Mon Jul 14 08:19:53 UTC 2025 I: starting to build mdanalysis/unstable/arm64 on jenkins on '2025-07-14 08:19' Mon Jul 14 08:19:53 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_2/102342/console.log Mon Jul 14 08:19:53 UTC 2025 I: Downloading source for unstable/mdanalysis=2.9.0-12 --2025-07-14 08:19:53-- http://deb.debian.org/debian/pool/main/m/mdanalysis/mdanalysis_2.9.0-12.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2945 (2.9K) [text/prs.lines.tag] Saving to: ‘mdanalysis_2.9.0-12.dsc’ 0K .. 100% 343M=0s 2025-07-14 08:19:53 (343 MB/s) - ‘mdanalysis_2.9.0-12.dsc’ saved [2945/2945] Mon Jul 14 08:19:53 UTC 2025 I: mdanalysis_2.9.0-12.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: mdanalysis Binary: python3-mdanalysis, python-mdanalysis-doc Architecture: any all Version: 2.9.0-12 Maintainer: Debichem Team Uploaders: Drew Parsons Homepage: https://www.mdanalysis.org/ Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/debichem-team/mdanalysis Vcs-Git: https://salsa.debian.org/debichem-team/mdanalysis.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@, python3-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) [amd64 arm64 armel armhf i386 mips64el ppc64el riscv64 s390x], python3-networkx, python3-griddataformats, python3-mmtf, python3-joblib, python3-scipy, python3-matplotlib, python3-mda-xdrlib, python3-tqdm, python3-threadpoolctl, python3-packaging, python3-filelock, 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: f2606c497528efce3e62fafbf7dc92d28d90d811 61025537 mdanalysis_2.9.0.orig.tar.gz 240d9e5287c77e6fc6708e2fadfd4b1d9185426a 13888 mdanalysis_2.9.0-12.debian.tar.xz Checksums-Sha256: 216c62feeaa75b810c5f6d539243d90ddea866ac06dbf73e38f8a864bfb4fb7d 61025537 mdanalysis_2.9.0.orig.tar.gz 009904701eef5802492559d4293454a4c32f7b170c91243454409f6aaeffd701 13888 mdanalysis_2.9.0-12.debian.tar.xz Files: 6bccd5d4b45aa8d56ea120c0674179fc 61025537 mdanalysis_2.9.0.orig.tar.gz 028468422ba3555926d89cbcd7e5bcfc 13888 mdanalysis_2.9.0-12.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAmhvhc4ACgkQVz7x5L1a AfoWIw//Zl+tDccNrXKyL6OGlP/Ppb24vyaO9YvjGLEefM6XkwpC4AYoLP8ZCvmZ B3HhTuhbROgJoumx5Gr9fNA5EvKC+xSanVEHS1MRb8wwLPrz7/scKZO7QghG0/3C EA9Mj8kJOXl/+oMPHp4FXmtypP8Gaoofbzun1pCgt0icXagiPhlC/Xw1nm1ERHFT YZfs7QOmwXbQuhcuwhxGft5YXDYYdjgx5nPCU2Gr2r0dFUcG+DWi469uI4i4ghvu GRMDcINCq3jKQHCcn9K9DmtR8M2PxUyaIAFy4I84SmW8KKjOvcqPm7zp2WqVPxcs VUXkrttBFxHQ2kBS2tYHnF3Mj3/afGHq5C45uYEWHoe2KHEm2nlXhT85ij2JcMH5 CkXAZitPKudPP5D1kC66cIAJ0wCQg6eT5b6L9OFtepD+kwiEmZZxHkStC0CUZvgv rKAnZjlJHAO94Xg63pAAK0wwoDP+ieCKCWZIfJLMUCQ6ANdEjdK1egvbtk09YAwT Q38xk7I0LWZqVMnWzvbKstygi+Rfnxd24WI1hWlyL0ti+M2a1Btws6JALuCYfIya CewF9QIlV041Lx+VarL4tKVLnXdqwXFld6Jt58R1FzIRN9zdqS+BISLdjj1spnZS 6AMHN1xx/W67prhYoNGmnqwQ3Sujw71mh4I3nW5+6rdOJVn+B4U= =dtf8 -----END PGP SIGNATURE----- Mon Jul 14 08:19:53 UTC 2025 I: Checking whether the package is not for us Mon Jul 14 08:19:53 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Mon Jul 14 08:19:53 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Mon Jul 14 08:26:26 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Aug 16 02:42:57 -12 2026 I: pbuilder-time-stamp: 1786891377 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [mdanalysis_2.9.0-12.dsc] I: copying [./mdanalysis_2.9.0.orig.tar.gz] I: copying [./mdanalysis_2.9.0-12.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.9.0-12.dsc: no acceptable signature found dpkg-source: info: extracting mdanalysis in mdanalysis-2.9.0 dpkg-source: info: unpacking mdanalysis_2.9.0.orig.tar.gz dpkg-source: info: unpacking mdanalysis_2.9.0-12.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 doc_no_mdanalysis_sphinx.patch dpkg-source: info: applying improve_test_timeout_PR4584.diff dpkg-source: info: applying skip_gsd_tests.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1015473/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='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='5ba14b1d6ca641578b62b1f541af23c1' 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='1015473' 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.gkCtXGsg/pbuilderrc_2Rnc --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.gkCtXGsg/b1 --logfile b1/build.log mdanalysis_2.9.0-12.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 codethink03-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1015473/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-filelock, 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 ... 19963 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-filelock; however: Package python3-filelock 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} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgcrypt20{a} libgfortran5{a} libglib2.0-0t64{a} libgnutls30t64{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhdf5-310{a} libhdf5-hl-310{a} libidn2-0{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} liblcms2-2{a} libldap2{a} liblerc4{a} liblzf1{a} libmagic-mgc{a} libmagic1t64{a} libnetcdf22{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libopenjp2-7{a} libp11-kit0{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} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{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} libtasn1-6{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{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} libzopfli1{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-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-filelock{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-jaraco.text{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-numpy-dev{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-platformdirs{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-pytz{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-tqdm{a} python3-typeguard{a} python3-typing-extensions{a} python3-ufolib2{a} python3-urllib3{a} python3-wheel{a} python3-yaml{a} python3-zipp{a} python3-zopfli{a} python3.13{a} python3.13-dev{a} python3.13-minimal{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 libgpg-error-l10n 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-pooch python3-psutil python3-pydot python3-pygraphviz python3-tables python3-tz shared-mime-info wget xdg-user-dirs 0 packages upgraded, 266 newly installed, 0 to remove and 0 not upgraded. Need to get 185 MB of archives. After unpacking 784 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.5-2 [856 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.7.1-1 [93.3 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.5-2 [2003 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.5-1 [27.2 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025b-4 [260 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.8-2 [21.3 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.5-2 [1892 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.5-2 [757 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.5-1 [10.2 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.5-1 [28.2 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1 [136 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.1-2 [104 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-19 [361 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:2.2.4+ds-1 [3604 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-8 [63.0 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-8 [873 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.5.1-1 [1457 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20250419 [162 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-5 [93.8 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [984 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.48-1 [274 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libfontenc1 arm64 1:1.1.8-1+b2 [22.5 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+24 [217 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 51 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-2.3 [318 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-2.3 [387 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.12-1 [343 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.12-1 [795 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.12-1 [27.0 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libxft2 arm64 2.3.6-1+b4 [51.6 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libxss1 arm64 1:1.2.3-1+b3 [17.1 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libtk8.6 arm64 8.6.16-1 [741 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-8 [537 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 blt arm64 2.5.3+dfsg-8 [5984 B] Get: 65 http://deb.debian.org/debian unstable/main arm64 cython3 arm64 3.0.11+dfsg-2+b1 [2255 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 72 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-1 [629 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250414 [116 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 fonts-lyx all 2.4.3-1 [190 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libaec0 arm64 1.1.3-1+b1 [22.5 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.4-1+b1 [483 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-3+b1 [24.9 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-2 [107 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.9-3 [1375 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 100 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1.1 [71.4 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.8.0-1 [63.2 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.11.0-1 [121 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.11.0-1 [28.2 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.14.1-2 [353 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.14.1-2 [359 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.7.1-1 [145 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libgpg-error0 arm64 1.51-4 [78.5 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.84.3-1 [1426 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.2.0-1+b1 [442 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libsz2 arm64 1.1.3-1+b1 [8044 B] Get: 123 http://deb.debian.org/debian unstable/main arm64 libhdf5-310 arm64 1.14.5+repack-3 [1155 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [66.1 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-4 [173 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 liblzf1 arm64 3.6-4+b3 [10.1 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libnetcdf22 arm64 1:4.9.3-1 [481 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.3-2 [190 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libpython3.13 arm64 3.13.5-2 [1976 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libpython3.13-dev arm64 3.13.5-2 [4890 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.13.5-1 [10.4 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libpython3-all-dev arm64 3.13.5-1 [1068 B] Get: 144 http://deb.debian.org/debian unstable/main arm64 libqhull-r8.0 arm64 2020.2-6+b2 [229 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.2-1 [13.6 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.7.0-3 [325 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [113 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.5.0-0.1 [125 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libxslt1.1 arm64 1.1.35-1.2 [221 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-2 [49.2 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libzopfli1 arm64 1.0.3-3 [95.2 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 25.0-1 [56.6 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 python3-wheel all 0.46.1-2 [21.7 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 python3-build all 1.2.2-2 [36.1 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 pybuild-plugin-pyproject all 6.20250414 [11.8 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 python-matplotlib-data all 3.10.1+dfsg1-4 [2737 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.13.5-1 [1044 B] Get: 164 http://deb.debian.org/debian unstable/main arm64 python3.13-dev arm64 3.13.5-2 [505 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.13.5-1 [26.1 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 python3-all-dev arm64 3.13.5-1 [1068 B] Get: 167 http://deb.debian.org/debian unstable/main arm64 python3-attr all 25.3.0-1 [69.5 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 python3-babel all 2.17.0-1 [117 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 python3-charset-normalizer arm64 3.4.2-1 [120 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 python3.13-tk arm64 3.13.5-2 [105 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 python3-tk arm64 3.13.5-1 [9604 B] Get: 173 http://deb.debian.org/debian unstable/main arm64 python3-pil.imagetk arm64 11.1.0-5+b1 [81.8 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 python3-pil arm64 11.1.0-5+b1 [495 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 python3-cairo arm64 1.27.0-2 [114 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 178 http://deb.debian.org/debian unstable/main arm64 python3-reportlab all 4.4.2-1 [1167 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 python3-biopython arm64 1.85+dfsg-4 [1657 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 python3-brotli arm64 1.1.0-2+b7 [300 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 183 http://deb.debian.org/debian unstable/main arm64 python3-cftime arm64 1.6.4-2 [183 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 python3-lxml arm64 5.4.0-1 [1139 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 python3-citeproc all 0.8.2-1 [99.0 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 python3-contourpy arm64 1.3.1-1+b1 [190 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 python3-cycler all 0.12.1-1 [9496 B] Get: 189 http://deb.debian.org/debian unstable/main arm64 python3-dateutil all 2.9.0-4 [79.4 kB] Get: 190 http://deb.debian.org/debian unstable/main arm64 python3-decorator all 5.2.1-2 [33.0 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 python3-roman all 5.0-1 [10.6 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 python3-looseversion all 1.3.0-3 [8964 B] Get: 195 http://deb.debian.org/debian unstable/main arm64 python3-idna all 3.10-1 [42.0 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 python3-urllib3 all 2.3.0-3 [115 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 python3-requests all 2.32.3+dfsg-5 [72.2 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 python3-duecredit all 0.10.2-2 [70.6 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 python3-monotonic all 1.6-3 [5340 B] Get: 200 http://deb.debian.org/debian unstable/main arm64 python3-fasteners all 0.18-2 [14.0 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 python3-filelock all 3.18.0-1 [12.8 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 python3-platformdirs all 4.3.7-1 [16.6 kB] Get: 203 http://deb.debian.org/debian unstable/main arm64 python3-fs all 2.4.16-7 [95.2 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 python3-lz4 arm64 4.4.0+dfsg-2 [25.3 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 python3-scipy arm64 1.15.3-1 [14.9 MB] Get: 206 http://deb.debian.org/debian unstable/main arm64 python3-mpmath all 1.3.0-1 [419 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 python3-sympy all 1.13.3-5 [4148 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.0 kB] Get: 209 http://deb.debian.org/debian unstable/main arm64 python3-zopfli arm64 0.2.3.post1-1 [10.2 kB] Get: 210 http://deb.debian.org/debian unstable/main