Sat Aug 16 13:29:05 UTC 2025 I: starting to build mdtraj/forky/arm64 on jenkins on '2025-08-16 13:28' Sat Aug 16 13:29:05 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_11/118222/console.log Sat Aug 16 13:29:05 UTC 2025 I: Downloading source for forky/mdtraj=1.11.0-1 --2025-08-16 13:29:05-- http://deb.debian.org/debian/pool/main/m/mdtraj/mdtraj_1.11.0-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2856 (2.8K) [text/prs.lines.tag] Saving to: ‘mdtraj_1.11.0-1.dsc’ 0K .. 100% 359M=0s 2025-08-16 13:29:05 (359 MB/s) - ‘mdtraj_1.11.0-1.dsc’ saved [2856/2856] Sat Aug 16 13:29:05 UTC 2025 I: mdtraj_1.11.0-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: mdtraj Binary: python3-mdtraj, python-mdtraj-doc Architecture: any-amd64 arm64 i386 all Version: 1.11.0-1 Maintainer: Debichem Team Uploaders: Drew Parsons Homepage: https://mdtraj.org/ Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/debichem-team/mdtraj Vcs-Git: https://salsa.debian.org/debichem-team/mdtraj.git Testsuite: autopkgtest Testsuite-Triggers: python3-gsd, python3-ipykernel, python3-jupyter-client, python3-matplotlib, python3-nbformat, python3-netcdf4, python3-packaging, python3-pandas, python3-pytest, python3-pytest-rerunfailures, python3-sklearn Build-Depends: debhelper-compat (= 13), dh-sequence-python3, dh-sequence-numpy3, cython3, python3-setuptools, python3-all-dev, python3-gsd, python3-numpy (>= 2.0.0~), python3-scipy, python3-nbsphinx, python3-nbsphinx-link, python3-netcdf4, python3-networkx, python3-packaging , python3-pandas, python3-pyparsing, python3-pytest , python3-pytest-rerunfailures , python3-sphinx, python3-tables, python3-versioneer, libjs-mathjax Build-Depends-Indep: pandoc, python3-msmb-theme, python3-ipykernel, python3-jupyter-client, python3-matplotlib, python3-nbconvert, python3-nbformat, python3-numpydoc, python3-sklearn Package-List: python-mdtraj-doc deb doc optional arch=all python3-mdtraj deb python optional arch=any-amd64,arm64,i386 Checksums-Sha1: 21e669632e858df798f129cfeb9a9a3d31ccb394 22723159 mdtraj_1.11.0.orig.tar.gz 02855388782c2563201868a1910b1feb3b82b6b5 298656 mdtraj_1.11.0-1.debian.tar.xz Checksums-Sha256: fefca787f882d0716a7aeb01b4d8e30caddbd2be0b2893acfa7201c31d13c786 22723159 mdtraj_1.11.0.orig.tar.gz adea16845a36ab69788ef02c54702a4fb881868452a22766fd4a0e67c93db9a3 298656 mdtraj_1.11.0-1.debian.tar.xz Files: 7ad9ab16d7cbca7b7aee5e88ff440586 22723159 mdtraj_1.11.0.orig.tar.gz 28bce5e968ca2d0bbbac38200c04aadf 298656 mdtraj_1.11.0-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAmiaL5MACgkQVz7x5L1a AfquEBAAoZ7blxVeg575mUvjXD45ruOTzf1qUNYRbeH6dDssWajqrYt1iKVOwjfo y2Av40xqSkovFzQSThIcUl9pILttHuo+FWpiYhkWk4/iu/H98Pirt+soxOQAfu7Q HDV1ZbeP2lz3hJvb65JEPMr6kOKrk3v0AEYVFIo7bBYJ5Ccbz+ZM/cQNzVMREmcB HChE+d0Q1/Fd8twCs3yp9/qOrER43p1zA0eFoq3DrvItLaagxaqnsPnjSqX6op5j RcHLT9GPsmhhCdco+Jn1zEP20DtspWba6dcPECORjHhqRhSA4t9KZVfv1RtWur93 FfP1tZNjUvTvE02Z0GA+DNUJhLjd6gfEi2KuxabPwoye9xwZzSl8Gtj7xhmuxglb r7BfDFzDQTvRx4tExK+QscQTV3IkX273AzLtiN6mL1lwRbtxLrmFW9CPSiaJe4zo 4O905aHoPap8F7noll16KdaOlQamHU+vHsmUsSsedULtLYVEhHZSF36OqabsUeqx 4cazf95FCQzFtIzgfqQtpW/VQxtPfQY58KV8hqHVaTFBsR4t9LpdVCos29n4heBz JBtI7RUQGGBB16fYFMV+N8dv79zqoTm6+Kbp0aNSGTMWYlIcOKzNEXnI7ExOrfn/ 0N8cHQPP/VsW4aaNqDIAOw9DQqbAfZAcE1zwTn6Y9gwmzrEODPI= =gjaZ -----END PGP SIGNATURE----- Sat Aug 16 13:29:05 UTC 2025 I: Checking whether the package is not for us Sat Aug 16 13:29:05 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Sat Aug 16 13:29:05 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Sat Aug 16 13:55:06 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Aug 16 01:29:07 -12 2025 I: pbuilder-time-stamp: 1755350947 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 [mdtraj_1.11.0-1.dsc] I: copying [./mdtraj_1.11.0.orig.tar.gz] I: copying [./mdtraj_1.11.0-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.11.0-1.dsc: no acceptable signature found dpkg-source: info: extracting mdtraj in mdtraj-1.11.0 dpkg-source: info: unpacking mdtraj_1.11.0.orig.tar.gz dpkg-source: info: unpacking mdtraj_1.11.0-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying docs_use_local_mathjax.patch dpkg-source: info: applying build_dir_pybuild.patch dpkg-source: info: applying python_hashbang.patch dpkg-source: info: applying 32bit_skip_image_molecule.patch dpkg-source: info: applying test_relax_tol.patch dpkg-source: info: applying rename-mdconvert-mdtraj.patch dpkg-source: info: applying drop_notebook_in_docs.patch dpkg-source: info: applying test_increase_timeout.patch dpkg-source: info: applying openmm_version_skip.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3339124/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='71d902da7ed441f6aa4155ff832ccb12' 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='3339124' 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.GWNZtOSj/pbuilderrc_JzAc --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.GWNZtOSj/b1 --logfile b1/build.log mdtraj_1.11.0-1.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' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3339124/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, dh-sequence-numpy3, cython3, python3-setuptools, python3-all-dev, python3-gsd, python3-numpy (>= 2.0.0~), python3-scipy, python3-nbsphinx, python3-nbsphinx-link, python3-netcdf4, python3-networkx, python3-packaging, python3-pandas, python3-pyparsing, python3-pytest, python3-pytest-rerunfailures, python3-sphinx, python3-tables, python3-versioneer, libjs-mathjax, pandoc, python3-msmb-theme, python3-ipykernel, python3-jupyter-client, python3-matplotlib, python3-nbconvert, python3-nbformat, python3-numpydoc, python3-sklearn dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19963 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-numpy3; however: Package dh-sequence-numpy3 is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools 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-gsd; however: Package python3-gsd is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy (>= 2.0.0~); however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-nbsphinx; however: Package python3-nbsphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-nbsphinx-link; however: Package python3-nbsphinx-link is not installed. pbuilder-satisfydepends-dummy depends on python3-netcdf4; however: Package python3-netcdf4 is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-packaging; however: Package python3-packaging is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-pyparsing; however: Package python3-pyparsing is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-rerunfailures; however: Package python3-pytest-rerunfailures is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-tables; however: Package python3-tables is not installed. pbuilder-satisfydepends-dummy depends on python3-versioneer; however: Package python3-versioneer is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax is not installed. pbuilder-satisfydepends-dummy depends on pandoc; however: Package pandoc 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-ipykernel; however: Package python3-ipykernel is not installed. pbuilder-satisfydepends-dummy depends on python3-jupyter-client; however: Package python3-jupyter-client is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-nbconvert; however: Package python3-nbconvert is not installed. pbuilder-satisfydepends-dummy depends on python3-nbformat; however: Package python3-nbformat is not installed. pbuilder-satisfydepends-dummy depends on python3-numpydoc; however: Package python3-numpydoc is not installed. pbuilder-satisfydepends-dummy depends on python3-sklearn; however: Package python3-sklearn 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} gdb{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libbabeltrace1{a} libblas3{a} libblosc1{a} libblosc2-4{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdebhelper-perl{a} libdebuginfod-common{a} libdebuginfod1t64{a} libdeflate0{a} libdw1t64{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgcrypt20{a} libgfortran5{a} libglib2.0-0t64{a} libgnutls30t64{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhdf5-310{a} libhdf5-hl-310{a} libidn2-0{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-c5{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} liblua5.4-0{a} liblzo2-2{a} libmagic-mgc{a} libmagic1t64{a} libnetcdf22{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnorm1t64{a} libnuma1{a} libopenjp2-7{a} libp11-kit0{a} libpgm-5.3-0t64{a} libpipeline1{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsnappy1v5{a} libsodium23{a} libsource-highlight-common{a} libsource-highlight4t64{a} libssh2-1t64{a} libsz2{a} libtasn1-6{a} libtcl8.6{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{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} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} libzmq5{a} libzopfli1{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} pandoc{a} pandoc-data{a} po-debconf{a} procps{a} python-babel-localedata{a} python-matplotlib-data{a} python-tables-data{a} python-tinycss2-common{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-asttokens{a} python3-attr{a} python3-autocommand{a} python3-babel{a} python3-bleach{a} python3-brotli{a} python3-bs4{a} python3-certifi{a} python3-cffi-backend{a} python3-cftime{a} python3-chardet{a} python3-charset-normalizer{a} python3-comm{a} python3-contourpy{a} python3-coverage{a} python3-cpuinfo{a} python3-cycler{a} python3-dateutil{a} python3-debugpy{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-executing{a} python3-fastjsonschema{a} python3-fonttools{a} python3-fs{a} python3-gsd{a} python3-html5lib{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-ipykernel{a} python3-ipython{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jedi{a} python3-jinja2{a} python3-joblib{a} python3-jsonschema{a} python3-jsonschema-specifications{a} python3-jupyter-client{a} python3-jupyter-core{a} python3-jupyterlab-pygments{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-markupsafe{a} python3-matplotlib{a} python3-matplotlib-inline{a} python3-minimal{a} python3-mistune{a} python3-more-itertools{a} python3-mpmath{a} python3-msmb-theme{a} python3-nbclient{a} python3-nbconvert{a} python3-nbformat{a} python3-nbsphinx{a} python3-nbsphinx-link{a} python3-nest-asyncio{a} python3-netcdf4{a} python3-networkx{a} python3-numexpr{a} python3-numpy{a} python3-numpy-dev{a} python3-numpydoc{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pandocfilters{a} python3-parso{a} python3-pexpect{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pluggy{a} python3-prompt-toolkit{a} python3-psutil{a} python3-ptyprocess{a} python3-pure-eval{a} python3-pygments{a} python3-pyparsing{a} python3-pytest{a} python3-pytest-rerunfailures{a} python3-pytz{a} python3-referencing{a} python3-requests{a} python3-roman{a} python3-rpds-py{a} python3-scipy{a} python3-setuptools{a} python3-sklearn{a} python3-sklearn-lib{a} python3-snowballstemmer{a} python3-soupsieve{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-sphinxcontrib.jquery{a} python3-stack-data{a} python3-sympy{a} python3-tables{a} python3-tables-lib{a} python3-tabulate{a} python3-threadpoolctl{a} python3-tinycss2{a} python3-tk{a} python3-tornado{a} python3-traitlets{a} python3-typeguard{a} python3-typeshed{a} python3-typing-extensions{a} python3-ufolib2{a} python3-urllib3{a} python3-versioneer{a} python3-wcwidth{a} python3-webencodings{a} python3-zipp{a} python3-zmq{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} ucf{a} unicode-data{a} x11-common{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl 