Fri Nov 21 02:35:57 UTC 2025 I: starting to build mdanalysis/forky/amd64 on jenkins on '2025-11-21 02:35' Fri Nov 21 02:35:57 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_36/91913/console.log Fri Nov 21 02:35:57 UTC 2025 I: Downloading source for forky/mdanalysis=2.9.0-12 --2025-11-21 02:35:57-- 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 2025-11-21 02:35:57 (343 MB/s) - ‘mdanalysis_2.9.0-12.dsc’ saved [2945/2945] Fri Nov 21 02:35:57 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----- Fri Nov 21 02:35:57 UTC 2025 I: Checking whether the package is not for us Fri Nov 21 02:35:57 UTC 2025 I: Starting 1st build on remote node infom02-amd64.debian.net. Fri Nov 21 02:35:57 UTC 2025 I: Preparing to do remote build '1' on infom02-amd64.debian.net. Fri Nov 21 02:43:59 UTC 2025 I: Deleting $TMPDIR on infom02-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Dec 23 20:58:59 -12 2026 I: pbuilder-time-stamp: 1798102739 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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/945172/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='96ab2897ffd742b39bda063adcdfcb43' 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='945172' 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.eVkdL12F/pbuilderrc_HjDh --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.eVkdL12F/b1 --logfile b1/build.log mdanalysis_2.9.0-12.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom02-amd64 6.12.57+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.57-1 (2025-11-05) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/945172/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cython3, dh-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 ... 19862 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} libabsl20240722{a} libaec0{a} libaom3{a} libarchive-zip-perl{a} libavif16{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdav1d7{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} libgav1-1{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-mathjax{a} libjs-sphinxdoc{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} libngtcp2-crypto-ossl0{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} librav1e0.8{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libsvtav1enc2{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} libxml2-16{a} libxrender1{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} libyuv0{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-numerals{a} python3-scipy{a} python3-seaborn{a} python3-setuptools{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-numba python3-numexpr python3-odf python3-olefile python3-openpyxl python3-pooch python3-psutil python3-pydot python3-pygraphviz python3-tables shared-mime-info wget xdg-user-dirs 0 packages upgraded, 272 newly installed, 0 to remove and 0 not upgraded. Need to get 211 MB of archives. After unpacking 849 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.3-1 [112 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libpython3.13-minimal amd64 3.13.9-1 [865 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 python3.13-minimal amd64 3.13.9-1 [2257 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 media-types all 14.0.0 [30.8 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 tzdata all 2025b-5 [260 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 libpython3.13-stdlib amd64 3.13.9-1 [1965 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 python3.13 amd64 3.13.9-1 [764 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 python3-numpy-dev amd64 1:2.3.4+ds-3 [138 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 libgfortran5 amd64 15.2.0-7 [862 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 python3-numpy amd64 1:2.3.4+ds-3 [5093 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 openssl amd64 3.5.4-1 [1496 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 ca-certificates all 20250419 [162 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.2-1 [245 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.2-4 [98.5 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-2 [325 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 38 http://deb.debian.org/debian forky/main amd64 automake all 1:1.18.1-2 [877 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.2-1 [772 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1041 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 x11-common all 1:7.7+26 [217 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 51 http://deb.debian.org/debian forky/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 54 http://deb.debian.org/debian forky/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 56 http://deb.debian.org/debian forky/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 libtk8.6 amd64 8.6.17-1 [794 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [591 kB] Get: 64 http://deb.debian.org/debian forky/main amd64 blt amd64 2.5.3+dfsg-8 [5984 B] Get: 65 http://deb.debian.org/debian forky/main amd64 cython3 amd64 3.1.6+dfsg-2 [2349 kB] Get: 66 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.28 [92.4 kB] Get: 67 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-7 [540 kB] Get: 68 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 69 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 70 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 71 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 72 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.194-1 [185 kB] Get: 73 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 74 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 75 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.15.1+dfsg-0.4 [640 kB] Get: 76 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.2-1 [1687 kB] Get: 77 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 78 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 79 http://deb.debian.org/debian forky/main amd64 debhelper all 13.28 [941 kB] Get: 80 http://deb.debian.org/debian forky/main amd64 dh-python all 6.20250414 [116 kB] Get: 81 http://deb.debian.org/debian forky/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 82 http://deb.debian.org/debian forky/main amd64 xml-core all 0.19 [20.1 kB] Get: 83 http://deb.debian.org/debian forky/main amd64 docutils-common all 0.22.3+dfsg-1 [128 kB] Get: 84 http://deb.debian.org/debian forky/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 85 http://deb.debian.org/debian forky/main amd64 fonts-lyx all 2.4.4-2 [190 kB] Get: 86 http://deb.debian.org/debian forky/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 87 http://deb.debian.org/debian forky/main amd64 libabsl20240722 amd64 20240722.0-4 [492 kB] Get: 88 http://deb.debian.org/debian