arm64 unicode-data all 15.1.0-1 [8547 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 python3-fonttools arm64 4.57.0-1 [1366 kB] Get: 212 http://deb.debian.org/debian unstable/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1023 kB] Get: 213 http://deb.debian.org/debian unstable/main arm64 python3-mrcfile all 1.5.4-2 [118 kB] Get: 214 http://deb.debian.org/debian unstable/main arm64 python3-griddataformats all 1.0.2-2 [2048 kB] Get: 215 http://deb.debian.org/debian unstable/main arm64 python3-gsd arm64 3.4.2-2+b1 [200 kB] Get: 216 http://deb.debian.org/debian unstable/main arm64 python3-h5py-serial arm64 3.13.0-1+b1 [953 kB] Get: 217 http://deb.debian.org/debian unstable/main arm64 python3-h5py all 3.13.0-1 [15.0 kB] Get: 218 http://deb.debian.org/debian unstable/main arm64 python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 219 http://deb.debian.org/debian unstable/main arm64 python3-hypothesis all 6.130.5-2 [336 kB] Get: 220 http://deb.debian.org/debian unstable/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 221 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.7.0-1 [67.4 kB] Get: 222 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.13.2-1 [90.5 kB] Get: 223 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 224 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 225 http://deb.debian.org/debian unstable/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 226 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 227 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 228 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 229 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 230 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 231 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 232 http://deb.debian.org/debian unstable/main arm64 python3-markupsafe arm64 2.1.5-1+b4 [14.1 kB] Get: 233 http://deb.debian.org/debian unstable/main arm64 python3-jinja2 all 3.1.6-1 [107 kB] Get: 234 http://deb.debian.org/debian unstable/main arm64 python3-joblib all 1.4.2-4 [216 kB] Get: 235 http://deb.debian.org/debian unstable/main arm64 python3-kiwisolver arm64 1.4.7-3+b1 [57.8 kB] Get: 236 http://deb.debian.org/debian unstable/main arm64 python3-latexcodec all 3.0.0-1 [17.5 kB] Get: 237 http://deb.debian.org/debian unstable/main arm64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 238 http://deb.debian.org/debian unstable/main arm64 python3-matplotlib arm64 3.10.1+dfsg1-4 [23.7 MB] Get: 239 http://deb.debian.org/debian unstable/main arm64 python3-mda-xdrlib all 0.2.0-3 [11.6 kB] Get: 240 http://deb.debian.org/debian unstable/main arm64 python3-msgpack arm64 1.0.3-3+b5 [77.4 kB] Get: 241 http://deb.debian.org/debian unstable/main arm64 python3-mmtf all 1.1.3-1 [17.0 kB] Get: 242 http://deb.debian.org/debian unstable/main arm64 sphinx-common all 8.1.3-5 [617 kB] Get: 243 http://deb.debian.org/debian unstable/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 244 http://deb.debian.org/debian unstable/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 245 http://deb.debian.org/debian unstable/main arm64 python3-sphinx all 8.1.3-5 [468 kB] Get: 246 http://deb.debian.org/debian unstable/main arm64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 247 http://deb.debian.org/debian unstable/main arm64 python3-sphinx-rtd-theme all 3.0.2+dfsg-3 [29.7 kB] Get: 248 http://deb.debian.org/debian unstable/main arm64 python3-msmb-theme all 1.2.0-4 [33.8 kB] Get: 249 http://deb.debian.org/debian unstable/main arm64 python3-netcdf4 arm64 1.7.2-1+b5 [542 kB] Get: 250 http://deb.debian.org/debian unstable/main arm64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 251 http://deb.debian.org/debian unstable/main arm64 python3-pytz all 2025.2-3 [152 kB] Get: 252 http://deb.debian.org/debian unstable/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-9 [3877 kB] Get: 253 http://deb.debian.org/debian unstable/main arm64 python3-pandas all 2.2.3+dfsg-9 [3097 kB] Get: 254 http://deb.debian.org/debian unstable/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 255 http://deb.debian.org/debian unstable/main arm64 python3-six all 1.17.0-1 [16.5 kB] Get: 256 http://deb.debian.org/debian unstable/main arm64 python3-yaml arm64 6.0.2-1+b2 [122 kB] Get: 257 http://deb.debian.org/debian unstable/main arm64 python3-pybtex all 0.24.0-4 [74.6 kB] Get: 258 http://deb.debian.org/debian unstable/main arm64 python3-pybtex-docutils all 1.0.2-1 [8064 B] Get: 259 http://deb.debian.org/debian unstable/main arm64 python3-pytest all 8.3.5-2 [250 kB] Get: 260 http://deb.debian.org/debian unstable/main arm64 python3-seaborn all 0.13.2-5 [215 kB] Get: 261 http://deb.debian.org/debian unstable/main arm64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 262 http://deb.debian.org/debian unstable/main arm64 python3-sklearn-lib arm64 1.4.2+dfsg-8 [3408 kB] Get: 263 http://deb.debian.org/debian unstable/main arm64 python3-sklearn all 1.4.2+dfsg-8 [2248 kB] Get: 264 http://deb.debian.org/debian unstable/main arm64 python3-sphinx-sitemap all 2.6.0-1 [8508 B] Get: 265 http://deb.debian.org/debian unstable/main arm64 python3-sphinxcontrib.bibtex all 2.6.2-1 [32.4 kB] Get: 266 http://deb.debian.org/debian unstable/main arm64 python3-tqdm all 4.67.1-5 [90.8 kB] Fetched 185 MB in 1s (203 MB/s) Preconfiguring packages ... 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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 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.5-2_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.5-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.5-2_arm64.deb ... Unpacking python3.13 (3.13.5-2) ... 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Unpacking libfontenc1:arm64 (1:1.1.8-1+b2) ... Selecting previously unselected package x11-common. Preparing to unpack .../032-x11-common_1%3a7.7+24_all.deb ... Unpacking x11-common (1:7.7+24) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../033-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 .../034-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 .../035-fonts-urw-base35_20200910-8_all.deb ... Unpacking fonts-urw-base35 (20200910-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../036-fontconfig-config_2.15.0-2.3_arm64.deb ... Unpacking fontconfig-config (2.15.0-2.3) ... Selecting previously unselected package libfontconfig1:arm64. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/mdanalysis-2.9.0/ && 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_2.9.0-12_source.changes dpkg-buildpackage: info: source package mdanalysis dpkg-buildpackage: info: source version 2.9.0-12 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-2.9.0/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-2.9.0' 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-2.9.0' 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 python3.13 with "build" module I: pybuild base:311: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_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:289: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) /usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! dist._finalize_license_expression() /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running bdist_wheel running build running build_py creating build/lib.linux-aarch64-cpython-313/MDAnalysis copying MDAnalysis/authors.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis copying MDAnalysis/version.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis copying MDAnalysis/units.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis copying MDAnalysis/exceptions.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis copying MDAnalysis/due.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis copying MDAnalysis/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis creating build/lib.linux-aarch64-cpython-313/doc/sphinx/source copying doc/sphinx/source/conf.py -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source creating build/lib.linux-aarch64-cpython-313/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/visualization copying MDAnalysis/visualization/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/visualization creating build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/wrap.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/translate.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/rotate.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/nojump.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/fit.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/base.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations creating build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/tables.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/guessers.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/core.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/base.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/GROParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology creating build/lib.linux-aarch64-cpython-313/MDAnalysis/tests copying MDAnalysis/tests/datafiles.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/tests copying MDAnalysis/tests/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/tests creating build/lib.linux-aarch64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/vmd.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/pymol.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/jmol.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/gromacs.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/charmm.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/base.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/selections creating build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/util.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/transformations.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/mdamath.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/log.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/distances.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/correlations.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_distopia.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib creating build/lib.linux-aarch64-cpython-313/MDAnalysis/guesser copying MDAnalysis/guesser/tables.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/guesser copying MDAnalysis/guesser/default_guesser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/guesser copying MDAnalysis/guesser/base.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/guesser copying MDAnalysis/guesser/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/guesser creating build/lib.linux-aarch64-cpython-313/MDAnalysis/core copying MDAnalysis/core/universe.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/core copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/core copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/core copying MDAnalysis/core/topology.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/core copying MDAnalysis/core/selection.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/core copying MDAnalysis/core/groups.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/core copying MDAnalysis/core/accessors.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/core copying MDAnalysis/core/_get_readers.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/core copying MDAnalysis/core/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/core creating build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/null.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/memory.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/core.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/chain.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/base.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRC.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TNG.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates creating build/lib.linux-aarch64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/base.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/RDKit.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/converters creating build/lib.linux-aarch64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/core.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/base.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/auxiliary creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/rms.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/results.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/rdf.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/psa.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/polymer.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/pca.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/msd.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/gnm.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/distances.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/dielectric.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/density.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/contacts.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/bat.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/base.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/backends.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/atomicdistances.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/align.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis creating build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/tpr creating build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/libmdanalysis copying MDAnalysis/lib/libmdanalysis/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/libmdanalysis creating build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/include copying MDAnalysis/lib/include/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/include creating build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats creating build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations creating build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src creating build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/legacy creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hydrogenbonds creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hole2 creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hbonds creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/dssp copying MDAnalysis/analysis/dssp/pydssp_numpy.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/dssp copying MDAnalysis/analysis/dssp/dssp.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/dssp copying MDAnalysis/analysis/dssp/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/dssp creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/data creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-aarch64-cpython-313/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/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/clustering/include/ap.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/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/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/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' copying doc/README -> build/lib.linux-aarch64-cpython-313/doc copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/data copying doc/sphinx/Makefile -> build/lib.linux-aarch64-cpython-313/doc/sphinx copying doc/sphinx/source/index.