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 psmisc publicsuffix python3-bottleneck python3-cssselect python3-fqdn python3-gdal python3-isoduration python3-json-pointer python3-odf python3-olefile python3-openpyxl python3-pooch python3-pydot python3-pygraphviz python3-rfc3339-validator python3-rfc3986-validator python3-rfc3987 python3-sphinxcontrib.bibtex python3-tz python3-uritemplate python3-webcolors python3-yaml shared-mime-info wget xdg-user-dirs 0 packages upgraded, 299 newly installed, 0 to remove and 0 not upgraded. Need to get 205 MB of archives. After unpacking 1016 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main arm64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian forky/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B] Get: 3 http://deb.debian.org/debian forky/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 4 http://deb.debian.org/debian forky/main arm64 libproc2-0 arm64 2:4.0.4-9 [62.8 kB] Get: 5 http://deb.debian.org/debian forky/main arm64 procps arm64 2:4.0.4-9 [871 kB] Get: 6 http://deb.debian.org/debian forky/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 7 http://deb.debian.org/debian forky/main arm64 ucf all 3.0052 [43.3 kB] Get: 8 http://deb.debian.org/debian forky/main arm64 libdebuginfod-common all 0.192-4 [23.7 kB] Get: 9 http://deb.debian.org/debian forky/main arm64 libexpat1 arm64 2.7.1-2 [93.3 kB] Get: 10 http://deb.debian.org/debian forky/main arm64 libpython3.13-minimal arm64 3.13.5-2 [856 kB] Get: 11 http://deb.debian.org/debian forky/main arm64 python3.13-minimal arm64 3.13.5-2 [2003 kB] Get: 12 http://deb.debian.org/debian forky/main arm64 python3-minimal arm64 3.13.5-1 [27.2 kB] Get: 13 http://deb.debian.org/debian forky/main arm64 media-types all 13.0.0 [29.3 kB] Get: 14 http://deb.debian.org/debian forky/main arm64 netbase all 6.5 [12.4 kB] Get: 15 http://deb.debian.org/debian forky/main arm64 tzdata all 2025b-4 [260 kB] Get: 16 http://deb.debian.org/debian forky/main arm64 libffi8 arm64 3.4.8-2 [21.3 kB] Get: 17 http://deb.debian.org/debian forky/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 18 http://deb.debian.org/debian forky/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 19 http://deb.debian.org/debian forky/main arm64 libpython3.13-stdlib arm64 3.13.5-2 [1892 kB] Get: 20 http://deb.debian.org/debian forky/main arm64 python3.13 arm64 3.13.5-2 [757 kB] Get: 21 http://deb.debian.org/debian forky/main arm64 libpython3-stdlib arm64 3.13.5-1 [10.2 kB] Get: 22 http://deb.debian.org/debian forky/main arm64 python3 arm64 3.13.5-1 [28.2 kB] Get: 23 http://deb.debian.org/debian forky/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1 [136 kB] Get: 24 http://deb.debian.org/debian forky/main arm64 libblas3 arm64 3.12.1-6 [104 kB] Get: 25 http://deb.debian.org/debian forky/main arm64 libgfortran5 arm64 14.2.0-19 [361 kB] Get: 26 http://deb.debian.org/debian forky/main arm64 liblapack3 arm64 3.12.1-6 [1820 kB] Get: 27 http://deb.debian.org/debian forky/main arm64 python3-numpy arm64 1:2.2.4+ds-1 [3604 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 openssl arm64 3.5.1-1 [1457 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 ca-certificates all 20250419 [162 kB] Get: 30 http://deb.debian.org/debian forky/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 31 http://deb.debian.org/debian forky/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 32 http://deb.debian.org/debian forky/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 33 http://deb.debian.org/debian forky/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 34 http://deb.debian.org/debian forky/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 35 http://deb.debian.org/debian forky/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 36 http://deb.debian.org/debian forky/main arm64 bsdextrautils arm64 2.41-5 [93.8 kB] Get: 37 http://deb.debian.org/debian forky/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 38 http://deb.debian.org/debian forky/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 39 http://deb.debian.org/debian forky/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 40 http://deb.debian.org/debian forky/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 41 http://deb.debian.org/debian forky/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 42 http://deb.debian.org/debian forky/main arm64 automake all 1:1.17-4 [862 kB] Get: 43 http://deb.debian.org/debian forky/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 44 http://deb.debian.org/debian forky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [984 kB] Get: 45 http://deb.debian.org/debian forky/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 46 http://deb.debian.org/debian forky/main arm64 libpng16-16t64 arm64 1.6.48-1 [274 kB] Get: 47 http://deb.debian.org/debian forky/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 48 http://deb.debian.org/debian forky/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 49 http://deb.debian.org/debian forky/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 50 http://deb.debian.org/debian forky/main arm64 fontconfig-config arm64 2.15.0-2.3 [318 kB] Get: 51 http://deb.debian.org/debian forky/main arm64 libfontconfig1 arm64 2.15.0-2.3 [387 kB] Get: 52 http://deb.debian.org/debian forky/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 53 http://deb.debian.org/debian forky/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 54 http://deb.debian.org/debian forky/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 55 http://deb.debian.org/debian forky/main arm64 libx11-data all 2:1.8.12-1 [343 kB] Get: 56 http://deb.debian.org/debian forky/main arm64 libx11-6 arm64 2:1.8.12-1 [795 kB] Get: 57 http://deb.debian.org/debian forky/main arm64 libxrender1 arm64 1:0.9.12-1 [27.0 kB] Get: 58 http://deb.debian.org/debian forky/main arm64 libxft2 arm64 2.3.6-1+b4 [51.6 kB] Get: 59 http://deb.debian.org/debian forky/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 60 http://deb.debian.org/debian forky/main arm64 x11-common all 1:7.7+24 [217 kB] Get: 61 http://deb.debian.org/debian forky/main arm64 libxss1 arm64 1:1.2.3-1+b3 [17.1 kB] Get: 62 http://deb.debian.org/debian forky/main arm64 libtk8.6 arm64 8.6.16-1 [741 kB] Get: 63 http://deb.debian.org/debian forky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-8 [537 kB] Get: 64 http://deb.debian.org/debian forky/main arm64 blt arm64 2.5.3+dfsg-8 [5984 B] Get: 65 http://deb.debian.org/debian forky/main arm64 cython3 arm64 3.0.11+dfsg-2+b1 [2255 kB] Get: 66 http://deb.debian.org/debian forky/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 67 http://deb.debian.org/debian forky/main arm64 libtool all 2.5.4-4 [539 kB] Get: 68 http://deb.debian.org/debian forky/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 69 http://deb.debian.org/debian forky/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 70 http://deb.debian.org/debian forky/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 71 http://deb.debian.org/debian forky/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 72 http://deb.debian.org/debian forky/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 73 http://deb.debian.org/debian forky/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 74 http://deb.debian.org/debian forky/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 75 http://deb.debian.org/debian forky/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-2.1 [630 kB] Get: 76 http://deb.debian.org/debian forky/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 77 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 78 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 79 http://deb.debian.org/debian forky/main arm64 debhelper all 13.24.2 [919 kB] Get: 80 http://deb.debian.org/debian forky/main arm64 dh-python all 6.20250414 [116 kB] Get: 81 http://deb.debian.org/debian forky/main arm64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 82 http://deb.debian.org/debian forky/main arm64 xml-core all 0.19 [20.1 kB] Get: 83 http://deb.debian.org/debian forky/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 84 http://deb.debian.org/debian forky/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 85 http://deb.debian.org/debian forky/main arm64 fonts-lyx all 2.4.3-1 [190 kB] Get: 86 http://deb.debian.org/debian forky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 87 http://deb.debian.org/debian forky/main arm64 libdw1t64 arm64 0.192-4 [237 kB] Get: 88 http://deb.debian.org/debian forky/main arm64 libglib2.0-0t64 arm64 2.84.3-1 [1426 kB] Get: 89 http://deb.debian.org/debian forky/main arm64 libbabeltrace1 arm64 1.5.11-4+b2 [164 kB] Get: 90 http://deb.debian.org/debian forky/main arm64 libidn2-0 arm64 2.3.8-2 [107 kB] Get: 91 http://deb.debian.org/debian forky/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 92 http://deb.debian.org/debian forky/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 93 http://deb.debian.org/debian forky/main arm64 libgnutls30t64 arm64 3.8.9-3 [1375 kB] Get: 94 http://deb.debian.org/debian forky/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 95 http://deb.debian.org/debian forky/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get: 96 http://deb.debian.org/debian forky/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 97 http://deb.debian.org/debian forky/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 98 http://deb.debian.org/debian forky/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 99 http://deb.debian.org/debian forky/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 