forky/main amd64 libaec0 amd64 1.1.4-2 [23.8 kB] Get: 89 http://deb.debian.org/debian forky/main amd64 libaom3 amd64 3.13.1-2 [1906 kB] Get: 90 http://deb.debian.org/debian forky/main amd64 libdav1d7 amd64 1.5.2-1 [564 kB] Get: 91 http://deb.debian.org/debian forky/main amd64 libgav1-1 amd64 0.19.0-3+b1 [353 kB] Get: 92 http://deb.debian.org/debian forky/main amd64 librav1e0.8 amd64 0.8.1-6 [978 kB] Get: 93 http://deb.debian.org/debian forky/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Get: 94 http://deb.debian.org/debian forky/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 95 http://deb.debian.org/debian forky/main amd64 libyuv0 amd64 0.0.1919.20250919-1 [175 kB] Get: 96 http://deb.debian.org/debian forky/main amd64 libavif16 amd64 1.3.0-1+b1 [137 kB] Get: 97 http://deb.debian.org/debian forky/main amd64 libpixman-1-0 amd64 0.46.4-1 [259 kB] Get: 98 http://deb.debian.org/debian forky/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 99 http://deb.debian.org/debian forky/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 100 http://deb.debian.org/debian forky/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get: 101 http://deb.debian.org/debian forky/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 102 http://deb.debian.org/debian forky/main amd64 libnghttp3-9 amd64 1.12.0-1 [68.4 kB] Get: 103 http://deb.debian.org/debian forky/main amd64 libngtcp2-16 amd64 1.16.0-1 [136 kB] Get: 104 http://deb.debian.org/debian forky/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 105 http://deb.debian.org/debian forky/main amd64 libp11-kit0 amd64 0.25.9-2 [443 kB] Get: 106 http://deb.debian.org/debian forky/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 107 http://deb.debian.org/debian forky/main amd64 libgnutls30t64 amd64 3.8.10-3 [1493 kB] Get: 108 http://deb.debian.org/debian forky/main amd64 libkrb5support0 amd64 1.22.1-2 [33.1 kB] Get: 109 http://deb.debian.org/debian forky/main amd64 libk5crypto3 amd64 1.22.1-2 [81.1 kB] Get: 110 http://deb.debian.org/debian forky/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 111 http://deb.debian.org/debian forky/main amd64 libkrb5-3 amd64 1.22.1-2 [337 kB] Get: 112 http://deb.debian.org/debian forky/main amd64 libgssapi-krb5-2 amd64 1.22.1-2 [139 kB] Get: 113 http://deb.debian.org/debian forky/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-10 [19.8 kB] Get: 114 http://deb.debian.org/debian forky/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-10 [57.8 kB] Get: 115 http://deb.debian.org/debian forky/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 116 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 117 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-gnutls8 amd64 1.16.0-1 [25.2 kB] Get: 118 http://deb.debian.org/debian forky/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 119 http://deb.debian.org/debian forky/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 120 http://deb.debian.org/debian forky/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 121 http://deb.debian.org/debian forky/main amd64 libcurl3t64-gnutls amd64 8.17.0-2 [401 kB] Get: 122 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-ossl0 amd64 1.16.0-1 [27.5 kB] Get: 123 http://deb.debian.org/debian forky/main amd64 libcurl4t64 amd64 8.17.0-2 [409 kB] Get: 124 http://deb.debian.org/debian forky/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 125 http://deb.debian.org/debian forky/main amd64 libexpat1-dev amd64 2.7.3-1 [165 kB] Get: 126 http://deb.debian.org/debian forky/main amd64 libfribidi0 amd64 1.0.16-3 [26.6 kB] Get: 127 http://deb.debian.org/debian forky/main amd64 libgpg-error0 amd64 1.56-2 [89.1 kB] Get: 128 http://deb.debian.org/debian forky/main amd64 libgcrypt20 amd64 1.11.2-3 [871 kB] Get: 129 http://deb.debian.org/debian forky/main amd64 libglib2.0-0t64 amd64 2.86.1-2 [1547 kB] Get: 130 http://deb.debian.org/debian forky/main amd64 libgraphite2-3 amd64 1.3.14-11 [76.7 kB] Get: 131 http://deb.debian.org/debian forky/main amd64 libharfbuzz0b amd64 12.1.0-1 [530 kB] Get: 132 http://deb.debian.org/debian forky/main amd64 libsz2 amd64 1.1.4-2 [8108 B] Get: 133 http://deb.debian.org/debian forky/main amd64 libhdf5-310 amd64 1.14.5+repack-4 [1448 kB] Get: 134 http://deb.debian.org/debian forky/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-4 [72.6 kB] Get: 135 http://deb.debian.org/debian forky/main amd64 libimagequant0 amd64 4.4.0-3 [251 kB] Get: 136 http://deb.debian.org/debian forky/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 137 http://deb.debian.org/debian forky/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Get: 138 http://deb.debian.org/debian forky/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 139 http://deb.debian.org/debian forky/main amd64 libjs-sphinxdoc all 8.2.3-9 [27.7 kB] Get: 140 http://deb.debian.org/debian forky/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 141 http://deb.debian.org/debian forky/main amd64 liblcms2-2 amd64 2.17-1 [163 kB] Get: 142 http://deb.debian.org/debian forky/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 143 http://deb.debian.org/debian forky/main amd64 liblzf1 amd64 3.6-4+b3 [10.1 kB] Get: 144 http://deb.debian.org/debian forky/main amd64 libnetcdf22 amd64 1:4.9.3-1+b1 [517 kB] Get: 145 http://deb.debian.org/debian forky/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [204 kB] Get: 146 http://deb.debian.org/debian forky/main amd64 libpython3.13 amd64 3.13.9-1 [2184 kB] Get: 147 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 148 http://deb.debian.org/debian forky/main amd64 libpython3.13-dev amd64 3.13.9-1 [5311 kB] Get: 149 http://deb.debian.org/debian forky/main amd64 libpython3-dev amd64 3.13.7-1 [10.5 kB] Get: 150 http://deb.debian.org/debian forky/main amd64 libpython3-all-dev amd64 3.13.7-1 [1068 B] Get: 151 http://deb.debian.org/debian forky/main amd64 libqhull-r8.0 amd64 2020.2-7 [248 kB] Get: 152 http://deb.debian.org/debian forky/main amd64 libraqm0 amd64 0.10.3-1 [14.0 kB] Get: 153 http://deb.debian.org/debian forky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 154 http://deb.debian.org/debian forky/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 155 http://deb.debian.org/debian forky/main amd64 libtiff6 amd64 4.7.1-1 [361 kB] Get: 156 http://deb.debian.org/debian forky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 157 http://deb.debian.org/debian forky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 158 http://deb.debian.org/debian forky/main amd64 libxslt1.1 amd64 1.1.43-0.3 [158 kB] Get: 159 http://deb.debian.org/debian forky/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get: 160 http://deb.debian.org/debian forky/main amd64 libzopfli1 amd64 1.0.3-3 [106 kB] Get: 161 