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source copying doc/sphinx/source/references.bib -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source creating build/lib.linux-aarch64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/AnalysisBase_parallel.png -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/RSMD_plot.png -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/janin_demo_plot.png -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/janin_ref_plot.png -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/msd_demo_plot.png -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/parallelization_time.png -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/rama_demo_plot.png -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/rama_ref_plot.png -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/images creating build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/analysis_modules.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/auxiliary_modules.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/converters.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/coordinates_modules.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/core_modules.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/exceptions.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/guesser_modules.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/lib_modules.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/overview.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/references.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/selections.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/selections_modules.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/topology.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/topology_modules.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/trajectory_transformations.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/units.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/version.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/visualization_modules.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages creating build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/streamlines.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/testing_streamline.png -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/visualization creating build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/base.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/fit.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/nojump.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/positionaveraging.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/rotate.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/translate.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/wrap.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/transformations creating build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/CRDParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/DMSParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/GMSParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/GROParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/GSDParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/ITPParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/MMTFParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/MinimalParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PDBParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PQRParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PSFParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/TOPParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/TPRParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/TXYZParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/XYZParser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/base.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/core.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/guessers.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/init.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/tables.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/tpr_util.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology creating build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/base.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/charmm.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/gromacs.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/jmol.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/pymol.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/vmd.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/selections creating build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/c_distances.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/correlations.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/distances.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/log.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/mdamath.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/nsgrid.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/pkdtree.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/qcprot.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/transformations.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/util.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib creating build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/base.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/init.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/tables.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules creating build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/accessors.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/groups.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/init.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/selection.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/topology.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/topologyattrs.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/topologyobjects.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/universe.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/core creating build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/CRD.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/DCD.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/DLPoly.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/DMS.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/FHIAIMS.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/GMS.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/GRO.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/GSD.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/H5MD.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/INPCRD.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/LAMMPS.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/MMTF.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/MOL2.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/NAMDBIN.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PDB.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PDBQT.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PQR.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TNG.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRC.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRJ.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRR.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRZ.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TXYZ.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XDR.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XTC.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XYZ.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/base.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/chain.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/chemfiles.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/core.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/init.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/memory.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/null.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/pickle_readers.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/timestep.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates creating build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/OpenMM.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/ParmEd.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/RDKit.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/base.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/converters creating build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/EDR.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/XVG.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/base.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/core.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/init.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary creating build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/align.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/atomicdistances.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/backends.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/base.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/bat.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/contacts.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/data.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/density.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/dielectric.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/diffusionmap.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/dihedrals.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/distances.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/dssp.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/encore.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/gnm.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel_deprecated.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/helix_analysis.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hole2.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hydrogenbonds.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/leaflet.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/legacy_modules.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/lineardensity.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/msd.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/nucleicacids.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/nuclinfo.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/parallelization.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/pca.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/polymer.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/psa.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/rdf.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/results.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/rms.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/waterdynamics.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/wbridge_analysis.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis creating build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats copying doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats copying doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats creating build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy copying doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy creating build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/confdistmatrix.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/covariance.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/utils.rst -> build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying MDAnalysis/lib/_augment.cpp -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_augment.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_cutil.cpp -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pxd -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pxd -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.cpp -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/qcprot.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/qcprot.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib copying MDAnalysis/coordinates/timestep.cpp -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pxd -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/libmdanalysis copying MDAnalysis/lib/include/calc_distances.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/include copying MDAnalysis/lib/formats/cython_util.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/src copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/src creating build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/include copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/include running build_ext building 'MDAnalysis.lib.formats.libdcd' extension creating build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -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-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/usr/include/python3.13 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libdcd.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/formats/libdcd.c:1261: /usr/lib/aarch64-linux-gnu/python3-numpy/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-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libdcd.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libdcd.cpython-313-aarch64-linux-gnu.so building 'MDAnalysis.lib.c_distances' extension aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include -I/usr/include/python3.13 -c MDAnalysis/lib/c_distances.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/c_distances.c:1263: /usr/lib/aarch64-linux-gnu/python3-numpy/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-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances.o -L/usr/lib/aarch64-linux-gnu -lm -o build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances.cpython-313-aarch64-linux-gnu.so building 'MDAnalysis.lib.c_distances_openmp' extension aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPARALLEL -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include -I/usr/include/python3.13 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/c_distances_openmp.c:1272: /usr/lib/aarch64-linux-gnu/python3-numpy/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-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances_openmp.o -L/usr/lib/aarch64-linux-gnu -lm -lgomp -o build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances_openmp.cpython-313-aarch64-linux-gnu.so -fopenmp building 'MDAnalysis.lib.qcprot' extension aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/lib/qcprot.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/qcprot.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/qcprot.c:1255: /usr/lib/aarch64-linux-gnu/python3-numpy/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-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/qcprot.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/qcprot.cpython-313-aarch64-linux-gnu.so building 'MDAnalysis.lib._transformations' extension creating build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations/transformations.