100 http://deb.debian.org/debian forky/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB] Get: 101 http://deb.debian.org/debian forky/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB] Get: 102 http://deb.debian.org/debian forky/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get: 103 http://deb.debian.org/debian forky/main arm64 libnghttp2-14 arm64 1.64.0-1.1 [71.4 kB] Get: 104 http://deb.debian.org/debian forky/main arm64 libnghttp3-9 arm64 1.8.0-1 [63.2 kB] Get: 105 http://deb.debian.org/debian forky/main arm64 libngtcp2-16 arm64 1.11.0-1 [121 kB] Get: 106 http://deb.debian.org/debian forky/main arm64 libngtcp2-crypto-gnutls8 arm64 1.11.0-1 [28.2 kB] Get: 107 http://deb.debian.org/debian forky/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 108 http://deb.debian.org/debian forky/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 109 http://deb.debian.org/debian forky/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 110 http://deb.debian.org/debian forky/main arm64 libcurl3t64-gnutls arm64 8.14.1-2 [353 kB] Get: 111 http://deb.debian.org/debian forky/main arm64 libjson-c5 arm64 0.18+ds-1 [45.2 kB] Get: 112 http://deb.debian.org/debian forky/main arm64 libdebuginfod1t64 arm64 0.192-4 [31.3 kB] Get: 113 http://deb.debian.org/debian forky/main arm64 libpython3.13 arm64 3.13.5-2 [1976 kB] Get: 114 http://deb.debian.org/debian forky/main arm64 libsource-highlight-common all 3.1.9-4.3 [77.5 kB] Get: 115 http://deb.debian.org/debian forky/main arm64 libsource-highlight4t64 arm64 3.1.9-4.3+b1 [294 kB] Get: 116 http://deb.debian.org/debian forky/main arm64 gdb arm64 16.3-1 [4552 kB] Get: 117 http://deb.debian.org/debian forky/main arm64 libaec0 arm64 1.1.3-1+b1 [22.5 kB] Get: 118 http://deb.debian.org/debian forky/main arm64 libsnappy1v5 arm64 1.2.2-1 [28.3 kB] Get: 119 http://deb.debian.org/debian forky/main arm64 libblosc1 arm64 1.21.5+ds-1+b2 [39.2 kB] Get: 120 http://deb.debian.org/debian forky/main arm64 libblosc2-4 arm64 2.17.1+ds-1 [166 kB] Get: 121 http://deb.debian.org/debian forky/main arm64 libcurl4t64 arm64 8.14.1-2 [359 kB] Get: 122 http://deb.debian.org/debian forky/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get: 123 http://deb.debian.org/debian forky/main arm64 libexpat1-dev arm64 2.7.1-2 [145 kB] Get: 124 http://deb.debian.org/debian forky/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 125 http://deb.debian.org/debian forky/main arm64 libgpg-error0 arm64 1.51-4 [78.5 kB] Get: 126 http://deb.debian.org/debian forky/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB] Get: 127 http://deb.debian.org/debian forky/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 128 http://deb.debian.org/debian forky/main arm64 libharfbuzz0b arm64 10.2.0-1+b1 [442 kB] Get: 129 http://deb.debian.org/debian forky/main arm64 libsz2 arm64 1.1.3-1+b1 [8044 B] Get: 130 http://deb.debian.org/debian forky/main arm64 libhdf5-310 arm64 1.14.5+repack-3 [1155 kB] Get: 131 http://deb.debian.org/debian forky/main arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [66.1 kB] Get: 132 http://deb.debian.org/debian forky/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 133 http://deb.debian.org/debian forky/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 134 http://deb.debian.org/debian forky/main arm64 libjpeg62-turbo arm64 1:2.1.5-4 [173 kB] Get: 135 http://deb.debian.org/debian forky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 136 http://deb.debian.org/debian forky/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 137 http://deb.debian.org/debian forky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 138 http://deb.debian.org/debian forky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 139 http://deb.debian.org/debian forky/main arm64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 140 http://deb.debian.org/debian forky/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 141 http://deb.debian.org/debian forky/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 142 http://deb.debian.org/debian forky/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 143 http://deb.debian.org/debian forky/main arm64 liblua5.4-0 arm64 5.4.7-1+b2 [134 kB] Get: 144 http://deb.debian.org/debian forky/main arm64 liblzo2-2 arm64 2.10-3+b1 [49.6 kB] Get: 145 http://deb.debian.org/debian forky/main arm64 libnetcdf22 arm64 1:4.9.3-1 [481 kB] Get: 146 http://deb.debian.org/debian forky/main arm64 libnorm1t64 arm64 1.5.9+dfsg-3.1+b2 [205 kB] Get: 147 http://deb.debian.org/debian forky/main arm64 libnuma1 arm64 2.0.19-1 [21.6 kB] Get: 148 http://deb.debian.org/debian forky/main arm64 libopenjp2-7 arm64 2.5.3-2 [190 kB] Get: 149 http://deb.debian.org/debian forky/main arm64 libpgm-5.3-0t64 arm64 5.3.128~dfsg-2.1+b1 [152 kB] Get: 150 http://deb.debian.org/debian forky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 151 http://deb.debian.org/debian forky/main arm64 libpython3.13-dev arm64 3.13.5-2 [4890 kB] Get: 152 http://deb.debian.org/debian forky/main arm64 libpython3-dev arm64 3.13.5-1 [10.4 kB] Get: 153 http://deb.debian.org/debian forky/main arm64 libpython3-all-dev arm64 3.13.5-1 [1068 B] Get: 154 http://deb.debian.org/debian forky/main arm64 libqhull-r8.0 arm64 2020.2-6+b2 [229 kB] Get: 155 http://deb.debian.org/debian forky/main arm64 libraqm0 arm64 0.10.2-1 [13.6 kB] Get: 156 http://deb.debian.org/debian forky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 157 http://deb.debian.org/debian forky/main arm64 libsodium23 arm64 1.0.18-1+b2 [121 kB] Get: 158 http://deb.debian.org/debian forky/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 159 http://deb.debian.org/debian forky/main arm64 libtiff6 arm64 4.7.0-3 [325 kB] Get: 160 http://deb.debian.org/debian forky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [113 kB] Get: 161 http://deb.debian.org/debian forky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [125 kB] Get: 162 http://deb.debian.org/debian forky/main arm64 libxslt1.1 arm64 1.1.35-1.2 [221 kB] Get: 163 http://deb.debian.org/debian forky/main arm64 libyaml-0-2 arm64 0.2.5-2 [49.2 kB] Get: 164 http://deb.debian.org/debian forky/main arm64 libzmq5 arm64 4.3.5-1+b3 [253 kB] Get: 165 http://deb.debian.org/debian forky/main arm64 libzopfli1 arm64 1.0.3-3 [95.2 kB] Get: 166 http://deb.debian.org/debian forky/main arm64 pandoc-data all 3.1.11.1-3 [459 kB] Get: 167 http://deb.debian.org/debian forky/main arm64 pandoc arm64 3.1.11.1+ds-2 [26.2 MB] Get: 168 http://deb.debian.org/debian forky/main arm64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 169 http://deb.debian.org/debian forky/main arm64 python-matplotlib-data all 3.10.1+dfsg1-4 [2737 kB] Get: 170 http://deb.debian.org/debian forky/main arm64 python-tables-data all 3.10.2-2 [47.3 kB] Get: 171 http://deb.debian.org/debian forky/main arm64 python-tinycss2-common all 1.4.0-2 [44.7 kB] Get: 172 http://deb.debian.org/debian forky/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 173 http://deb.debian.org/debian forky/main arm64 python3-all arm64 3.13.5-1 [1044 B] Get: 174 http://deb.debian.org/debian forky/main arm64 python3.13-dev arm64 3.13.5-2 [505 kB] Get: 175 http://deb.debian.org/debian forky/main arm64 python3-dev arm64 3.13.5-1 [26.1 kB] Get: 176 http://deb.debian.org/debian forky/main arm64 python3-all-dev arm64 3.13.5-1 [1068 B] Get: 177 http://deb.debian.org/debian forky/main arm64 python3-asttokens all 3.0.0-1 [20.1 kB] Get: 178 http://deb.debian.org/debian forky/main arm64 python3-attr all 25.3.0-1 [69.5 kB] Get: 179 http://deb.debian.org/debian forky/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 180 http://deb.debian.org/debian forky/main arm64 python3-babel all 2.17.0-1 [117 kB] Get: 181 http://deb.debian.org/debian forky/main arm64 python3-webencodings all 0.5.1-5 [11.1 kB] Get: 182 http://deb.debian.org/debian forky/main arm64 python3-html5lib all 1.2-2 [92.1 kB] Get: 183 http://deb.debian.org/debian forky/main arm64 python3-bleach all 6.2.0-1 [51.2 kB] Get: 184 http://deb.debian.org/debian forky/main arm64 python3-brotli arm64 1.1.0-2+b7 [300 kB] Get: 185 http://deb.debian.org/debian forky/main arm64 python3-soupsieve all 2.7-1 [39.0 kB] Get: 186 http://deb.debian.org/debian forky/main arm64 python3-typing-extensions all 4.13.2-1 [90.5 kB] Get: 187 http://deb.debian.org/debian forky/main arm64 python3-bs4 all 4.13.4-2 [167 kB] Get: 188 http://deb.debian.org/debian forky/main arm64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 189 http://deb.debian.org/debian forky/main arm64 python3-cffi-backend arm64 1.17.1-3 [93.0 kB] Get: 190 http://deb.debian.org/debian forky/main arm64 python3-cftime arm64 1.6.4-2 [183 kB] Get: 191 http://deb.debian.org/debian forky/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 192 http://deb.debian.org/debian forky/main arm64 python3-charset-normalizer arm64 3.4.2-1 [120 kB] Get: 193 http://deb.debian.org/debian forky/main arm64 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB] Get: 194 http://deb.debian.org/debian forky/main arm64 python3-comm all 0.2.1-1 [8104 B] Get: 195 http://deb.debian.org/debian forky/main arm64 python3-contourpy arm64 1.3.1-1+b1 [190 kB] Get: 196 http://deb.debian.org/debian forky/main arm64 python3-coverage arm64 7.8.2+dfsg1-1 [182 kB] Get: 197 http://deb.debian.org/debian forky/main arm64 python3-cpuinfo all 9.0.0+git20221119-3 [23.5 kB] Get: 198 http://deb.debian.org/debian forky/main arm64 python3-cycler all 0.12.1-1 [9496 B] Get: 199 http://deb.debian.org/debian forky/main arm64 python3-dateutil all 2.9.0-4 [79.4 kB] Get: 200 http://deb.debian.org/debian forky/main arm64 python3-debugpy arm64 1.8.12+ds-1 [692 kB] Get: 201 http://deb.debian.org/debian forky/main arm64 python3-decorator all 5.2.1-2 [33.0 kB] Get: 202 http://deb.debian.org/debian forky/main arm64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 203 http://deb.debian.org/debian forky/main arm64 python3-roman all 5.0-1 [10.6 kB] Get: 204 http://deb.debian.org/debian forky/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 205 http://deb.debian.org/debian forky/main arm64 python3-executing all 2.2.0-0.1 [24.5 kB] Get: 206 http://deb.debian.org/debian forky/main arm64 python3-fastjsonschema all 2.21.1-1 [22.4 kB] Get: 207 http://deb.debian.org/debian forky/main arm64 python3-platformdirs all 4.3.7-1 [16.6 kB] Get: 208 http://deb.debian.org/debian forky/main arm64 python3-fs all 2.4.16-7 [95.2 kB] Get: 209 http://deb.debian.org/debian forky/main arm64 python3-lxml arm64 5.4.0-1 [1139 kB] Get: 210 http://deb.debian.org/debian forky/main arm64 python3-lz4 arm64 4.4.0+dfsg-2 [25.3 kB] Get: 211 