http://deb.debian.org/debian forky/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get: 162 http://deb.debian.org/debian forky/main amd64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Get: 163 http://deb.debian.org/debian forky/main amd64 python3-wheel all 0.46.1-2 [21.7 kB] Get: 164 http://deb.debian.org/debian forky/main amd64 python3-build all 1.2.2-4 [36.2 kB] Get: 165 http://deb.debian.org/debian forky/main amd64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 166 http://deb.debian.org/debian forky/main amd64 pybuild-plugin-pyproject all 6.20250414 [11.8 kB] Get: 167 http://deb.debian.org/debian forky/main amd64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 168 http://deb.debian.org/debian forky/main amd64 python-matplotlib-data all 3.10.7+dfsg1-1 [2737 kB] Get: 169 http://deb.debian.org/debian forky/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 170 http://deb.debian.org/debian forky/main amd64 python3-all amd64 3.13.7-1 [1048 B] Get: 171 http://deb.debian.org/debian forky/main amd64 python3.13-dev amd64 3.13.9-1 [504 kB] Get: 172 http://deb.debian.org/debian forky/main amd64 python3-dev amd64 3.13.7-1 [26.1 kB] Get: 173 http://deb.debian.org/debian forky/main amd64 python3-all-dev amd64 3.13.7-1 [1068 B] Get: 174 http://deb.debian.org/debian forky/main amd64 python3-attr all 25.4.0-1 [73.1 kB] Get: 175 http://deb.debian.org/debian forky/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 176 http://deb.debian.org/debian forky/main amd64 python3-babel all 2.17.0-1 [117 kB] Get: 177 http://deb.debian.org/debian forky/main amd64 python3-charset-normalizer amd64 3.4.3-1 [131 kB] Get: 178 http://deb.debian.org/debian forky/main amd64 python3.13-tk amd64 3.13.9-1 [108 kB] Get: 179 http://deb.debian.org/debian forky/main amd64 python3-tk amd64 3.13.9-1 [8688 B] Get: 180 http://deb.debian.org/debian forky/main amd64 python3-pil.imagetk amd64 11.3.0-1 [81.1 kB] Get: 181 http://deb.debian.org/debian forky/main amd64 python3-pil amd64 11.3.0-1 [526 kB] Get: 182 http://deb.debian.org/debian forky/main amd64 python3-cairo amd64 1.27.0-2 [114 kB] Get: 183 http://deb.debian.org/debian forky/main amd64 python3-freetype all 2.5.1-2 [89.4 kB] Get: 184 http://deb.debian.org/debian forky/main amd64 python3-rlpycairo all 0.3.0-4 [10.1 kB] Get: 185 http://deb.debian.org/debian forky/main amd64 python3-reportlab all 4.4.4-2 [1170 kB] Get: 186 http://deb.debian.org/debian forky/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 187 http://deb.debian.org/debian forky/main amd64 python3-biopython amd64 1.86+dfsg-1 [1612 kB] Get: 188 http://deb.debian.org/debian forky/main amd64 python3-brotli amd64 1.1.0-2+b7 [320 kB] Get: 189 http://deb.debian.org/debian forky/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 190 http://deb.debian.org/debian forky/main amd64 python3-cftime amd64 1.6.5-1 [396 kB] Get: 191 http://deb.debian.org/debian forky/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 192 http://deb.debian.org/debian forky/main amd64 python3-lxml amd64 6.0.2-1 [1447 kB] Get: 193 http://deb.debian.org/debian forky/main amd64 python3-citeproc all 0.9.0-1 [100 kB] Get: 194 http://deb.debian.org/debian forky/main amd64 python3-contourpy amd64 1.3.1-2 [215 kB] Get: 195 http://deb.debian.org/debian forky/main amd64 python3-cycler all 0.12.1-2 [9616 B] Get: 196 http://deb.debian.org/debian forky/main amd64 python3-dateutil all 2.9.0-4 [79.4 kB] Get: 197 http://deb.debian.org/debian forky/main amd64 python3-decorator all 5.2.1-2 [33.0 kB] Get: 198 http://deb.debian.org/debian forky/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 199 http://deb.debian.org/debian forky/main amd64 python3-roman-numerals all 3.1.0-2 [8740 B] Get: 200 http://deb.debian.org/debian forky/main amd64 python3-docutils all 0.22.3+dfsg-1 [432 kB] Get: 201 http://deb.debian.org/debian forky/main amd64 python3-looseversion all 1.3.0-3 [8964 B] Get: 202 http://deb.debian.org/debian forky/main amd64 python3-idna all 3.10-1 [42.0 kB] Get: 203 http://deb.debian.org/debian forky/main amd64 python3-urllib3 all 2.5.0-1 [116 kB] Get: 204 http://deb.debian.org/debian forky/main amd64 python3-requests all 2.32.5+dfsg-1 [72.4 kB] Get: 205 http://deb.debian.org/debian forky/main amd64 python3-duecredit all 0.10.2-2 [70.6 kB] Get: 206 http://deb.debian.org/debian forky/main amd64 python3-monotonic all 1.6-3 [5340 B] Get: 207 http://deb.debian.org/debian forky/main amd64 python3-fasteners all 0.19-2 [14.4 kB] Get: 208 http://deb.debian.org/debian forky/main amd64 python3-filelock all 3.20.0-1 [12.6 kB] Get: 209 http://deb.debian.org/debian forky/main amd64 python3-platformdirs all 4.4.0-1 [16.7 kB] Get: 210 http://deb.debian.org/debian forky/main amd64 python3-fs all 2.4.16-9 [95.5 kB] Get: 211 http://deb.debian.org/debian forky/main amd64 python3-lz4 amd64 4.4.4+dfsg-3 [25.6 kB] Get: 212 http://deb.debian.org/debian forky/main amd64 python3-scipy amd64 1.16.3-1 [15.7 MB] Get: 213 http://deb.debian.org/debian forky/main amd64 python3-mpmath all 1.3.0-2 [419 kB] Get: 214 http://deb.debian.org/debian forky/main amd64 python3-sympy all 1.14.0-2 [4228 kB] Get: 215 http://deb.debian.org/debian forky/main amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.0 kB] Get: 216 http://deb.debian.org/debian forky/main amd64 python3-zopfli amd64 0.4.0-1 [10.5 kB] Get: 217 http://deb.debian.org/debian forky/main amd64 unicode-data all 16.0.0-1 [9197 kB] Get: 218 http://deb.debian.org/debian forky/main amd64 python3-fonttools amd64 4.57.0-2 [1457 kB] Get: 219 http://deb.debian.org/debian forky/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1023 kB] Get: 220 http://deb.debian.org/debian forky/main amd64 python3-mrcfile all 1.5.4-2 [118 kB] Get: 221 http://deb.debian.org/debian forky/main amd64 python3-griddataformats all 1.0.2-2 [2048 kB] Get: 222 http://deb.debian.org/debian forky/main amd64 python3-gsd amd64 4.2.0-1 [206 kB] Get: 223 http://deb.debian.org/debian forky/main amd64 python3-h5py-serial amd64 3.15.1-3 [976 kB] Get: 224 http://deb.debian.org/debian forky/main amd64 python3-h5py all 3.15.1-3 [18.8 kB] Get: 225 http://deb.debian.org/debian forky/main amd64 python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 226 http://deb.debian.org/debian forky/main amd64 python3-hypothesis all 6.142.2-1 [364 kB] Get: 227 http://deb.debian.org/debian forky/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 228 http://deb.debian.org/debian forky/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 229 http://deb.debian.org/debian forky/main amd64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 230 http://deb.debian.org/debian forky/main amd64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 231 http://deb.debian.org/debian