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/src/transformations/transformations.c:73: /usr/lib/aarch64-linux-gnu/python3-numpy/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-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations/transformations.o -L/usr/lib/aarch64-linux-gnu -lm -o build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_transformations.cpython-313-aarch64-linux-gnu.so building 'MDAnalysis.lib.formats.libmdaxdr' extension creating build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -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-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/formats/libmdaxdr.c:1282: /usr/lib/aarch64-linux-gnu/python3-numpy/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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -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-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/trr_seek.o -std=c11 -O3 -funroll-loops -fsigned-zeros aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -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-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xdrfile.o -std=c11 -O3 -funroll-loops -fsigned-zeros aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -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-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_trr.o -std=c11 -O3 -funroll-loops -fsigned-zeros aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -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-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_xtc.o -std=c11 -O3 -funroll-loops -fsigned-zeros aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -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-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/include/python3.13 -c MDAnalysis/lib/formats/src/xtc_seek.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xtc_seek.o -std=c11 -O3 -funroll-loops -fsigned-zeros 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-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/trr_seek.o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xdrfile.o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_trr.o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_xtc.o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xtc_seek.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.cpython-313-aarch64-linux-gnu.so building 'MDAnalysis.lib.formats.cython_util' extension aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/lib/formats/cython_util.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/cython_util.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/formats/cython_util.c:1272: /usr/lib/aarch64-linux-gnu/python3-numpy/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-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/formats/cython_util.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/cython_util.cpython-313-aarch64-linux-gnu.so building 'MDAnalysis.analysis.encore.cutils' extension creating build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/cutils.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/cutils.o -std=c11 -funroll-loops -fsigned-zeros -O1 In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/analysis/encore/cutils.c:1255: /usr/lib/aarch64-linux-gnu/python3-numpy/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-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/cutils.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/cutils.cpython-313-aarch64-linux-gnu.so building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension creating build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering creating build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/src aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/clustering/affinityprop.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.o -std=c11 -funroll-loops -fsigned-zeros -O1 In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/analysis/encore/clustering/affinityprop.c:1261: /usr/lib/aarch64-linux-gnu/python3-numpy/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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/clustering/src/ap.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/src/ap.o -std=c11 -funroll-loops -fsigned-zeros -O1 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-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.o build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/src/ap.o -L/usr/lib/aarch64-linux-gnu -lm -o build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-313-aarch64-linux-gnu.so building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension creating build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -std=c11 -funroll-loops -fsigned-zeros -O1 aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.13 -c MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -o build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -std=c11 -funroll-loops -fsigned-zeros -O1 In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:1261: /usr/lib/aarch64-linux-gnu/python3-numpy/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-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o build/temp.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -L/usr/lib/aarch64-linux-gnu -lm -o build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-313-aarch64-linux-gnu.so building 'MDAnalysis.lib._cutil' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include -I/usr/include/python3.13 -c MDAnalysis/lib/_cutil.cpp -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/_cutil.o -O3 -funroll-loops -fsigned-zeros -std=c++11 In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/_cutil.cpp:1273: /usr/lib/aarch64-linux-gnu/python3-numpy/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-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/_cutil.o -L/usr/lib/aarch64-linux-gnu -lm -o build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_cutil.cpython-313-aarch64-linux-gnu.so building 'MDAnalysis.lib._augment' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/lib/_augment.cpp -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/_augment.o -O3 -funroll-loops -fsigned-zeros -std=c++11 In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/_augment.cpp:1268: /usr/lib/aarch64-linux-gnu/python3-numpy/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-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/_augment.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_augment.cpython-313-aarch64-linux-gnu.so building 'MDAnalysis.lib.nsgrid' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/include -I/usr/include/python3.13 -c MDAnalysis/lib/nsgrid.cpp -o build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/nsgrid.o -O3 -funroll-loops -fsigned-zeros -std=c++11 aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/lib/nsgrid.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/nsgrid.cpython-313-aarch64-linux-gnu.so building 'MDAnalysis.coordinates.timestep' extension creating build/temp.linux-aarch64-cpython-313/MDAnalysis/coordinates aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/coordinates/timestep.cpp -o build/temp.linux-aarch64-cpython-313/MDAnalysis/coordinates/timestep.o -O3 -funroll-loops -fsigned-zeros -std=c++11 In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/coordinates/timestep.cpp:1269: /usr/lib/aarch64-linux-gnu/python3-numpy/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-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/MDAnalysis/coordinates/timestep.o -L/usr/lib/aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/timestep.cpython-313-aarch64-linux-gnu.so installing to build/bdist.linux-aarch64/wheel running install running install_lib creating build/bdist.linux-aarch64/wheel creating build/bdist.linux-aarch64/wheel/doc copying build/lib.linux-aarch64-cpython-313/doc/README -> build/bdist.linux-aarch64/wheel/./doc creating build/bdist.linux-aarch64/wheel/doc/sphinx copying build/lib.linux-aarch64-cpython-313/doc/sphinx/Makefile -> build/bdist.linux-aarch64/wheel/./doc/sphinx creating build/bdist.linux-aarch64/wheel/doc/sphinx/source creating build/bdist.linux-aarch64/wheel/doc/sphinx/source/documentation_pages creating build/bdist.linux-aarch64/wheel/doc/sphinx/source/documentation_pages/analysis creating build/bdist.linux-aarch64/wheel/doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/utils.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/covariance.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/confdistmatrix.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis/encore creating build/bdist.linux-aarch64/wheel/doc/sphinx/source/documentation_pages/analysis/legacy copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis/legacy copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/wbridge_analysis.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/waterdynamics.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/rms.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/results.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/rdf.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/psa.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/polymer.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/pca.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/parallelization.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/nuclinfo.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/nucleicacids.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/msd.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/lineardensity.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy_modules.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/leaflet.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hydrogenbonds.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hole2.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/helix_analysis.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel_deprecated.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/gnm.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/dssp.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/distances.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/dihedrals.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/diffusionmap.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/dielectric.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/density.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/data.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/contacts.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/bat.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/base.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/backends.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/atomicdistances.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis/align.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/analysis creating build/bdist.linux-aarch64/wheel/doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/init.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/core.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/base.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/XVG.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/auxiliary copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary/EDR.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/auxiliary creating build/bdist.linux-aarch64/wheel/doc/sphinx/source/documentation_pages/converters copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/converters/base.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/converters copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/converters/RDKit.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/converters copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/converters/ParmEd.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/converters copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/converters/OpenMM.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/converters creating build/bdist.linux-aarch64/wheel/doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/timestep.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/pickle_readers.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/null.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/memory.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/init.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/core.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/chemfiles.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/chain.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/base.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/XYZ.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/XTC.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/XDR.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TXYZ.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRZ.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRR.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRJ.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TRC.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/TNG.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/PQR.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/PDBQT.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/PDB.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/NAMDBIN.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/MOL2.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/MMTF.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/LAMMPS.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/INPCRD.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/H5MD.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/GSD.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/GRO.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/GMS.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/FHIAIMS.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/DMS.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/DLPoly.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/DCD.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates/CRD.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/coordinates creating build/bdist.linux-aarch64/wheel/doc/sphinx/source/documentation_pages/core copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/core/universe.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/core/topologyobjects.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/core/topologyattrs.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/core/topology.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/core/selection.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/core/init.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/core/groups.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/core copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/core/accessors.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/core creating build/bdist.linux-aarch64/wheel/doc/sphinx/source/documentation_pages/guesser_modules copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/tables.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/init.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules/base.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/guesser_modules creating build/bdist.linux-aarch64/wheel/doc/sphinx/source/documentation_pages/lib creating build/bdist.linux-aarch64/wheel/doc/sphinx/source/documentation_pages/lib/formats copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/lib/formats copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/lib/formats copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib/util.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib/transformations.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib/qcprot.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib/pkdtree.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib/nsgrid.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib/mdamath.