http://deb.debian.org/debian forky/main arm64 python3-scipy arm64 1.15.3-1 [14.9 MB] Get: 212 http://deb.debian.org/debian forky/main arm64 python3-mpmath all 1.3.0-1 [419 kB] Get: 213 http://deb.debian.org/debian forky/main arm64 python3-sympy all 1.13.3-5 [4148 kB] Get: 214 http://deb.debian.org/debian forky/main arm64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.0 kB] Get: 215 http://deb.debian.org/debian forky/main arm64 python3-zopfli arm64 0.2.3.post1-1 [10.2 kB] Get: 216 http://deb.debian.org/debian forky/main arm64 unicode-data all 15.1.0-1 [8547 kB] Get: 217 http://deb.debian.org/debian forky/main arm64 python3-fonttools arm64 4.57.0-1 [1366 kB] Get: 218 http://deb.debian.org/debian forky/main arm64 python3-gsd arm64 3.4.2-2+b1 [200 kB] Get: 219 http://deb.debian.org/debian forky/main arm64 python3-idna all 3.10-1 [42.0 kB] Get: 220 http://deb.debian.org/debian forky/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 221 http://deb.debian.org/debian forky/main arm64 python3-more-itertools all 10.7.0-1 [67.4 kB] Get: 222 http://deb.debian.org/debian forky/main arm64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 223 http://deb.debian.org/debian forky/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 224 http://deb.debian.org/debian forky/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 225 http://deb.debian.org/debian forky/main arm64 python3-parso all 0.8.4-1 [67.8 kB] Get: 226 http://deb.debian.org/debian forky/main arm64 python3-typeshed all 0.0~git20241223.ea91db2-3 [1531 kB] Get: 227 http://deb.debian.org/debian forky/main arm64 python3-jedi all 0.19.1+ds1-1 [691 kB] Get: 228 http://deb.debian.org/debian forky/main arm64 python3-matplotlib-inline all 0.1.7-1 [9032 B] Get: 229 http://deb.debian.org/debian forky/main arm64 python3-wcwidth all 0.2.13+dfsg1-1 [24.9 kB] Get: 230 http://deb.debian.org/debian forky/main arm64 python3-prompt-toolkit all 3.0.51-2 [278 kB] Get: 231 http://deb.debian.org/debian forky/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 232 http://deb.debian.org/debian forky/main arm64 python3-pure-eval all 0.2.3-1 [11.2 kB] Get: 233 http://deb.debian.org/debian forky/main arm64 python3-stack-data all 0.6.3-1 [21.6 kB] Get: 234 http://deb.debian.org/debian forky/main arm64 python3-ptyprocess all 0.7.0-6 [14.5 kB] Get: 235 http://deb.debian.org/debian forky/main arm64 python3-pexpect all 4.9-3 [55.6 kB] Get: 236 http://deb.debian.org/debian forky/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 237 http://deb.debian.org/debian forky/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 238 http://deb.debian.org/debian forky/main arm64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 239 http://deb.debian.org/debian forky/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 240 http://deb.debian.org/debian forky/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 241 http://deb.debian.org/debian forky/main arm64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 242 http://deb.debian.org/debian forky/main arm64 python3-ipython all 8.35.0-1 [576 kB] Get: 243 http://deb.debian.org/debian forky/main arm64 python3-jupyter-core all 5.7.2-5 [35.3 kB] Get: 244 http://deb.debian.org/debian forky/main arm64 python3-psutil arm64 7.0.0-2 [220 kB] Get: 245 http://deb.debian.org/debian forky/main arm64 python3-tornado arm64 6.4.2-3 [350 kB] Get: 246 http://deb.debian.org/debian forky/main arm64 python3-zmq arm64 26.4.0-1 [163 kB] Get: 247 http://deb.debian.org/debian forky/main arm64 python3-jupyter-client all 8.6.3-2 [92.4 kB] Get: 248 http://deb.debian.org/debian forky/main arm64 python3-nest-asyncio all 1.5.4-1 [6248 B] Get: 249 http://deb.debian.org/debian forky/main arm64 python3-packaging all 25.0-1 [56.6 kB] Get: 250 http://deb.debian.org/debian forky/main arm64 python3-ipykernel all 6.29.5-2 [102 kB] Get: 251 http://deb.debian.org/debian forky/main arm64 python3-markupsafe arm64 2.1.5-1+b4 [14.1 kB] Get: 252 http://deb.debian.org/debian forky/main arm64 python3-jinja2 all 3.1.6-1 [107 kB] Get: 253 http://deb.debian.org/debian forky/main arm64 python3-joblib all 1.4.2-4 [216 kB] Get: 254 http://deb.debian.org/debian forky/main arm64 python3-rpds-py arm64 0.21.0-2+b1 [226 kB] Get: 255 http://deb.debian.org/debian forky/main arm64 python3-referencing all 0.36.2-1 [23.7 kB] Get: 256 http://deb.debian.org/debian forky/main arm64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B] Get: 257 http://deb.debian.org/debian forky/main arm64 python3-jsonschema all 4.19.2-6 [71.4 kB] Get: 258 http://deb.debian.org/debian forky/main arm64 python3-jupyterlab-pygments all 0.2.2-3 [6096 B] Get: 259 http://deb.debian.org/debian forky/main arm64 python3-kiwisolver arm64 1.4.7-3+b1 [57.8 kB] Get: 260 http://deb.debian.org/debian forky/main arm64 python3-pil arm64 11.1.0-5+b1 [495 kB] Get: 261 http://deb.debian.org/debian forky/main arm64 python3.13-tk arm64 3.13.5-2 [105 kB] Get: 262 http://deb.debian.org/debian forky/main arm64 python3-tk arm64 3.13.5-1 [9604 B] Get: 263 http://deb.debian.org/debian forky/main arm64 python3-pil.imagetk arm64 11.1.0-5+b1 [81.8 kB] Get: 264 http://deb.debian.org/debian forky/main arm64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 265 http://deb.debian.org/debian forky/main arm64 python3-matplotlib arm64 3.10.1+dfsg1-4 [23.7 MB] Get: 266 http://deb.debian.org/debian forky/main arm64 python3-mistune all 3.1.3-1 [35.5 kB] Get: 267 http://deb.debian.org/debian forky/main arm64 sphinx-common all 8.1.3-5 [617 kB] Get: 268 http://deb.debian.org/debian forky/main arm64 python3-urllib3 all 2.3.0-3 [115 kB] Get: 269 http://deb.debian.org/debian forky/main arm64 python3-requests all 2.32.3+dfsg-5 [72.2 kB] Get: 270 http://deb.debian.org/debian forky/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 271 http://deb.debian.org/debian forky/main arm64 python3-sphinx all 8.1.3-5 [468 kB] Get: 272 http://deb.debian.org/debian forky/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1023 kB] Get: 273 http://deb.debian.org/debian forky/main arm64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 274 http://deb.debian.org/debian forky/main arm64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [29.7 kB] Get: 275 http://deb.debian.org/debian forky/main arm64 python3-msmb-theme all 1.2.0-4 [33.8 kB] Get: 276 http://deb.debian.org/debian forky/main arm64 python3-nbformat all 5.9.1-1 [45.1 kB] Get: 277 http://deb.debian.org/debian forky/main arm64 python3-nbclient all 0.8.0-2 [62.2 kB] Get: 278 http://deb.debian.org/debian forky/main arm64 python3-tinycss2 all 1.4.0-2 [25.0 kB] Get: 279 http://deb.debian.org/debian forky/main arm64 python3-pandocfilters all 1.5.1-1 [23.7 kB] Get: 280 http://deb.debian.org/debian forky/main arm64 python3-nbconvert all 7.16.6-1 [160 kB] Get: 281 http://deb.debian.org/debian forky/main arm64 python3-nbsphinx all 0.9.5+ds-1 [39.9 kB] Get: 282 http://deb.debian.org/debian forky/main arm64 python3-nbsphinx-link all 1.3.0-4 [6264 B] Get: 283 http://deb.debian.org/debian forky/main arm64 python3-netcdf4 arm64 1.7.2-1+b5 [542 kB] Get: 284 http://deb.debian.org/debian forky/main arm64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 285 http://deb.debian.org/debian forky/main arm64 python3-numexpr arm64 2.11.0-1 [125 kB] Get: 286 http://deb.debian.org/debian forky/main arm64 python3-tabulate all 0.9.0-1 [45.9 kB] Get: 287 http://deb.debian.org/debian forky/main arm64 python3-numpydoc all 1.8.0-1 [51.4 kB] Get: 288 http://deb.debian.org/debian forky/main arm64 python3-pytz all 2025.2-3 [152 kB] Get: 289 http://deb.debian.org/debian forky/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-9 [3877 kB] Get: 290 http://deb.debian.org/debian forky/main arm64 python3-pandas all 2.2.3+dfsg-9 [3097 kB] Get: 291 http://deb.debian.org/debian forky/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 292 http://deb.debian.org/debian forky/main arm64 python3-pytest all 8.3.5-2 [250 kB] Get: 293 http://deb.debian.org/debian forky/main arm64 python3-pytest-rerunfailures all 15.0-1 [16.8 kB] Get: 294 http://deb.debian.org/debian forky/main arm64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 295 http://deb.debian.org/debian forky/main arm64 python3-sklearn-lib arm64 1.4.2+dfsg-8 [3408 kB] Get: 296 http://deb.debian.org/debian forky/main arm64 python3-sklearn all 1.4.2+dfsg-8 [2248 kB] Get: 297 http://deb.debian.org/debian forky/main arm64 python3-tables-lib arm64 3.10.2-2+b1 [427 kB] Get: 298 http://deb.debian.org/debian forky/main arm64 python3-tables all 3.10.2-2 [353 kB] Get: 299 http://deb.debian.org/debian forky/main arm64 python3-versioneer all 0.29-1 [43.0 kB] Fetched 205 MB in 2s (103 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 ... 19963 files and directories currently installed.) Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libtext-charwidth-perl:arm64. Preparing to unpack .../01-libtext-charwidth-perl_0.04-11+b4_arm64.deb ... Unpacking libtext-charwidth-perl:arm64 (0.04-11+b4) ... 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(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 ... 20594 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.5-1_arm64.deb ... Unpacking python3-minimal (3.13.5-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... 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/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.5-2_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.5-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.5-2_arm64.deb ... Unpacking python3.13 (3.13.5-2) ... 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Selecting previously unselected package python3-numpy-dev:arm64. Preparing to unpack .../001-python3-numpy-dev_1%3a2.2.4+ds-1_arm64.deb ... Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../002-libblas3_3.12.1-6_arm64.deb ... Unpacking libblas3:arm64 (3.12.1-6) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../003-libgfortran5_14.2.0-19_arm64.deb ... Unpacking libgfortran5:arm64 (14.2.0-19) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../004-liblapack3_3.12.1-6_arm64.deb ... Unpacking liblapack3:arm64 (3.12.1-6) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../005-python3-numpy_1%3a2.2.4+ds-1_arm64.deb ... Unpacking python3-numpy (1:2.2.4+ds-1) ... Selecting previously unselected package openssl. Preparing to unpack .../006-openssl_3.5.1-1_arm64.deb ... Unpacking openssl (3.5.1-1) ... 