forky/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 232 http://deb.debian.org/debian forky/main amd64 python3-iniconfig all 2.1.0-1 [7432 B] Get: 233 http://deb.debian.org/debian forky/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 234 http://deb.debian.org/debian forky/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 235 http://deb.debian.org/debian forky/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 236 http://deb.debian.org/debian forky/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 237 http://deb.debian.org/debian forky/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 238 http://deb.debian.org/debian forky/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 239 http://deb.debian.org/debian forky/main amd64 python3-markupsafe amd64 3.0.3-1 [13.8 kB] Get: 240 http://deb.debian.org/debian forky/main amd64 python3-jinja2 all 3.1.6-1 [107 kB] Get: 241 http://deb.debian.org/debian forky/main amd64 python3-joblib all 1.4.2-5 [216 kB] Get: 242 http://deb.debian.org/debian forky/main amd64 python3-kiwisolver amd64 1.4.10~rc0-1 [61.9 kB] Get: 243 http://deb.debian.org/debian forky/main amd64 python3-latexcodec all 3.0.0-1 [17.5 kB] Get: 244 http://deb.debian.org/debian forky/main amd64 python3-pyparsing all 3.1.3-1 [148 kB] Get: 245 http://deb.debian.org/debian forky/main amd64 python3-matplotlib amd64 3.10.7+dfsg1-1 [22.6 MB] Get: 246 http://deb.debian.org/debian forky/main amd64 python3-mda-xdrlib all 0.2.0-3 [11.6 kB] Get: 247 http://deb.debian.org/debian forky/main amd64 python3-msgpack amd64 1.0.3-3+b4 [84.5 kB] Get: 248 http://deb.debian.org/debian forky/main amd64 python3-mmtf all 1.1.3-1 [17.0 kB] Get: 249 http://deb.debian.org/debian forky/main amd64 sphinx-common all 8.2.3-9 [619 kB] Get: 250 http://deb.debian.org/debian forky/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 251 http://deb.debian.org/debian forky/main amd64 python3-snowballstemmer all 3.0.1-1 [63.5 kB] Get: 252 http://deb.debian.org/debian forky/main amd64 python3-sphinx all 8.2.3-9 [477 kB] Get: 253 http://deb.debian.org/debian forky/main amd64 python3-sphinxcontrib.jquery all 4.1-6 [7496 B] Get: 254 http://deb.debian.org/debian forky/main amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-3 [29.7 kB] Get: 255 http://deb.debian.org/debian forky/main amd64 python3-msmb-theme all 1.2.0-4 [33.8 kB] Get: 256 http://deb.debian.org/debian forky/main amd64 python3-netcdf4 amd64 1.7.3-1 [625 kB] Get: 257 http://deb.debian.org/debian forky/main amd64 python3-networkx all 3.4.2-2 [24.2 MB] Get: 258 http://deb.debian.org/debian forky/main amd64 python3-pytz all 2025.2-4 [31.8 kB] Get: 259 http://deb.debian.org/debian forky/main amd64 python3-pandas-lib amd64 2.3.3+dfsg-2 [4362 kB] Get: 260 http://deb.debian.org/debian forky/main amd64 python3-pandas all 2.3.3+dfsg-2 [2935 kB] Get: 261 http://deb.debian.org/debian forky/main amd64 python3-pluggy all 1.6.0-1 [27.1 kB] Get: 262 http://deb.debian.org/debian forky/main amd64 python3-yaml amd64 6.0.2-2 [137 kB] Get: 263 http://deb.debian.org/debian forky/main amd64 python3-pybtex all 0.25.1-1 [75.2 kB] Get: 264 http://deb.debian.org/debian forky/main amd64 python3-pybtex-docutils all 1.0.3-1 [8224 B] Get: 265 http://deb.debian.org/debian forky/main amd64 python3-pytest all 8.4.2-1 [266 kB] Get: 266 http://deb.debian.org/debian forky/main amd64 python3-seaborn all 0.13.2-5 [215 kB] Get: 267 http://deb.debian.org/debian forky/main amd64 python3-sklearn-lib amd64 1.7.2+dfsg-3 [3530 kB] Get: 268 http://deb.debian.org/debian forky/main amd64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 269 http://deb.debian.org/debian forky/main amd64 python3-sklearn all 1.7.2+dfsg-3 [2601 kB] Get: 270 http://deb.debian.org/debian forky/main amd64 python3-sphinx-sitemap all 2.6.0-1 [8508 B] Get: 271 http://deb.debian.org/debian forky/main amd64 python3-sphinxcontrib.bibtex all 2.6.5-3 [33.2 kB] Get: 272 http://deb.debian.org/debian forky/main amd64 python3-tqdm all 4.67.1-6 [90.9 kB] Fetched 211 MB in 5s (41.7 MB/s) Preconfiguring packages ... Selecting previously unselected package fonts-lato. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19862 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.7.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.3-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.9-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.9-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.9-1_amd64.deb ... Unpacking python3.13-minimal (3.13.9-1) ... Setting up libpython3.13-minimal:amd64 (3.13.9-1) ... Setting up libexpat1:amd64 (2.7.3-1) ... Setting up python3.13-minimal (3.13.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20222 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_14.0.0_all.deb ... Unpacking media-types (14.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.9-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.9-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.9-1_amd64.deb ... Unpacking python3.13 (3.13.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21237 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.7-1_amd64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package python3-numpy-dev:amd64. Preparing to unpack .../001-python3-numpy-dev_1%3a2.3.4+ds-3_amd64.deb ... Unpacking python3-numpy-dev:amd64 (1:2.3.4+ds-3) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../002-libblas3_3.12.1-7_amd64.deb ... Unpacking libblas3:amd64 (3.12.1-7) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../003-libgfortran5_15.2.0-7_amd64.deb ... Unpacking libgfortran5:amd64 (15.2.0-7) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../004-liblapack3_3.12.1-7_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-7) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../005-python3-numpy_1%3a2.3.4+ds-3_amd64.deb ... Unpacking python3-numpy (1:2.3.4+ds-3) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../006-libproc2-0_2%3a4.0.4-9_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-9) ... Selecting previously unselected package procps. 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Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../014-gettext-base_0.23.2-1_amd64.deb ... Unpacking gettext-base (0.23.2-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../015-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../016-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../017-bsdextrautils_2.41.2-4_amd64.deb ... Unpacking bsdextrautils (2.41.2-4) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../018-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../019-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... 