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib/log.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib/distances.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib/correlations.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib/c_distances.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/lib copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/lib creating build/bdist.linux-aarch64/wheel/doc/sphinx/source/documentation_pages/selections copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/selections/vmd.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/selections copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/selections/pymol.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/selections copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/selections/jmol.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/selections copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/selections/gromacs.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/selections copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/selections/charmm.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/selections copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/selections/base.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/selections creating build/bdist.linux-aarch64/wheel/doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/tpr_util.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/tables.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/init.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/guessers.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/core.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/base.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/XYZParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/TXYZParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/TPRParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/TOPParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/PSFParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/PQRParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/PDBParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/MinimalParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/MMTFParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/ITPParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/GSDParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/GROParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/GMSParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/DMSParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology/CRDParser.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/topology creating build/bdist.linux-aarch64/wheel/doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/transformations/wrap.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/transformations/translate.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/transformations/rotate.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/transformations/positionaveraging.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/transformations/nojump.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/transformations/fit.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/transformations copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/transformations/base.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/transformations creating build/bdist.linux-aarch64/wheel/doc/sphinx/source/documentation_pages/visualization copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/visualization/testing_streamline.png -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/visualization copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/visualization copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/visualization copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/visualization/streamlines.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages/visualization copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/visualization_modules.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/version.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/units.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/trajectory_transformations.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology_modules.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/topology.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/selections_modules.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/selections.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/references.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/overview.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/lib_modules.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/exceptions.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/core_modules.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/coordinates_modules.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/converters.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary_modules.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/documentation_pages/analysis_modules.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/documentation_pages creating build/bdist.linux-aarch64/wheel/doc/sphinx/source/images copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/images/rama_ref_plot.png -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/images copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/images/rama_demo_plot.png -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/images copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/images/parallelization_time.png -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/images copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/images/msd_demo_plot.png -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/images copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/images/janin_ref_plot.png -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/images copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/images/janin_demo_plot.png -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/images copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/images/RSMD_plot.png -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/images copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/images/AnalysisBase_parallel.png -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source/images copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/references.bib -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/index.rst -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source copying build/lib.linux-aarch64-cpython-313/doc/sphinx/source/conf.py -> build/bdist.linux-aarch64/wheel/./doc/sphinx/source creating build/bdist.linux-aarch64/wheel/MDAnalysis creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/data copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/data copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/data copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/data copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/data creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/dssp copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/dssp/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/dssp copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/dssp/dssp.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/dssp copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/dssp/pydssp_numpy.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/dssp creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/cutils.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/cutils.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-aarch64-cpython-313/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-313/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/clustering/include copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/include/ap.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering/include creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/clustering/src copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/src/ap.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering/src copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/clustering copying build/lib.linux-aarch64-cpython-313/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-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-313-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/include copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction/include creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction/src copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore/dimensionality_reduction copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/encore copying build/lib.linux-aarch64-cpython-313/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-313/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hbonds copying build/lib.linux-aarch64-cpython-313/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-313/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hole2 creating build/bdist.linux-aarch64/wheel/MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/hydrogenbonds copying build/lib.linux-aarch64-cpython-313/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-313/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/legacy copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis/legacy copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/align.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/atomicdistances.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/backends.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/bat.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/contacts.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/density.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/dielectric.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/distances.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/gnm.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/msd.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/nucleicacids.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/pca.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/polymer.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/psa.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/rdf.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/results.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/analysis/rms.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/analysis copying build/lib.linux-aarch64-cpython-313/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-313/MDAnalysis/auxiliary/EDR.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-aarch64-cpython-313/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-aarch64-cpython-313/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-aarch64-cpython-313/MDAnalysis/auxiliary/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/auxiliary copying build/lib.linux-aarch64-cpython-313/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-313/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters copying build/lib.linux-aarch64-cpython-313/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters copying build/lib.linux-aarch64-cpython-313/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters copying build/lib.linux-aarch64-cpython-313/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters copying build/lib.linux-aarch64-cpython-313/MDAnalysis/converters/RDKit.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters copying build/lib.linux-aarch64-cpython-313/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters copying build/lib.linux-aarch64-cpython-313/MDAnalysis/converters/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/converters copying build/lib.linux-aarch64-cpython-313/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-313/MDAnalysis/coordinates/timestep.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/timestep.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/timestep.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/timestep.cpp -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/H5MD.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/TNG.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/TRC.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/chain.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/core.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/MDAnalysis/coordinates/memory.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/coordinates copying build/lib.linux-aarch64-cpython-313/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-313/MDAnalysis/core/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core copying build/lib.linux-aarch64-cpython-313/MDAnalysis/core/_get_readers.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core copying build/lib.linux-aarch64-cpython-313/MDAnalysis/core/accessors.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core copying build/lib.linux-aarch64-cpython-313/MDAnalysis/core/groups.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core copying build/lib.linux-aarch64-cpython-313/MDAnalysis/core/selection.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core copying build/lib.linux-aarch64-cpython-313/MDAnalysis/core/topology.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core copying build/lib.linux-aarch64-cpython-313/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core copying build/lib.linux-aarch64-cpython-313/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core copying build/lib.linux-aarch64-cpython-313/MDAnalysis/core/universe.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/core creating build/bdist.linux-aarch64/wheel/MDAnalysis/guesser copying build/lib.linux-aarch64-cpython-313/MDAnalysis/guesser/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/guesser copying build/lib.linux-aarch64-cpython-313/MDAnalysis/guesser/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/guesser copying build/lib.linux-aarch64-cpython-313/MDAnalysis/guesser/default_guesser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/guesser copying build/lib.linux-aarch64-cpython-313/MDAnalysis/guesser/tables.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/guesser creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/nsgrid.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_augment.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_cutil.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_transformations.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/qcprot.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances_openmp.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/qcprot.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/qcprot.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/nsgrid.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/nsgrid.cpp -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances_openmp.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances_openmp.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/c_distances.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_cutil.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_cutil.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_cutil.cpp -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_augment.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_augment.cpp -> 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-313/MDAnalysis/lib/src/transformations/transformations.