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Setting up libyaml-0-2:arm64 (0.2.5-2) ... Setting up fonts-lyx (2.4.3-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libbrotli1:arm64 (1.1.0-2+b7) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up x11-common (1:7.7+24) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:arm64 (1.64.0-1.1) ... Setting up libdeflate0:arm64 (1.23-2) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up libgcrypt20:arm64 (1.11.0-7) ... Setting up libqhull-r8.0:arm64 (2020.2-6+b2) ... Setting up liblzo2-2:arm64 (2.10-3+b1) ... Setting up libcom-err2:arm64 (1.47.2-3+b3) ... Setting up file (1:5.46-5) ... Setting up libtext-wrapi18n-perl (0.06-10) ... Setting up libjbig0:arm64 (2.1-6.1+b2) ... Setting up libaec0:arm64 (1.1.3-1+b1) ... Setting up libsource-highlight-common (3.1.9-4.3) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up python-babel-localedata (2.17.0-1) ... Setting up libsnappy1v5:arm64 (1.2.2-1) ... Setting up libkrb5support0:arm64 (1.21.3-5) ... Setting up libdw1t64:arm64 (0.192-4) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-9) ... Setting up tzdata (2025b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Aug 16 13:30:18 UTC 2025. Universal Time is now: Sat Aug 16 13:30:18 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... Setting up libpgm-5.3-0t64:arm64 (5.3.128~dfsg-2.1+b1) ... Setting up libblosc2-4:arm64 (2.17.1+ds-1) ... Setting up autotools-dev (20240727.1) ... Setting up libblas3:arm64 (3.12.1-6) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libexpat1-dev:arm64 (2.7.1-2) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-4) ... Setting up libzopfli1 (1.0.3-3) ... 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Setting up libtiff6:arm64 (4.7.0-3) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-9) ... Setting up python-tinycss2-common (1.4.0-2) ... Setting up libjson-perl (4.10000-1) ... Setting up libblosc1:arm64 (1.21.5+ds-1+b2) ... Setting up libtasn1-6:arm64 (4.20.0-2) ... Setting up liblua5.4-0:arm64 (5.4.7-1+b2) ... Setting up libopenjp2-7:arm64 (2.5.3-2) ... Setting up libx11-6:arm64 (2:1.8.12-1) ... Setting up netbase (6.5) ... Setting up libngtcp2-16:arm64 (1.11.0-1) ... Setting up sgml-base (1.31+nmu1) ... Setting up libkrb5-3:arm64 (1.21.3-5) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up pandoc-data (3.1.11.1-3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.10.1+dfsg1-4) ... Setting up openssl (3.5.1-1) ... Setting up libwebpmux3:arm64 (1.5.0-0.1) ... Setting up libjson-c5:arm64 (0.18+ds-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up python-tables-data (3.10.2-2) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (3.0.2+dfsg-2) ... Setting up libldap2:arm64 (2.6.10+dfsg-1) ... Setting up libsz2:arm64 (1.1.3-1+b1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:arm64 (3.12.1-6) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.23.1-2) ... Setting up libxrender1:arm64 (1:0.9.12-1) ... Setting up libtool (2.5.4-4) ... Setting up fontconfig-config (2.15.0-2.3) ... Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... Setting up libxext6:arm64 (2:1.3.4-1+b3) ... Setting up libidn2-0:arm64 (2.3.8-2) ... Setting up libsource-highlight4t64:arm64 (3.1.9-4.3+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up libglib2.0-0t64:arm64 (2.84.3-1) ... No schema files found: doing nothing. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up pandoc (3.1.11.1+ds-2) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-5) ... Setting up ucf (3.0052) ... Setting up libbabeltrace1:arm64 (1.5.11-4+b2) ... Setting up libjs-sphinxdoc (8.1.3-5) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:arm64 (1.1.35-1.2) ... Setting up libharfbuzz0b:arm64 (10.2.0-1+b1) ... Setting up libxss1:arm64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:arm64 (2.15.0-2.3) ... Setting up libpython3.13-stdlib:arm64 (3.13.5-2) ... Setting up libpython3-stdlib:arm64 (3.13.5-1) ... Setting up libpython3.13:arm64 (3.13.5-2) ... Setting up libgnutls30t64:arm64 (3.8.9-3) ... Setting up libxft2:arm64 (2.3.6-1+b4) ... Setting up libzmq5:arm64 (4.3.5-1+b3) ... Setting up libdebuginfod-common (0.192-4) ... Setting up python3.13 (3.13.5-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:arm64 (8.6.16-1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.5-1) ... Setting up python3-pandocfilters (1.5.1-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-markupsafe (2.1.5-1+b4) ... Setting up python3-webencodings (0.5.1-5) ... Setting up python3.13-tk (3.13.5-2) ... Setting up python3-platformdirs (4.3.7-1) ... Setting up python3-psutil (7.0.0-2) ... Setting up python3-zopfli (0.2.3.post1-1) ... Setting up python3-fs (2.4.16-7) ... Setting up python3-roman (5.0-1) ... Setting up python3-decorator (5.2.1-2) ... Setting up python3-jinja2 (3.1.6-1) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up python3-packaging (25.0-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-wcwidth (0.2.13+dfsg1-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-certifi (2025.1.31+ds-1) ... Setting up python3-typeshed (0.0~git20241223.ea91db2-3) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up python3-nest-asyncio (1.5.4-1) ... Setting up python3-brotli (1.1.0-2+b7) ... Setting up libraqm0:arm64 (0.10.2-1) ... Setting up libpython3.13-dev:arm64 (3.13.5-2) ... Setting up sphinx-common (8.1.3-5) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.7-3+b1) ... Setting up python3-idna (3.10-1) ... Setting up cython3 (3.0.11+dfsg-2+b1) ... Setting up python3-typing-extensions (4.13.2-1) ... Setting up python3-cpuinfo (9.0.0+git20221119-3) ... Setting up python3-html5lib (1.2-2) ... Setting up python3-numpy (1:2.2.4+ds-1) ... Setting up python3-urllib3 (2.3.0-3) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-rpds-py (0.21.0-2+b1) ... Setting up python3-fastjsonschema (2.21.1-1) ... Setting up python3-lxml:arm64 (5.4.0-1) ... Setting up python3-traitlets (5.14.3+really5.14.3-1) ... Setting up python3-dateutil (2.9.0-4) ... Setting up python3-contourpy (1.3.1-1+b1) ... Setting up python3-versioneer (0.29-1) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-mistune (3.1.3-1) ... Setting up python3-soupsieve (2.7-1) ... Setting up python3-jupyter-core (5.7.2-5) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.11.0-1) ... Setting up python3-cffi-backend:arm64 (1.17.1-3) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-ptyprocess (0.7.0-6) ... Setting up python3-prompt-toolkit (3.0.51-2) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.7.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sympy (1.13.3-5) ... Setting up python3-attr (25.3.0-1) ... Setting up python3-tornado (6.4.2-3) ... Setting up python3-pure-eval (0.2.3-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... Setting up python3-tinycss2 (1.4.0-2) ... Setting up python3-scipy (1.15.3-1) ... Setting up libpython3-dev:arm64 (3.13.5-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up libcurl4t64:arm64 (8.14.1-2) ... Setting up python3-joblib (1.4.2-4) ... Setting up python3-parso (0.8.4-1) ... Setting up python3-babel (2.17.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-lz4 (4.4.0+dfsg-2) ... Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-asttokens (3.0.0-1) ... Setting up python3-charset-normalizer (3.4.2-1) ... Setting up python3.13-dev (3.13.5-2) ... Setting up python3-pytest (8.3.5-2) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up blt (2.5.3+dfsg-8) ... Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-9) ... Setting up python3-typeguard (4.4.2-1) ... Setting up python3-threadpoolctl (3.1.0-1) ... Setting up libcurl3t64-gnutls:arm64 (8.14.1-2) ... Setting up python3-sklearn-lib:arm64 (1.4.2+dfsg-8) ... Setting up python3-tabulate (0.9.0-1) ... Setting up python3-all (3.13.5-1) ... Setting up python3-coverage (7.8.2+dfsg1-1) ... Setting up python3-tk:arm64 (3.13.5-1) ... Setting up debhelper (13.24.2) ... Setting up python3-gsd (3.4.2-2+b1) ... Setting up python3-pytz (2025.2-3) ... Setting up python3-bs4 (4.13.4-2) ... Setting up python3-bleach (6.2.0-1) ... Setting up python3-matplotlib-inline (0.1.7-1) ... Setting up python3-comm (0.2.1-1) ... Setting up python3-jupyterlab-pygments (0.2.2-3) ... Setting up python3-pil:arm64 (11.1.0-5+b1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pandas (2.2.3+dfsg-9) ... Setting up python3-pil.imagetk:arm64 (11.1.0-5+b1) ... Setting up python3-executing (2.2.0-0.1) ... Setting up libpython3-all-dev:arm64 (3.13.5-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pexpect (4.9-3) ... Setting up python3-zmq (26.4.0-1) ... Setting up python3-dev (3.13.5-1) ... Setting up python3-requests (2.32.3+dfsg-5) ... Setting up python3-sklearn (1.4.2+dfsg-8) ... Setting up python3-cftime (1.6.4-2) ... Setting up python3-numexpr (2.11.0-1) ... Setting up libhdf5-310:arm64 (1.14.5+repack-3) ... Setting up python3-jupyter-client (8.6.3-2) ... Setting up python3-stack-data (0.6.3-1) ... Setting up python3-referencing (0.36.2-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-all-dev (3.13.5-1) ... Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3) ... Setting up libdebuginfod1t64:arm64 (0.192-4) ... Setting up python3-pytest-rerunfailures (15.0-1) ... Setting up python3-setuptools (78.1.1-0.1) ... Setting up python3-jedi (0.19.1+ds1-1) ... Setting up python3-tables-lib (3.10.2-2+b1) ... Setting up libnetcdf22:arm64 (1:4.9.3-1) ... Setting up python3-tables (3.10.2-2) ... Setting up python3-networkx (3.2.1-5) ... Setting up gdb (16.3-1) ... Setting up python3-ipython (8.35.0-1) ... Setting up python3-jsonschema-specifications (2023.12.1-2) ... Setting up python3-netcdf4 (1.7.2-1+b5) ... Setting up python3-debugpy (1.8.12+ds-1) ... Setting up python3-jsonschema (4.19.2-6) ... Setting up python3-ipykernel (6.29.5-2) ... Setting up python3-nbformat (5.9.1-1) ... Setting up python3-nbclient (0.8.0-2) ... Setting up python3-nbconvert (7.16.6-1) ... Setting up python3-fonttools (4.57.0-1) ... Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... Setting up python3-matplotlib (3.10.1+dfsg1-4) ... Processing triggers for libc-bin (2.41-12) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.1.3-5) ... Setting up python3-nbsphinx (0.9.5+ds-1) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-numpydoc (1.8.0-1) ... Setting up python3-nbsphinx-link (1.3.0-4) ... Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... Setting up python3-msmb-theme (1.2.0-4) ... Processing triggers for ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/mdtraj-1.11.0/ && 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 > ../mdtraj_1.11.0-1_source.changes dpkg-buildpackage: info: source package mdtraj dpkg-buildpackage: info: source version 1.11.