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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 amd64 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:273:0: 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:300:0: 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-x86_64-cpython-313/MDAnalysis copying MDAnalysis/due.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/authors.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/exceptions.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/units.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis copying MDAnalysis/version.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/results.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/density.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/contacts.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/backends.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/dielectric.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/rdf.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/msd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/atomicdistances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/align.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/rms.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/bat.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/gnm.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/pca.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/psa.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/polymer.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/distances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis creating build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/RDKit.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/converters creating build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/chain.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRC.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/null.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/TNG.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/memory.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates creating build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser copying MDAnalysis/guesser/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser copying MDAnalysis/guesser/tables.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser copying MDAnalysis/guesser/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser copying MDAnalysis/guesser/default_guesser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/guesser creating build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/vmd.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/pymol.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/gromacs.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/charmm.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections copying MDAnalysis/selections/jmol.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/selections creating build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/auxiliary creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/transformations.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/util.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/correlations.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/mdamath.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/log.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_distopia.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/distances.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib creating build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/translate.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/nojump.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/fit.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/rotate.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations copying MDAnalysis/transformations/wrap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/transformations creating build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/selection.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/topology.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/accessors.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/groups.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/_get_readers.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/universe.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core copying MDAnalysis/core/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/core creating build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/base.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/GROParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/core.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/tables.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/guessers.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology creating build/lib.linux-x86_64-cpython-313/MDAnalysis/tests copying MDAnalysis/tests/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/tests copying MDAnalysis/tests/datafiles.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/tests creating build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization copying MDAnalysis/visualization/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/visualization creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp copying MDAnalysis/analysis/dssp/dssp.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp copying MDAnalysis/analysis/dssp/pydssp_numpy.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp copying MDAnalysis/analysis/dssp/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/dssp creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hbonds creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/legacy creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hole2 creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/hydrogenbonds creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis copying MDAnalysis/lib/libmdanalysis/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include copying MDAnalysis/lib/include/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include creating build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations creating build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-x86_64-cpython-313/MDAnalysis/topology/tpr creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source copying doc/sphinx/source/conf.py -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source 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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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 MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/data copying doc/README -> build/lib.linux-x86_64-cpython-313/doc copying MDAnalysis/coordinates/timestep.