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/src/transformations copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations/LICENCE -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/src/transformations copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations/AUTHOR -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/src/transformations copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/src/transformations/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/src/transformations creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/cython_util.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libdcd.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libmdaxdr.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libdcd.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libdcd.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/libdcd.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/cython_util.pyx -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/cython_util.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/cython_util.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/formats/include copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include/xtc_seek.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include/xdrfile.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include/trr_seek.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include/readdcd.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include/fastio.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include/endianswap.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/include/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/include creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/formats/src copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xtc_seek.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/xdrfile.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/trr_seek.c -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/src/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats/src copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/formats creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/include copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/include/calc_distances.h -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/include copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/include/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/include creating build/bdist.linux-aarch64/wheel/MDAnalysis/lib/libmdanalysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/libmdanalysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/libmdanalysis/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib/libmdanalysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/_distopia.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/correlations.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/distances.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/log.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/mdamath.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/MDAnalysis/lib/transformations.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/lib copying build/lib.linux-aarch64-cpython-313/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-313/MDAnalysis/selections/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections copying build/lib.linux-aarch64-cpython-313/MDAnalysis/selections/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections copying build/lib.linux-aarch64-cpython-313/MDAnalysis/selections/charmm.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections copying build/lib.linux-aarch64-cpython-313/MDAnalysis/selections/gromacs.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections copying build/lib.linux-aarch64-cpython-313/MDAnalysis/selections/jmol.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections copying build/lib.linux-aarch64-cpython-313/MDAnalysis/selections/pymol.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/selections copying build/lib.linux-aarch64-cpython-313/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-313/MDAnalysis/tests/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/tests copying build/lib.linux-aarch64-cpython-313/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-313/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology/tpr copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/GROParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/core.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/MDAnalysis/topology/guessers.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/topology copying build/lib.linux-aarch64-cpython-313/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-313/MDAnalysis/transformations/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations copying build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations/base.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations copying build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations copying build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations/fit.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations copying build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations/nojump.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations copying build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations copying build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations/rotate.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations copying build/lib.linux-aarch64-cpython-313/MDAnalysis/transformations/translate.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/transformations copying build/lib.linux-aarch64-cpython-313/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-313/MDAnalysis/visualization/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/visualization copying build/lib.linux-aarch64-cpython-313/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/visualization copying build/lib.linux-aarch64-cpython-313/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis/visualization copying build/lib.linux-aarch64-cpython-313/MDAnalysis/__init__.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/due.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/exceptions.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/units.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/version.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis copying build/lib.linux-aarch64-cpython-313/MDAnalysis/authors.py -> build/bdist.linux-aarch64/wheel/./MDAnalysis running install_egg_info Copying MDAnalysis.egg-info to build/bdist.linux-aarch64/wheel/./MDAnalysis-2.9.0.egg-info running install_scripts creating build/bdist.linux-aarch64/wheel/mdanalysis-2.9.0.dist-info/WHEEL creating '/build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/.tmp-qryeo1kg/mdanalysis-2.9.0-cp313-cp313-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/backends.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/results.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/dssp/__init__.py' adding 'MDAnalysis/analysis/dssp/dssp.py' adding 'MDAnalysis/analysis/dssp/pydssp_numpy.py' 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-313-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-313-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-313-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/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-313-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/guesser/__init__.py' adding 'MDAnalysis/guesser/base.py' adding 'MDAnalysis/guesser/default_guesser.py' adding 'MDAnalysis/guesser/tables.py' adding 'MDAnalysis/lib/NeighborSearch.py' adding 'MDAnalysis/lib/__init__.py' adding 'MDAnalysis/lib/_augment.cpp' adding 'MDAnalysis/lib/_augment.cpython-313-aarch64-linux-gnu.so' adding 'MDAnalysis/lib/_augment.pyx' adding 'MDAnalysis/lib/_cutil.cpp' adding 'MDAnalysis/lib/_cutil.cpython-313-aarch64-linux-gnu.so' adding 'MDAnalysis/lib/_cutil.pxd' adding 'MDAnalysis/lib/_cutil.pyx' adding 'MDAnalysis/lib/_distopia.py' adding 'MDAnalysis/lib/_transformations.cpython-313-aarch64-linux-gnu.so' adding 'MDAnalysis/lib/c_distances.c' adding 'MDAnalysis/lib/c_distances.cpython-313-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-313-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-313-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-313-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-313-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-313-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-313-aarch64-linux-gnu.so' adding 'MDAnalysis/lib/formats/libmdaxdr.pxd' adding 'MDAnalysis/lib/formats/libmdaxdr.pyx' adding 'MDAnalysis/lib/formats/include/__init__.py' 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/__init__.py' 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/__init__.py' adding 'MDAnalysis/lib/include/calc_distances.h' adding 'MDAnalysis/lib/libmdanalysis/__init__.pxd' adding 'MDAnalysis/lib/libmdanalysis/__init__.py' adding 'MDAnalysis/lib/src/transformations/AUTHOR' adding 'MDAnalysis/lib/src/transformations/LICENCE' adding 'MDAnalysis/lib/src/transformations/__init__.py' 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 'doc/README' adding 'doc/sphinx/Makefile' adding 'doc/sphinx/source/conf.py' adding 'doc/sphinx/source/index.rst' adding 'doc/sphinx/source/references.bib' adding 'doc/sphinx/source/documentation_pages/analysis_modules.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary_modules.rst' adding 'doc/sphinx/source/documentation_pages/converters.rst' adding 'doc/sphinx/source/documentation_pages/coordinates_modules.rst' adding 'doc/sphinx/source/documentation_pages/core_modules.rst' adding 'doc/sphinx/source/documentation_pages/exceptions.rst' adding 'doc/sphinx/source/documentation_pages/guesser_modules.rst' adding 'doc/sphinx/source/documentation_pages/lib_modules.rst' adding 'doc/sphinx/source/documentation_pages/overview.rst' adding 'doc/sphinx/source/documentation_pages/references.rst' adding 'doc/sphinx/source/documentation_pages/selections.rst' adding 'doc/sphinx/source/documentation_pages/selections_modules.rst' adding 'doc/sphinx/source/documentation_pages/topology.rst' adding 'doc/sphinx/source/documentation_pages/topology_modules.rst' adding 'doc/sphinx/source/documentation_pages/trajectory_transformations.rst' adding 'doc/sphinx/source/documentation_pages/units.rst' adding 'doc/sphinx/source/documentation_pages/version.rst' adding 'doc/sphinx/source/documentation_pages/visualization_modules.rst' adding 'doc/sphinx/source/documentation_pages/analysis/align.rst' adding 'doc/sphinx/source/documentation_pages/analysis/atomicdistances.rst' adding 'doc/sphinx/source/documentation_pages/analysis/backends.rst' adding 'doc/sphinx/source/documentation_pages/analysis/base.rst' adding 'doc/sphinx/source/documentation_pages/analysis/bat.rst' adding 'doc/sphinx/source/documentation_pages/analysis/contacts.rst' adding 'doc/sphinx/source/documentation_pages/analysis/data.rst' adding 'doc/sphinx/source/documentation_pages/analysis/density.rst' adding 'doc/sphinx/source/documentation_pages/analysis/dielectric.rst' adding 'doc/sphinx/source/documentation_pages/analysis/diffusionmap.rst' adding 'doc/sphinx/source/documentation_pages/analysis/dihedrals.rst' adding 'doc/sphinx/source/documentation_pages/analysis/distances.rst' adding 'doc/sphinx/source/documentation_pages/analysis/dssp.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore.rst' adding 'doc/sphinx/source/documentation_pages/analysis/gnm.rst' adding 'doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel.rst' adding 'doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel_deprecated.rst' adding 'doc/sphinx/source/documentation_pages/analysis/helix_analysis.rst' adding 'doc/sphinx/source/documentation_pages/analysis/hole2.rst' adding 'doc/sphinx/source/documentation_pages/analysis/hydrogenbonds.rst' adding 'doc/sphinx/source/documentation_pages/analysis/leaflet.rst' adding 'doc/sphinx/source/documentation_pages/analysis/legacy_modules.rst' adding 'doc/sphinx/source/documentation_pages/analysis/lineardensity.rst' adding 'doc/sphinx/source/documentation_pages/analysis/msd.rst' adding 'doc/sphinx/source/documentation_pages/analysis/nucleicacids.rst' adding 'doc/sphinx/source/documentation_pages/analysis/nuclinfo.rst' adding 'doc/sphinx/source/documentation_pages/analysis/parallelization.rst' adding 'doc/sphinx/source/documentation_pages/analysis/pca.rst' adding 'doc/sphinx/source/documentation_pages/analysis/polymer.rst' adding 'doc/sphinx/source/documentation_pages/analysis/psa.rst' adding 'doc/sphinx/source/documentation_pages/analysis/rdf.rst' adding 'doc/sphinx/source/documentation_pages/analysis/results.rst' adding 'doc/sphinx/source/documentation_pages/analysis/rms.rst' adding 'doc/sphinx/source/documentation_pages/analysis/waterdynamics.rst' adding 'doc/sphinx/source/documentation_pages/analysis/wbridge_analysis.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/confdistmatrix.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/covariance.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst' adding 'doc/sphinx/source/documentation_pages/analysis/encore/utils.rst' adding 'doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary/EDR.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary/XVG.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary/base.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary/core.rst' adding 'doc/sphinx/source/documentation_pages/auxiliary/init.rst' adding 'doc/sphinx/source/documentation_pages/converters/OpenMM.rst' adding 'doc/sphinx/source/documentation_pages/converters/ParmEd.rst' adding 'doc/sphinx/source/documentation_pages/converters/RDKit.rst' adding 'doc/sphinx/source/documentation_pages/converters/base.rst' adding 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'doc/sphinx/source/documentation_pages/coordinates/PDB.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/PDBQT.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/PQR.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TNG.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TRC.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TRJ.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TRR.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TRZ.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/TXYZ.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/XDR.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/XTC.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/XYZ.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/base.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/chain.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/chemfiles.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/core.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/init.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/memory.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/null.