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Drew Parsons dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 dpkg-source: info: using options from mdtraj-1.11.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild pybuild --clean -i python{version} -p 3.13 I: pybuild base:311: python3.13 setup.py clean Using built-in specs. COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/14/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-19) /build/reproducible-path/mdtraj-1.11.0/basesetup.py:483: UserWarning: Unrecognized setuptools command ('clean'), proceeding with generating Cython sources and expanding templates warnings.warn( warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired. Possible solutions: 1. Declare 'make_whole' 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 'make_whole' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired. Possible solutions: 1. Declare 'anchor_dists' 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 'anchor_dists' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired. Possible solutions: 1. Declare 'wrap_mols' 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 'wrap_mols' to allow an error code to be returned. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE2 support... Did not detect SSE2 support Attempting to autodetect SSE3 support... Did not detect SSE3 support Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support Attempting to autodetect NEON support... Compiler supports NEON [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx [ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 5/10] Cythonizing mdtraj/geometry/drid.pyx [ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx /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 v2 or later (LGPLv2+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running clean removing '/build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/mdtraj-1.11.0' for f in mdtraj/formats/binpos/binpos.c \ mdtraj/formats/dcd/dcd.c \ mdtraj/formats/dtr/dtr.cpp \ mdtraj/formats/tng/tng.c \ mdtraj/formats/xtc/trr.c \ mdtraj/formats/xtc/xtc.c \ mdtraj/geometry/drid.cpp \ mdtraj/geometry/neighborlist.cpp \ mdtraj/geometry/neighbors.cpp \ mdtraj/geometry/src/_geometry.cpp \ mdtraj/rmsd/_lprmsd.cpp \ mdtraj/rmsd/_rmsd.cpp \ mdtraj/version.py; \ do rm -f $f; done rm -rf mdtraj/core/lib rm -rf docs/api/generated rm -rf __pycache__ .pybuild find . -name "lib*.a" -delete make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.11.0' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/python3-mdtraj.substvars debian/python-mdtraj-doc.substvars debian/files rm -fr -- debian/python3-mdtraj/ debian/tmp/ debian/python-mdtraj-doc/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) 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 pybuild --configure -i python{version} -p 3.13 I: pybuild base:311: python3.13 setup.py config Using built-in specs. COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/14/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-19) /build/reproducible-path/mdtraj-1.11.0/basesetup.py:483: UserWarning: Unrecognized setuptools command ('config'), proceeding with generating Cython sources and expanding templates warnings.warn( warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired. Possible solutions: 1. Declare 'make_whole' 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 'make_whole' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired. Possible solutions: 1. Declare 'anchor_dists' 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 'anchor_dists' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired. Possible solutions: 1. Declare 'wrap_mols' 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 'wrap_mols' to allow an error code to be returned. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE2 support... Did not detect SSE2 support Attempting to autodetect SSE3 support... Did not detect SSE3 support Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support Attempting to autodetect NEON support... Compiler supports NEON [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx [ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 5/10] Cythonizing mdtraj/geometry/drid.pyx [ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx /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 v2 or later (LGPLv2+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running config dh_auto_build -O--buildsystem=pybuild pybuild --build -i python{version} -p 3.13 I: pybuild base:311: /usr/bin/python3 setup.py build Using built-in specs. COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/14/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-19) warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired. Possible solutions: 1. Declare 'make_whole' 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 'make_whole' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired. Possible solutions: 1. Declare 'anchor_dists' 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 'anchor_dists' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired. Possible solutions: 1. Declare 'wrap_mols' 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 'wrap_mols' to allow an error code to be returned. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE2 support... Did not detect SSE2 support Attempting to autodetect SSE3 support... Did not detect SSE3 support Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support Attempting to autodetect NEON support... Compiler supports NEON [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx [ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 5/10] Cythonizing mdtraj/geometry/drid.pyx [ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx /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 v2 or later (LGPLv2+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_py creating /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj copying mdtraj/io.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj copying mdtraj/_version.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj copying mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj creating /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils copying mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils copying mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils copying mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils copying mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils copying mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils copying mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils copying mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils creating /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing copying mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing copying mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing copying mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing copying mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing creating /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/pi_stacking.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats creating /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core copying mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core copying mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core copying mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core copying mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core copying mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core copying mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core creating /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/pdbxfile.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/pdbx.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/PdbxReader.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdbx copying mdtraj/formats/pdbx/PdbxContainers.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdbx creating /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/data UPDATING /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_version.py set /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_version.py to '1.11.0' running build_ext building 'mdtraj.formats.xtc' extension creating build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/xtc.c:1263: /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/xtc.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so building 'mdtraj.formats.trr' extension aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/trr.c:1265: /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/trr.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so building 'mdtraj.formats.dcd' extension creating build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd creating build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/src aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from mdtraj/formats/dcd/dcd.c:1260: /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/dcd.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so building 'mdtraj.formats.dtr' extension creating build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr creating build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr/src aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from mdtraj/formats/dtr/dtr.cpp:1279: /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/dtr/src/dtrplugin.cxx: In member function 'bool desres::molfile::Timekeys::init(const std::string&)': mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format '%d' expects argument of type 'int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 706 | sprintf(sub, "%03x/", i); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 706 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:970, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(subsub, "%03x", j); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 714 | sprintf(subsub, "%03x", j); | ^~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 4 and 9 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 667 | sprintf(answer, "%03x/", d1); | ^ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:667:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: '%03x' directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ In function 'std::string DDreldir(const std::string&, int, int)', inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:665:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 9 and 19 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr/dtr.