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/coordinates copying MDAnalysis/lib/_augment.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_augment.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_cutil.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.cpp -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/qcprot.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/lib/qcprot.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/src creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/clustering/include creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/src creating build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/analysis/encore/dimensionality_reduction/include copying MDAnalysis/lib/formats/cython_util.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/libmdanalysis copying MDAnalysis/lib/include/calc_distances.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/include copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/include copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations copying doc/sphinx/Makefile -> build/lib.linux-x86_64-cpython-313/doc/sphinx copying doc/sphinx/source/index.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source copying doc/sphinx/source/references.bib -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/AnalysisBase_parallel.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/RSMD_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/janin_demo_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/janin_ref_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/msd_demo_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/parallelization_time.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/rama_demo_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images copying doc/sphinx/source/images/rama_ref_plot.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/images creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/analysis_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/auxiliary_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/converters.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/coordinates_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/core_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/exceptions.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/guesser_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/lib_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/overview.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/references.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/selections.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/selections_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/topology.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/topology_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/trajectory_transformations.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/units.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/version.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/visualization_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/align.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/atomicdistances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/backends.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/bat.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/contacts.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/data.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/density.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/dielectric.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/diffusionmap.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/dihedrals.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/distances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/dssp.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/encore.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/gnm.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel_deprecated.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/helix_analysis.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hole2.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hydrogenbonds.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/leaflet.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/legacy_modules.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/lineardensity.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/msd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/nucleicacids.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/nuclinfo.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/parallelization.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/pca.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/polymer.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/psa.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/rdf.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/results.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/rms.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/waterdynamics.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/wbridge_analysis.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/OpenMM.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/ParmEd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/RDKit.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/converters creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/CRD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/DCD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/DLPoly.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/DMS.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/FHIAIMS.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/GMS.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/GRO.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/GSD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/H5MD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/INPCRD.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/LAMMPS.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/MMTF.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/MOL2.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/NAMDBIN.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PDB.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PDBQT.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PQR.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TNG.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRC.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRJ.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRR.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRZ.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TXYZ.