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/pickle_readers.rst' adding 'doc/sphinx/source/documentation_pages/coordinates/timestep.rst' adding 'doc/sphinx/source/documentation_pages/core/accessors.rst' adding 'doc/sphinx/source/documentation_pages/core/groups.rst' adding 'doc/sphinx/source/documentation_pages/core/init.rst' adding 'doc/sphinx/source/documentation_pages/core/selection.rst' adding 'doc/sphinx/source/documentation_pages/core/topology.rst' adding 'doc/sphinx/source/documentation_pages/core/topologyattrs.rst' adding 'doc/sphinx/source/documentation_pages/core/topologyobjects.rst' adding 'doc/sphinx/source/documentation_pages/core/universe.rst' adding 'doc/sphinx/source/documentation_pages/guesser_modules/base.rst' adding 'doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst' adding 'doc/sphinx/source/documentation_pages/guesser_modules/init.rst' adding 'doc/sphinx/source/documentation_pages/guesser_modules/tables.rst' adding 'doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst' adding 'doc/sphinx/source/documentation_pages/lib/c_distances.rst' adding 'doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst' adding 'doc/sphinx/source/documentation_pages/lib/correlations.rst' adding 'doc/sphinx/source/documentation_pages/lib/distances.rst' adding 'doc/sphinx/source/documentation_pages/lib/log.rst' adding 'doc/sphinx/source/documentation_pages/lib/mdamath.rst' adding 'doc/sphinx/source/documentation_pages/lib/nsgrid.rst' adding 'doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst' adding 'doc/sphinx/source/documentation_pages/lib/pkdtree.rst' adding 'doc/sphinx/source/documentation_pages/lib/qcprot.rst' adding 'doc/sphinx/source/documentation_pages/lib/transformations.rst' adding 'doc/sphinx/source/documentation_pages/lib/util.rst' adding 'doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst' adding 'doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst' adding 'doc/sphinx/source/documentation_pages/selections/base.rst' adding 'doc/sphinx/source/documentation_pages/selections/charmm.rst' adding 'doc/sphinx/source/documentation_pages/selections/gromacs.rst' adding 'doc/sphinx/source/documentation_pages/selections/jmol.rst' adding 'doc/sphinx/source/documentation_pages/selections/pymol.rst' adding 'doc/sphinx/source/documentation_pages/selections/vmd.rst' adding 'doc/sphinx/source/documentation_pages/topology/CRDParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/DMSParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/GMSParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/GROParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/GSDParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/ITPParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/MMTFParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst' adding 'doc/sphinx/source/documentation_pages/topology/MinimalParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/PDBParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/PQRParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/PSFParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/TOPParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/TPRParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/TXYZParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/XYZParser.rst' adding 'doc/sphinx/source/documentation_pages/topology/base.rst' adding 'doc/sphinx/source/documentation_pages/topology/core.rst' adding 'doc/sphinx/source/documentation_pages/topology/guessers.rst' adding 'doc/sphinx/source/documentation_pages/topology/init.rst' adding 'doc/sphinx/source/documentation_pages/topology/tables.rst' adding 'doc/sphinx/source/documentation_pages/topology/tpr_util.rst' adding 'doc/sphinx/source/documentation_pages/transformations/base.rst' adding 'doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst' adding 'doc/sphinx/source/documentation_pages/transformations/fit.rst' adding 'doc/sphinx/source/documentation_pages/transformations/nojump.rst' adding 'doc/sphinx/source/documentation_pages/transformations/positionaveraging.rst' adding 'doc/sphinx/source/documentation_pages/transformations/rotate.rst' adding 'doc/sphinx/source/documentation_pages/transformations/translate.rst' adding 'doc/sphinx/source/documentation_pages/transformations/wrap.rst' adding 'doc/sphinx/source/documentation_pages/visualization/streamlines.rst' adding 'doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst' adding 'doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png' adding 'doc/sphinx/source/documentation_pages/visualization/testing_streamline.png' adding 'doc/sphinx/source/images/AnalysisBase_parallel.png' adding 'doc/sphinx/source/images/RSMD_plot.png' adding 'doc/sphinx/source/images/janin_demo_plot.png' adding 'doc/sphinx/source/images/janin_ref_plot.png' adding 'doc/sphinx/source/images/msd_demo_plot.png' adding 'doc/sphinx/source/images/parallelization_time.png' adding 'doc/sphinx/source/images/rama_demo_plot.png' adding 'doc/sphinx/source/images/rama_ref_plot.png' adding 'mdanalysis-2.9.0.dist-info/licenses/AUTHORS' adding 'mdanalysis-2.9.0.dist-info/licenses/LICENSE' adding 'mdanalysis-2.9.0.dist-info/METADATA' adding 'mdanalysis-2.9.0.dist-info/WHEEL' adding 'mdanalysis-2.9.0.dist-info/top_level.txt' adding 'mdanalysis-2.9.0.dist-info/RECORD' removing build/bdist.linux-aarch64/wheel Successfully built mdanalysis-2.9.0-cp313-cp313-linux_aarch64.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.13 with "installer" module debian/rules execute_after_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.9.0' PYTHONPATH=/build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build make html -C package/doc/sphinx/ BUILDDIR=/build/reproducible-path/mdanalysis-2.9.0/.pybuild # HTML generator make[2]: Entering directory '/build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx' sphinx-build -v -b html source /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html Running Sphinx v8.1.3 loading translations [en]... locale_dir /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist locale_dir /build/reproducible-path/mdanalysis-2.9.0/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-2.9.0/package/doc/sphinx/source/references.bib... parsed 69 entries locale_dir /build/reproducible-path/mdanalysis-2.9.0/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 ... loading intersphinx inventory 'maplotlib' from https://matplotlib.org/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 'griddataformats' from https://mdanalysis.org/GridDataFormats/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://gsd.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='gsd.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by ProxyError('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://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 'numpy' from https://numpy.org/doc/stable/objects.inv ... loading intersphinx inventory 'networkx' from https://networkx.org/documentation/stable/objects.inv ... 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://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 'waterdynamics' from https://www.mdanalysis.org/waterdynamics/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://networkx.org/documentation/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='networkx.org', port=443): Max retries exceeded with url: /documentation/stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) loading intersphinx inventory 'mdahole2' from https://www.mdanalysis.org/mdahole2/objects.inv ... loading intersphinx inventory 'pathsimanalysis' from https://www.mdanalysis.org/PathSimAnalysis/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://matplotlib.org/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='matplotlib.org', port=443): Max retries exceeded with url: /stable/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) 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'))) loading intersphinx inventory 'parmed' from https://parmed.github.io/ParmEd/html/objects.inv ... 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'))) loading intersphinx inventory 'dask' from https://docs.dask.org/en/stable/objects.inv ... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://www.mdanalysis.org/waterdynamics/objects.inv' not fetchable due to : HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /waterdynamics/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://www.mdanalysis.org/PathSimAnalysis/objects.inv' not fetchable due to : HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /PathSimAnalysis/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://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'))) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://www.mdanalysis.org/mdahole2/objects.inv' not fetchable due to : HTTPSConnectionPool(host='www.mdanalysis.org', port=443): Max retries exceeded with url: /mdahole2/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://docs.dask.org/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.dask.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'))) locale_dir /build/reproducible-path/mdanalysis-2.9.0/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 177 source files that are out of date updating environment: locale_dir /build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx/source/locales/en/LC_MESSAGES does not exist [new config] 177 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/backends 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... [ 3%] 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 Didn't find Contacts.n_initial_contacts in MDAnalysis.analysis.contacts Didn't find Contacts.r0 in MDAnalysis.analysis.contacts reading sources... [ 4%] documentation_pages/analysis/data reading sources... [ 5%] 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... [ 6%] 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 mkdir -p failed for path /nonexistent/first-build/.config/matplotlib: [Errno 13] Permission denied: '/nonexistent' Matplotlib created a temporary cache directory at /tmp/matplotlib-_e273v5a because there was an issue with the default path (/nonexistent/first-build/.config/matplotlib); 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/dssp Didn't find DSSP.results.dssp in MDAnalysis.analysis.dssp.dssp Didn't find DSSP.results.dssp_ndarray in MDAnalysis.analysis.dssp.dssp Didn't find DSSP.results.resids in MDAnalysis.analysis.dssp.dssp reading sources... [ 8%] documentation_pages/analysis/encore reading sources... [ 8%] documentation_pages/analysis/encore/bootstrap /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/encore/__init__.py:45: DeprecationWarning: Deprecation in version 2.8.0 MDAnalysis.analysis.encore is deprecated in favour of the MDAKit mdaencore (https://www.mdanalysis.org/mdaencore/) and will be removed in MDAnalysis version 3.0.0. warnings.warn(wmsg, category=DeprecationWarning) reading sources... [ 9%] 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... [ 10%] documentation_pages/analysis/encore/confdistmatrix reading sources... [ 10%] documentation_pages/analysis/encore/covariance reading sources... [ 11%] documentation_pages/analysis/encore/dimensionality_reduction reading sources... [ 11%] documentation_pages/analysis/encore/similarity reading sources... [ 12%] 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... [ 13%] documentation_pages/analysis/hbond_autocorrel reading sources... [ 14%] documentation_pages/analysis/hbond_autocorrel_deprecated /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:54: 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... [ 15%] documentation_pages/analysis/hole2 /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/hole2/__init__.py:50: UserWarning: Please install the mdahole2 mdakit to use it in MDAnalysis. More details can be found here: https://www.mdanalysis.org/mdahole2/getting_started.html warnings.warn(wmsg, category=UserWarning) reading sources... [ 15%] documentation_pages/analysis/hydrogenbonds Didn't find HydrogenBondAnalysis.results.hbonds in MDAnalysis.analysis.hydrogenbonds.hbond_analysis reading sources... [ 16%] 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... [ 18%] 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... [ 19%] 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/parallelization 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... [ 21%] 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 /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/psa.py:72: UserWarning: Please install the PathSimAnalysis mdakit to use it in MDAnalysis. More details can be found here: https://www.mdanalysis.org/PathSimAnalysis/getting_started.html warnings.warn(wmsg, category=UserWarning) reading sources... [ 22%] 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... [ 23%] documentation_pages/analysis/results reading sources... [ 23%] 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... [ 24%] documentation_pages/analysis/waterdynamics /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/waterdynamics.py:57: UserWarning: Please install the waterdynamics mdakit to use it in MDAnalysis. More details can be found here: https://www.mdanalysis.org/waterdynamics/getting_started.html warnings.warn(wmsg, category=UserWarning) reading sources... [ 24%] 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... [ 25%] documentation_pages/analysis_modules reading sources... [ 25%] 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... [ 26%] documentation_pages/auxiliary/XVG reading sources... [ 27%] 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... [ 27%] documentation_pages/auxiliary/core reading sources... [ 28%] documentation_pages/auxiliary/init reading sources... [ 28%] documentation_pages/auxiliary_modules reading sources... [ 29%] documentation_pages/converters reading sources... [ 29%] documentation_pages/converters/OpenMM reading sources... [ 30%] documentation_pages/converters/ParmEd reading sources... [ 31%] documentation_pages/converters/RDKit reading sources... [ 31%] documentation_pages/converters/base reading sources... [ 32%] documentation_pages/coordinates/CRD reading sources... [ 32%] documentation_pages/coordinates/DCD reading sources... [ 33%] documentation_pages/coordinates/DLPoly reading sources... [ 33%] documentation_pages/coordinates/DMS reading sources... [ 34%] documentation_pages/coordinates/FHIAIMS reading sources... [ 34%] documentation_pages/coordinates/GMS reading sources... [ 35%] documentation_pages/coordinates/GRO reading sources... [ 36%] documentation_pages/coordinates/GSD reading sources... [ 36%] documentation_pages/coordinates/H5MD reading sources... [ 37%] 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... [ 40%] documentation_pages/coordinates/PDB reading sources... [ 40%] documentation_pages/coordinates/PDBQT reading sources... [ 41%] 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... [ 44%] 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... [ 47%] 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... [ 50%] documentation_pages/coordinates/pickle_readers reading sources... [ 51%] documentation_pages/coordinates/timestep reading sources... [ 51%] documentation_pages/coordinates_modules reading sources... [ 52%] documentation_pages/core/accessors reading sources... [ 53%] documentation_pages/core/groups reading sources... [ 53%] documentation_pages/core/init reading sources... [ 54%] documentation_pages/core/selection reading sources... [ 54%] documentation_pages/core/topology Didn't find TransTable.n_atoms in MDAnalysis.core.topology Didn't find TransTable.n_residues in MDAnalysis.core.topology Didn't find TransTable.n_segments in MDAnalysis.core.topology reading sources... [ 55%] documentation_pages/core/topologyattrs reading sources... [ 55%] documentation_pages/core/topologyobjects reading sources... [ 56%] documentation_pages/core/universe Didn't find Universe.atoms in MDAnalysis.core.universe Didn't find Universe.residues in MDAnalysis.core.universe Didn't find Universe.segments in MDAnalysis.core.universe reading sources... [ 56%] documentation_pages/core_modules