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so building 'mdtraj._rmsd' extension creating build/temp.linux-aarch64-cpython-313/mdtraj/rmsd creating build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from mdtraj/rmsd/_rmsd.cpp:1298: /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/_rmsd.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so building 'mdtraj._lprmsd' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from mdtraj/rmsd/_lprmsd.cpp:1305: /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/_lprmsd.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/Munkres.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/fancy_index.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so building 'mdtraj.core.lib.libtheobald' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -O3 -funroll-loops --std=c++11 aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o -O3 -funroll-loops --std=c++11 aarch64-linux-gnu-gcc-ar rcs /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/lib/libtheobald.a build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o building 'mdtraj.geometry._geometry' extension creating build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from mdtraj/geometry/src/_geometry.cpp:1287: /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/_geometry.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/dssp.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/geometry.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/sasa.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so building 'mdtraj.geometry.drid' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/drid.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/geometry/drid.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/dridkernels.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/moments.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so building 'mdtraj.geometry.neighbors' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/geometry/neighbors.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/neighbors.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/geometry/neighborlist.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/neighborlist.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so dh_auto_test -O--buildsystem=pybuild pybuild --test --test-pytest -i python{version} -p 3.13 I: pybuild base:311: cd /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build; python3.13 -m pytest -k 'not (mdconvert or pi_stacking.ipynb or nmr.ipynb or test_image_molecules) and not (test_3 or test_pdb_from_url or test_1vii_url_and_gz)' ============================= test session starts ============================== platform linux -- Python 3.13.5, pytest-8.3.5, pluggy-1.5.0 -- /usr/bin/python3.13 cachedir: .pytest_cache rootdir: /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build configfile: pyproject.toml testpaths: tests, examples plugins: rerunfailures-15.0, typeguard-4.4.2 collecting ... collected 1161 items / 22 deselected / 1139 selected tests/test_alignment.py::test_rmsd_zero PASSED [ 0%] tests/test_alignment.py::test_rmsd_nonzero PASSED [ 0%] tests/test_alignment.py::test_transform PASSED [ 0%] tests/test_alignment.py::test_transform2 PASSED [ 0%] tests/test_angles.py::test_angle_pbc_0 PASSED [ 0%] tests/test_angles.py::test_generator PASSED [ 0%] tests/test_angles.py::test_angle_180[True] PASSED [ 0%] tests/test_angles.py::test_angle_180[False] PASSED [ 0%] tests/test_arc.py::test_read_0 PASSED [ 0%] tests/test_arc.py::test_read_arctraj PASSED [ 0%] tests/test_arc.py::test_read_arctraj_top PASSED [ 0%] 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[ 44%] tests/test_topology.py::test_topology_openmm_formal_charges SKIPPED [ 44%] tests/test_topology.py::test_topology_dataframe_formal_charges PASSED [ 44%] tests/test_topology.py::test_topology_pandas PASSED [ 44%] tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 44%] tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 44%] tests/test_topology.py::test_topology_numbers PASSED [ 44%] tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 44%] tests/test_topology.py::test_chain PASSED [ 44%] tests/test_topology.py::test_residue PASSED [ 45%] tests/test_topology.py::test_segment_id PASSED [ 45%] tests/test_topology.py::test_nonconsective_resSeq PASSED [ 45%] tests/test_topology.py::test_pickle PASSED [ 45%] tests/test_topology.py::test_atoms_by_name PASSED [ 45%] tests/test_topology.py::test_select_atom_indices PASSED [ 45%] tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 45%] tests/test_topology.py::test_n_bonds PASSED [ 45%] tests/test_topology.py::test_load_unknown_topology PASSED [ 45%] tests/test_topology.py::test_unique_pairs PASSED [ 45%] tests/test_topology.py::test_select_pairs PASSED [ 45%] tests/test_topology.py::test_to_fasta PASSED [ 46%] tests/test_topology.py::test_subset PASSED [ 46%] tests/test_topology.py::test_subset_re_index_residues PASSED [ 46%] tests/test_topology.py::test_molecules PASSED [ 46%] tests/test_topology.py::test_copy_and_hash PASSED [ 46%] tests/test_topology.py::test_copy[traj.h5] PASSED [ 46%] tests/test_topology.py::test_copy[1ply_charge.pdb] PASSED [ 46%] tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 46%] tests/test_topology.py::test_topology_join PASSED [ 46%] tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 46%] tests/test_topology.py::test_topology_join_formal_charge PASSED [ 46%] tests/test_topology.py::test_delete_atom_by_index PASSED [ 46%] tests/test_trajectory.py::test_mismatch PASSED [ 47%] tests/test_trajectory.py::test_box PASSED [ 47%] tests/test_trajectory.py::test_load_pdb_box PASSED [ 47%] tests/test_trajectory.py::test_load_pdb_gz PASSED [ 47%] tests/test_trajectory.py::test_box_load_save[nc] PASSED [ 47%] tests/test_trajectory.py::test_box_load_save[h5] PASSED [ 47%] tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 47%] tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 47%] tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 47%] tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 47%] tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 47%] tests/test_trajectory.py::test_box_load_save[xyz] SKIPPED (xyz does ...) [ 48%] tests/test_trajectory.py::test_box_load_save[xyz.gz] SKIPPED (xyz.gz...) [ 48%] tests/test_trajectory.py::test_box_load_save[lammpstrj] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[lh5] SKIPPED (lh5 does ...) [ 48%] tests/test_trajectory.py::test_box_load_save[pdb] SKIPPED (pdb does ...) [ 48%] tests/test_trajectory.py::test_box_load_save[pdb.gz] SKIPPED (pdb.gz...) [ 48%] tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 48%] tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 48%] tests/test_trajectory.py::test_slice PASSED [ 48%] tests/test_trajectory.py::test_slice2 PASSED [ 48%] tests/test_trajectory.py::test_read_path[nc] PASSED [ 48%] tests/test_trajectory.py::test_read_path[h5] PASSED [ 49%] tests/test_trajectory.py::test_read_path[xtc] PASSED [ 49%] tests/test_trajectory.py::test_read_path[trr] PASSED [ 49%] tests/test_trajectory.py::test_read_path[dcd] PASSED [ 49%] tests/test_trajectory.py::test_read_path[mdcrd] PASSED [ 49%] tests/test_trajectory.py::test_read_path[dtr] PASSED [ 49%] tests/test_trajectory.py::test_read_path[xyz] PASSED [ 49%] tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 49%] tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 49%] tests/test_trajectory.py::test_read_path[lh5] PASSED [ 49%] tests/test_trajectory.py::test_read_path[pdb] PASSED [ 49%] tests/test_trajectory.py::test_read_path[pdb.gz] PASSED [ 50%] tests/test_trajectory.py::test_read_path[ncrst] XFAIL (These referen...) [ 50%] tests/test_trajectory.py::test_read_path[rst7] XFAIL (These referenc...) [ 50%] tests/test_trajectory.py::test_read_path[gro] PASSED [ 50%] tests/test_trajectory.py::test_write_path[nc] PASSED [ 50%] tests/test_trajectory.py::test_write_path[h5] PASSED [ 50%] tests/test_trajectory.py::test_write_path[xtc] PASSED [ 50%] tests/test_trajectory.py::test_write_path[trr] PASSED [ 50%] tests/test_trajectory.py::test_write_path[dcd] PASSED [ 50%] tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 50%] tests/test_trajectory.py::test_write_path[dtr] PASSED [ 50%] tests/test_trajectory.py::test_write_path[xyz] PASSED [ 51%] tests/test_trajectory.py::test_write_path[xyz.gz] PASSED [ 51%] tests/test_trajectory.py::test_write_path[lammpstrj] PASSED [ 51%] tests/test_trajectory.py::test_write_path[lh5] PASSED [ 51%] tests/test_trajectory.py::test_write_path[pdb] PASSED [ 51%] tests/test_trajectory.py::test_write_path[pdb.gz] PASSED [ 51%] tests/test_trajectory.py::test_write_path[ncrst] SKIPPED (ncrst can ...) [ 51%] tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 51%] tests/test_trajectory.py::test_write_path[gro] PASSED [ 51%] tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 51%] tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 51%] tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 51%] tests/test_trajectory.py::test_read_write[nc-trr] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-dcd] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-mdcrd] SKIPPED (mdcrd c...) [ 52%] tests/test_trajectory.py::test_read_write[nc-dtr] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-xyz] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-xyz.gz] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-lammpstrj] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 52%] tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 52%] tests/test_trajectory.py::test_read_write[nc-rst7] SKIPPED (rst7 can...) [ 53%] tests/test_trajectory.py::test_read_write[nc-gro] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-nc] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-h5] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-xtc] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-trr] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-dcd] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 53%] tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 53%] tests/test_trajectory.py::test_read_write[h5-lh5] PASSED [ 54%] tests/test_trajectory.py::test_read_write[h5-pdb] PASSED [ 54%] tests/test_trajectory.py::test_read_write[h5-pdb.gz] PASSED [ 54%] tests/test_trajectory.py::test_read_write[h5-ncrst] SKIPPED (ncrst c...) [ 54%] tests/test_trajectory.py::test_read_write[h5-rst7] SKIPPED (rst7 can...) [ 54%] tests/test_trajectory.py::test_read_write[h5-gro] PASSED [ 54%] tests/test_trajectory.py::test_read_write[xtc-nc] PASSED [ 54%] tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 54%] tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 