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XDR.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XTC.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XYZ.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/chain.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/chemfiles.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/core.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/memory.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/null.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/pickle_readers.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/timestep.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/coordinates creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/charmm.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/gromacs.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/jmol.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/pymol.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/vmd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/selections creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/EDR.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/XVG.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/core.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/auxiliary creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/c_distances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/correlations.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/distances.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/log.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/mdamath.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/nsgrid.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/pkdtree.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/qcprot.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/transformations.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/util.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/fit.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/nojump.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/positionaveraging.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/rotate.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/translate.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/wrap.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/transformations creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/tables.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/guesser_modules creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/accessors.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/groups.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/selection.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/topology.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/topologyattrs.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/topologyobjects.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/universe.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/core creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/CRDParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/DMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/GMSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/GROParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/GSDParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/ITPParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/MMTFParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/MinimalParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PDBParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PQRParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PSFParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/TOPParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/TPRParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/TXYZParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/XYZParser.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/base.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/core.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/guessers.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/init.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/tables.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/tpr_util.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/topology creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/streamlines.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/testing_streamline.png -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/visualization creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/confdistmatrix.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/covariance.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/utils.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/encore creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy copying doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/analysis/legacy creating build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats copying doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats copying doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst -> build/lib.linux-x86_64-cpython-313/doc/sphinx/source/documentation_pages/lib/formats running build_ext building 'MDAnalysis.lib.formats.libdcd' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/reproducible-path/mdanalysis-2.9.0/package/MDAnalysis/lib/formats -I/usr/lib/x86_64-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-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.o -std=c11 -O3 -funroll-loops -fsigned-zeros x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/formats/libdcd.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib.c_distances' extension x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-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-x86_64-cpython-313/MDAnalysis/lib/c_distances.o -std=c11 -O3 -funroll-loops -fsigned-zeros x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.o -L/usr/lib/x86_64-linux-gnu -lm -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib.c_distances_openmp' extension x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPARALLEL -I/usr/lib/x86_64-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-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c11 -O3 -funroll-loops -fsigned-zeros x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.o -L/usr/lib/x86_64-linux-gnu -lm -lgomp -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/c_distances_openmp.cpython-313-x86_64-linux-gnu.so -fopenmp building 'MDAnalysis.lib.qcprot' extension x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/lib/qcprot.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.o -std=c11 -O3 -funroll-loops -fsigned-zeros x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdanalysis-2.9.