reading sources... [ 57%] documentation_pages/exceptions reading sources... [ 58%] documentation_pages/guesser_modules reading sources... [ 58%] documentation_pages/guesser_modules/base reading sources... [ 59%] documentation_pages/guesser_modules/default_guesser reading sources... [ 59%] documentation_pages/guesser_modules/init reading sources... [ 60%] documentation_pages/guesser_modules/tables reading sources... [ 60%] documentation_pages/lib/NeighborSearch reading sources... [ 61%] documentation_pages/lib/c_distances reading sources... [ 62%] documentation_pages/lib/c_distances_openmp reading sources... [ 62%] documentation_pages/lib/correlations reading sources... [ 63%] documentation_pages/lib/distances reading sources... [ 63%] documentation_pages/lib/formats/libdcd reading sources... [ 64%] documentation_pages/lib/formats/libmdaxdr reading sources... [ 64%] documentation_pages/lib/log reading sources... [ 65%] documentation_pages/lib/mdamath reading sources... [ 66%] documentation_pages/lib/nsgrid reading sources... [ 66%] documentation_pages/lib/picklable_file_io reading sources... [ 67%] documentation_pages/lib/pkdtree reading sources... [ 67%] documentation_pages/lib/qcprot reading sources... [ 68%] documentation_pages/lib/transformations reading sources... [ 68%] documentation_pages/lib/util reading sources... [ 69%] documentation_pages/lib_modules reading sources... [ 69%] documentation_pages/overview reading sources... [ 70%] documentation_pages/references reading sources... [ 71%] documentation_pages/selections reading sources... [ 71%] documentation_pages/selections/base reading sources... [ 72%] documentation_pages/selections/charmm reading sources... [ 72%] documentation_pages/selections/gromacs reading sources... [ 73%] documentation_pages/selections/jmol reading sources... [ 73%] documentation_pages/selections/pymol reading sources... [ 74%] documentation_pages/selections/vmd reading sources... [ 75%] documentation_pages/selections_modules reading sources... [ 75%] documentation_pages/topology reading sources... [ 76%] documentation_pages/topology/CRDParser reading sources... [ 76%] documentation_pages/topology/DLPolyParser reading sources... [ 77%] documentation_pages/topology/DMSParser reading sources... [ 77%] documentation_pages/topology/ExtendedPDBParser reading sources... [ 78%] documentation_pages/topology/FHIAIMSParser reading sources... [ 79%] documentation_pages/topology/GMSParser reading sources... [ 79%] documentation_pages/topology/GROParser reading sources... [ 80%] documentation_pages/topology/GSDParser reading sources... [ 80%] documentation_pages/topology/HoomdXMLParser reading sources... [ 81%] documentation_pages/topology/ITPParser reading sources... [ 81%] documentation_pages/topology/LAMMPSParser reading sources... [ 82%] documentation_pages/topology/MMTFParser reading sources... [ 82%] documentation_pages/topology/MOL2Parser reading sources... [ 83%] documentation_pages/topology/MinimalParser reading sources... [ 84%] documentation_pages/topology/PDBParser reading sources... [ 84%] documentation_pages/topology/PDBQTParser reading sources... [ 85%] documentation_pages/topology/PQRParser reading sources... [ 85%] documentation_pages/topology/PSFParser reading sources... [ 86%] documentation_pages/topology/TOPParser reading sources... [ 86%] documentation_pages/topology/TPRParser reading sources... [ 87%] documentation_pages/topology/TXYZParser reading sources... [ 88%] documentation_pages/topology/XYZParser reading sources... [ 88%] documentation_pages/topology/base reading sources... [ 89%] documentation_pages/topology/core reading sources... [ 89%] documentation_pages/topology/guessers reading sources... [ 90%] documentation_pages/topology/init reading sources... [ 90%] documentation_pages/topology/tables /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/topology/tables.py:52: DeprecationWarning: Deprecated in version 2.8.0 MDAnalysis.topology.tables has been moved to MDAnalysis.guesser.tables. This import point will be removed in MDAnalysis version 3.0.0 warnings.warn(wmsg, category=DeprecationWarning) reading sources... [ 91%] documentation_pages/topology/tpr_util reading sources... [ 92%] documentation_pages/topology_modules reading sources... [ 92%] documentation_pages/trajectory_transformations reading sources... [ 93%] documentation_pages/transformations/base reading sources... [ 93%] documentation_pages/transformations/boxdimensions reading sources... [ 94%] documentation_pages/transformations/fit reading sources... [ 94%] documentation_pages/transformations/nojump reading sources... [ 95%] documentation_pages/transformations/positionaveraging reading sources... [ 95%] documentation_pages/transformations/rotate reading sources... [ 96%] documentation_pages/transformations/translate reading sources... [ 97%] documentation_pages/transformations/wrap reading sources... [ 97%] documentation_pages/units reading sources... [ 98%] documentation_pages/version reading sources... [ 98%] documentation_pages/visualization/streamlines reading sources... [ 99%] documentation_pages/visualization/streamlines_3D reading sources... [ 99%] documentation_pages/visualization_modules reading sources... [100%] index /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/analysis/dssp/dssp.py:docstring of MDAnalysis.analysis.dssp.dssp:25: WARNING: Explicit markup ends without a blank line; unexpected unindent. [docutils] WARNING: autodoc: failed to import module 'utils' from module 'MDAnalysis.analysis.hole2'; the following exception was raised: No module named 'MDAnalysis.analysis.hole2.utils' [autodoc.import_object] WARNING: autodoc: failed to import module 'templates' from module 'MDAnalysis.analysis.hole2'; the following exception was raised: No module named 'MDAnalysis.analysis.hole2.templates' [autodoc.import_object] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/core/universe.py:docstring of MDAnalysis.core.universe.Universe:127: WARNING: Definition list ends without a blank line; unexpected unindent. [docutils] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/core/universe.py:docstring of MDAnalysis.core.universe.Universe:127: WARNING: Inline strong start-string without end-string. [docutils] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/guesser/default_guesser.py:docstring of MDAnalysis.guesser.default_guesser.DefaultGuesser:5: ERROR: Unexpected indentation. [docutils] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/topology/ExtendedPDBParser.py:docstring of MDAnalysis.topology.ExtendedPDBParser.ExtendedPDBParser:29: CRITICAL: Unexpected section title. See Also -------- [docutils] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/topology/TPRParser.py:docstring of MDAnalysis.topology.TPRParser:46: WARNING: Footnote [*] is not referenced. [ref.footnote] docstring of MDAnalysis.topology.tables.atomelements:3: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.atomelements:4: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] docstring of MDAnalysis.topology.tables.atomelements:7: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.atomelements:8: WARNING: Inline strong start-string without end-string. [docutils] docstring of MDAnalysis.topology.tables.masses:3: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.masses:4: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] docstring of MDAnalysis.topology.tables.masses:7: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.masses:8: WARNING: Inline strong start-string without end-string. [docutils] docstring of MDAnalysis.topology.tables.vdwradii:3: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.vdwradii:4: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] docstring of MDAnalysis.topology.tables.vdwradii:7: ERROR: Unexpected indentation. [docutils] docstring of MDAnalysis.topology.tables.vdwradii:8: WARNING: Inline strong start-string without end-string. [docutils] 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... Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/basic.css Writing evaluated template result to /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html/_static/alabaster.css copying static files: done copying extra files... copying extra files: done copying assets: done writing output... 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[100%] index /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.openany:3: WARNING: unknown keyword: 'with' [ref.keyword] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.anyopen:25: WARNING: unknown keyword: 'with' [ref.keyword] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.NamedStream:32: WARNING: unknown keyword: 'with' [ref.keyword] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.NamedStream:67: WARNING: unknown keyword: 'with' [ref.keyword] /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis/build/MDAnalysis/lib/util.py:docstring of MDAnalysis.lib.util.NamedStream:74: WARNING: unknown keyword: 'with' [ref.keyword] generating indices... genindex py-modindex done highlighting module code... 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The HTML pages are in /build/reproducible-path/mdanalysis-2.9.0/.pybuild/html. make[2]: Leaving directory '/build/reproducible-path/mdanalysis-2.9.0/package/doc/sphinx' make[1]: Leaving directory '/build/reproducible-path/mdanalysis-2.9.0' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild plugin_pyproject:178: Copying package built for python3.13 to destdir dh_installdocs -O--buildsystem=pybuild dh_installdocs: warning: Cannot auto-detect main package for python-mdanalysis-doc. If the default is wrong, please use --doc-main-package dh_sphinxdoc -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/mdanalysis-2.9.0' dh_numpy3 Possible precedence issue with control flow operator (return) at /usr/bin/dh_numpy3 line 57. rm -rf debian/python3-mdanalysis/usr/lib/python3.* make[1]: Leaving directory '/build/reproducible-path/mdanalysis-2.9.0' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package python-mdanalysis-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-mdanalysis-dbgsym' in '../python3-mdanalysis-dbgsym_2.9.0-12_arm64.deb'. dpkg-deb: building package 'python3-mdanalysis' in '../python3-mdanalysis_2.9.0-12_arm64.deb'. dpkg-deb: building package 'python-mdanalysis-doc' in '../python-mdanalysis-doc_2.9.0-12_all.deb'. dpkg-genbuildinfo --build=binary -O../mdanalysis_2.9.0-12_arm64.buildinfo dpkg-genchanges --build=binary -O../mdanalysis_2.9.0-12_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from mdanalysis-2.9.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1015473 and its subdirectories I: Current time: Sun Aug 16 02:49:22 -12 2026 I: pbuilder-time-stamp: 1786891762 Mon Jul 14 08:26:27 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Mon Jul 14 08:26:27 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Mon Jul 14 08:32:43 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Mon Jul 14 08:32:44 UTC 2025 I: mdanalysis_2.9.0-12_arm64.changes: Format: 1.8 Date: Thu, 10 Jul 2025 11:07:57 +0200 Source: mdanalysis Binary: python-mdanalysis-doc python3-mdanalysis python3-mdanalysis-dbgsym Architecture: all arm64 Version: 2.9.0-12 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Drew Parsons Description: python-mdanalysis-doc - analyse molecular dynamics files and trajectories ( documentation python3-mdanalysis - analyse molecular dynamics files and trajectories Changes: mdanalysis (2.9.0-12) unstable; urgency=medium . * skip all tests, both build-time and run-time. See Bug#1108309. Checksums-Sha1: 2f8fa2f0ec0e7e25cdf87cea3d275a3bd59486ef 12775 mdanalysis_2.9.0-12_arm64.buildinfo 39e226ddeb3888a98d8c059f16845ae4ff341d4a 3504268 python-mdanalysis-doc_2.9.0-12_all.deb 7c250f0f918f17a6b271332d1749b752ae1e1241 5507980 python3-mdanalysis-dbgsym_2.9.0-12_arm64.deb ba48b5ca49f394512b02f5b9d620310f95d6c551 4147688 python3-mdanalysis_2.9.0-12_arm64.deb Checksums-Sha256: 8cfc3f220aae00934592c23c3771be148af65b6f817066252be5bffd81a2cbab 12775 mdanalysis_2.9.0-12_arm64.buildinfo 3265cce1cd904438f681e64ce97cba2e60a110b9a5c7d882fc5883c1433022c7 3504268 python-mdanalysis-doc_2.9.0-12_all.deb 187ba7e6df2ea8b5ef80d809881cea44081943ff3bef6b050de166c1f2d2b21d 5507980 python3-mdanalysis-dbgsym_2.9.0-12_arm64.deb 4fb90f22a7a696389e75d6e55731b89ac06010d923d4b902d5260126de5e15c9 4147688 python3-mdanalysis_2.9.0-12_arm64.deb Files: 9cffe8f2dd48c22d8ab8dc82c15ea487 12775 python optional mdanalysis_2.9.0-12_arm64.buildinfo ffa6e21739df87e79e9dc6310573dbc8 3504268 doc optional python-mdanalysis-doc_2.9.0-12_all.deb 8dd09530c3f9a283d52fb611022b751b 5507980 debug optional python3-mdanalysis-dbgsym_2.9.0-12_arm64.deb b07bebad3ad50242948153d2f257deae 4147688 python optional python3-mdanalysis_2.9.0-12_arm64.deb Mon Jul 14 08:32:45 UTC 2025 I: diffoscope 301 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_2-102342.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.gkCtXGsg/mdanalysis_2.9.0-12.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.gkCtXGsg/mdanalysis_2.9.0-12.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.gkCtXGsg/mdanalysis_2.9.0-12.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.gkCtXGsg/b1/mdanalysis_2.9.0-12_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.gkCtXGsg/b2/mdanalysis_2.9.0-12_arm64.changes ## close_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer ## command (total time: 0.674s) 0.311s 7 calls diff 0.267s 6 calls xz 0.036s 4 calls cmp 0.036s 4 calls cmp (external) 0.023s 11 calls html2text 0.001s 16 calls cmp (internal) ## compare_files (cumulative) (total time: 4.271s) 1.225s 1 call abc.DotChangesFile 1.176s 1 call abc.DebFile 1.025s 2 calls abc.XzFile 0.700s 1 call abc.DebDataTarFile 0.103s 1 call abc.HtmlFile 0.030s 1 call abc.TarFile 0.013s 1 call abc.Md5sumsFile ## container_extract (total time: 0.526s) 0.267s 6 calls diffoscope.comparators.xz.XzContainer 0.248s 1062 calls diffoscope.comparators.deb.DebTarContainer 0.009s 8 calls diffoscope.comparators.deb.DebContainer 0.002s 6 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 0.329s) 0.329s 11 calls linediff ## has_same_content_as (total time: 0.038s) 0.026s 1 call abc.DebDataTarFile 0.009s 3 calls abc.DebFile 0.002s 1 call abc.HtmlFile 0.000s 4 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 2 calls abc.Md5sumsFile 0.000s 2 calls abc.TextFile 0.000s 1 call diffoscope.comparators.binary.FilesystemFile 0.000s 2 calls abc.XzFile 0.000s 1 call abc.DotChangesFile 0.000s 1 call abc.TarFile ## main (total time: 7.193s) 7.192s 2 calls outputs 0.001s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer ## output (total time: 0.375s) 0.374s 1 call html 0.000s 1 call text 0.000s 1 call json ## recognizes (total time: 0.152s) 0.091s 12 calls diffoscope.comparators.binary.FilesystemFile 0.030s 550 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.017s 162 calls diffoscope.comparators.debian.DebControlMember 0.013s 264 calls diffoscope.comparators.utils.archive.ArchiveMember ## specialize (total time: 5.638s) 5.638s 17 calls specialize Finished with result: success Main processes terminated with: code=exited/status=1 Service runtime: 7.516s CPU time consumed: 2.064s Mon Jul 14 08:32:52 UTC 2025 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Mon Jul 14 08:32:52 UTC 2025 E: mdanalysis failed to build reproducibly in unstable on arm64. Mon Jul 14 08:32:53 UTC 2025 I: Removing signed mdanalysis_2.9.0-12_arm64.buildinfo.asc files: removed './b1/mdanalysis_2.9.0-12_arm64.buildinfo.asc' removed './b2/mdanalysis_2.9.0-12_arm64.buildinfo.asc'