrals writing output... [ 7%] documentation_pages/analysis/distances writing output... 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