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/MDAnalysis/lib/qcprot.cpython-313-x86_64-linux-gnu.so building 'MDAnalysis.lib._transformations' extension creating build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.linux-x86_64-cpython-313/MDAnalysis/lib/src/transformations/transformations.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from MDAnalysis/lib/src/transformations/transformations.c:73: MDAnalysis/lib/src/transformations/transformations.c: In function 'PyConverter_DoubleArray': MDAnalysis/lib/src/transformations/transformations.c:778:53: error: 'NPY_IN_ARRAY' undeclared (first use in this function) 778 | *address = PyArray_FROM_OTF(object, NPY_DOUBLE, NPY_IN_ARRAY); | ^~~~~~~~~~~~ /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28: note: in definition of macro 'PyArray_FROM_OTF' 91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \ | ^~~~~ MDAnalysis/lib/src/transformations/transformations.c:778:53: note: each undeclared identifier is reported only once for each function it appears in 778 | *address = PyArray_FROM_OTF(object, NPY_DOUBLE, NPY_IN_ARRAY); | ^~~~~~~~~~~~ /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28: note: in definition of macro 'PyArray_FROM_OTF' 91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \ | ^~~~~ MDAnalysis/lib/src/transformations/transformations.c: In function 'PyConverter_AnyDoubleArray': MDAnalysis/lib/src/transformations/transformations.c:794:57: error: 'NPY_ALIGNED' undeclared (first use in this function); did you mean 'Py_ALIGNED'? 794 | *address = PyArray_FROM_OTF(object, NPY_DOUBLE, NPY_ALIGNED); | ^~~~~~~~~~~ /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28: note: in definition of macro 'PyArray_FROM_OTF' 91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \ | ^~~~~ MDAnalysis/lib/src/transformations/transformations.c: In function 'PyConverter_DoubleArrayOrNone': MDAnalysis/lib/src/transformations/transformations.c:811:57: error: 'NPY_IN_ARRAY' undeclared (first use in this function) 811 | *address = PyArray_FROM_OTF(object, NPY_DOUBLE, NPY_IN_ARRAY); | ^~~~~~~~~~~~ /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28: note: in definition of macro 'PyArray_FROM_OTF' 91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \ | ^~~~~ MDAnalysis/lib/src/transformations/transformations.c: In function 'PyConverter_DoubleMatrix44': MDAnalysis/lib/src/transformations/transformations.c:826:53: error: 'NPY_IN_ARRAY' undeclared (first use in this function) 826 | *address = PyArray_FROM_OTF(object, NPY_DOUBLE, NPY_IN_ARRAY); | ^~~~~~~~~~~~ /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28: note: in definition of macro 'PyArray_FROM_OTF' 91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \ | ^~~~~ MDAnalysis/lib/src/transformations/transformations.c: In function 'PyConverter_DoubleMatrix44Copy': MDAnalysis/lib/src/transformations/transformations.c:849:33: error: 'NPY_ENSURECOPY' undeclared (first use in this function) 849 | NPY_ENSURECOPY|NPY_IN_ARRAY); | ^~~~~~~~~~~~~~ /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28: note: in definition of macro 'PyArray_FROM_OTF' 91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \ | ^~~~~ MDAnalysis/lib/src/transformations/transformations.c:849:48: error: 'NPY_IN_ARRAY' undeclared (first use in this function) 849 | NPY_ENSURECOPY|NPY_IN_ARRAY); | ^~~~~~~~~~~~ /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28: note: in definition of macro 'PyArray_FROM_OTF' 91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \ | ^~~~~ MDAnalysis/lib/src/transformations/transformations.c: In function 'PyConverter_DoubleVector3': MDAnalysis/lib/src/transformations/transformations.c:871:53: error: 'NPY_IN_ARRAY' undeclared (first use in this function) 871 | *address = PyArray_FROM_OTF(object, NPY_DOUBLE, NPY_IN_ARRAY); | ^~~~~~~~~~~~ /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28: note: in definition of macro 'PyArray_FROM_OTF' 91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \ | ^~~~~ MDAnalysis/lib/src/transformations/transformations.c: In function 'PyConverter_DoubleVector4': MDAnalysis/lib/src/transformations/transformations.c:893:53: error: 'NPY_IN_ARRAY' undeclared (first use in this function) 893 | *address = PyArray_FROM_OTF(object, NPY_DOUBLE, NPY_IN_ARRAY); | ^~~~~~~~~~~~ /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28: note: in definition of macro 'PyArray_FROM_OTF' 91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \ | ^~~~~ MDAnalysis/lib/src/transformations/transformations.c: In function 'PyConverter_DoubleVector4Copy': MDAnalysis/lib/src/transformations/transformations.c:916:33: error: 'NPY_ENSURECOPY' undeclared (first use in this function) 916 | NPY_ENSURECOPY|NPY_IN_ARRAY); | ^~~~~~~~~~~~~~ /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28: note: in definition of macro 'PyArray_FROM_OTF' 91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \ | ^~~~~ MDAnalysis/lib/src/transformations/transformations.c:916:48: error: 'NPY_IN_ARRAY' undeclared (first use in this function) 916 | NPY_ENSURECOPY|NPY_IN_ARRAY); | ^~~~~~~~~~~~ /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28: note: in definition of macro 'PyArray_FROM_OTF' 91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \ | ^~~~~ MDAnalysis/lib/src/transformations/transformations.c: In function 'PyConverter_DoubleVector3OrNone': MDAnalysis/lib/src/transformations/transformations.c:941:57: error: 'NPY_IN_ARRAY' undeclared (first use in this function) 941 | *address = PyArray_FROM_OTF(object, NPY_DOUBLE, NPY_IN_ARRAY); | ^~~~~~~~~~~~ /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28: note: in definition of macro 'PyArray_FROM_OTF' 91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \ | ^~~~~ MDAnalysis/lib/src/transformations/transformations.c: In function 'py_inverse_matrix': MDAnalysis/lib/src/transformations/transformations.c:3140:48: error: 'NPY_IN_ARRAY' undeclared (first use in this function) 3140 | NPY_IN_ARRAY); | ^~~~~~~~~~~~ /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28: note: in definition of macro 'PyArray_FROM_OTF' 91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \ | ^~~~~ error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1 ERROR Backend subprocess exited when trying to invoke build_wheel E: pybuild pybuild:389: build: plugin pyproject failed with: exit code=1: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis dh_auto_build: error: pybuild --build -i python{version} -p 3.13 returned exit code 13 make: *** [debian/rules:100: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/945172 and its subdirectories Fri Nov 21 02:43:59 UTC 2025 W: No second build log, what happened?