54%] tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 54%] tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 54%] tests/test_trajectory.py::test_read_write[xtc-mdcrd] SKIPPED (mdcrd ...) [ 55%] tests/test_trajectory.py::test_read_write[xtc-dtr] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-xyz] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-xyz.gz] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-lammpstrj] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-lh5] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-pdb] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 55%] tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 55%] tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 55%] tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 55%] tests/test_trajectory.py::test_read_write[trr-nc] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-h5] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-xtc] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-trr] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-dcd] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-mdcrd] SKIPPED (mdcrd ...) [ 56%] tests/test_trajectory.py::test_read_write[trr-dtr] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-xyz] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 56%] tests/test_trajectory.py::test_read_write[trr-pdb.gz] PASSED [ 57%] tests/test_trajectory.py::test_read_write[trr-ncrst] SKIPPED (ncrst ...) [ 57%] tests/test_trajectory.py::test_read_write[trr-rst7] SKIPPED (rst7 ca...) [ 57%] tests/test_trajectory.py::test_read_write[trr-gro] PASSED [ 57%] tests/test_trajectory.py::test_read_write[dcd-nc] PASSED [ 57%] tests/test_trajectory.py::test_read_write[dcd-h5] PASSED [ 57%] tests/test_trajectory.py::test_read_write[dcd-xtc] PASSED [ 57%] tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 57%] tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 57%] tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 57%] tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 57%] tests/test_trajectory.py::test_read_write[dcd-xyz] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-xyz.gz] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-lammpstrj] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-lh5] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-pdb] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-pdb.gz] PASSED [ 58%] tests/test_trajectory.py::test_read_write[dcd-ncrst] SKIPPED (ncrst ...) [ 58%] tests/test_trajectory.py::test_read_write[dcd-rst7] SKIPPED (rst7 ca...) [ 58%] tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 58%] tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 58%] tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 58%] tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 58%] tests/test_trajectory.py::test_read_write[mdcrd-trr] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-dcd] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-mdcrd] SKIPPED (mdcr...) [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-dtr] SKIPPED (dtr ne...) [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-xyz] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-xyz.gz] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-lammpstrj] SKIPPED (...) [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 59%] tests/test_trajectory.py::test_read_write[mdcrd-rst7] SKIPPED (rst7 ...) [ 60%] tests/test_trajectory.py::test_read_write[mdcrd-gro] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-nc] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-h5] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-xtc] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-trr] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-dcd] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-mdcrd] SKIPPED (mdcrd ...) [ 60%] tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 60%] tests/test_trajectory.py::test_read_write[dtr-lammpstrj] PASSED [ 61%] tests/test_trajectory.py::test_read_write[dtr-lh5] PASSED [ 61%] tests/test_trajectory.py::test_read_write[dtr-pdb] PASSED [ 61%] tests/test_trajectory.py::test_read_write[dtr-pdb.gz] PASSED [ 61%] tests/test_trajectory.py::test_read_write[dtr-ncrst] SKIPPED (ncrst ...) [ 61%] tests/test_trajectory.py::test_read_write[dtr-rst7] SKIPPED (rst7 ca...) [ 61%] tests/test_trajectory.py::test_read_write[dtr-gro] PASSED [ 61%] tests/test_trajectory.py::test_read_write[xyz-nc] PASSED [ 61%] tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 61%] tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 61%] tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 61%] tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 61%] tests/test_trajectory.py::test_read_write[xyz-mdcrd] SKIPPED (mdcrd ...) [ 62%] tests/test_trajectory.py::test_read_write[xyz-dtr] SKIPPED (dtr need...) [ 62%] tests/test_trajectory.py::test_read_write[xyz-xyz] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-xyz.gz] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-lammpstrj] SKIPPED (la...) [ 62%] tests/test_trajectory.py::test_read_write[xyz-lh5] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-pdb] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-pdb.gz] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 62%] tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 62%] tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 62%] tests/test_trajectory.py::test_read_write[xyz.gz-nc] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-h5] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-xtc] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-trr] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-dcd] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-mdcrd] SKIPPED (mdc...) [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-dtr] SKIPPED (dtr n...) [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-xyz] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 63%] tests/test_trajectory.py::test_read_write[xyz.gz-pdb] PASSED [ 64%] tests/test_trajectory.py::test_read_write[xyz.gz-pdb.gz] PASSED [ 64%] tests/test_trajectory.py::test_read_write[xyz.gz-ncrst] SKIPPED (ncr...) [ 64%] tests/test_trajectory.py::test_read_write[xyz.gz-rst7] SKIPPED (rst7...) [ 64%] tests/test_trajectory.py::test_read_write[xyz.gz-gro] PASSED [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-nc] PASSED [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-h5] PASSED [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-xtc] PASSED [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-trr] PASSED [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 64%] tests/test_trajectory.py::test_read_write[lammpstrj-xyz] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-xyz.gz] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-lammpstrj] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-lh5] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-pdb] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-pdb.gz] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-ncrst] SKIPPED (...) [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-rst7] SKIPPED (r...) [ 65%] tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 65%] tests/test_trajectory.py::test_read_write[lh5-xtc] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-trr] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-dcd] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-mdcrd] SKIPPED (mdcrd ...) [ 66%] tests/test_trajectory.py::test_read_write[lh5-dtr] SKIPPED (dtr need...) [ 66%] tests/test_trajectory.py::test_read_write[lh5-xyz] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-xyz.gz] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-lammpstrj] SKIPPED (la...) [ 66%] tests/test_trajectory.py::test_read_write[lh5-lh5] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 66%] tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 66%] tests/test_trajectory.py::test_read_write[lh5-rst7] SKIPPED (rst7 ca...) [ 67%] tests/test_trajectory.py::test_read_write[lh5-gro] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-nc] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-h5] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-xtc] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-trr] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-dcd] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-mdcrd] SKIPPED (mdcrd ...) [ 67%] tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 67%] tests/test_trajectory.py::test_read_write[pdb-lammpstrj] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb-lh5] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb-pdb] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb-pdb.gz] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb-ncrst] SKIPPED (ncrst ...) [ 68%] tests/test_trajectory.py::test_read_write[pdb-rst7] SKIPPED (rst7 ca...) [ 68%] tests/test_trajectory.py::test_read_write[pdb-gro] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb.gz-nc] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb.gz-h5] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 68%] tests/test_trajectory.py::test_read_write[pdb.gz-dcd] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-mdcrd] SKIPPED (mdc...) [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-dtr] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-xyz] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-xyz.gz] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-lammpstrj] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-lh5] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-pdb] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-pdb.gz] PASSED [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 69%] tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 69%] tests/test_trajectory.py::test_read_write[ncrst-nc] XFAIL (These ref...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-h5] XFAIL (These ref...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-xtc] XFAIL (These re...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-trr] XFAIL (These re...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-dcd] XFAIL (These re...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-mdcrd] XFAIL (These ...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-dtr] XFAIL (These re...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-xyz] XFAIL (These re...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] XFAIL (These...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 70%] tests/test_trajectory.py::test_read_write[ncrst-pdb] XFAIL (These re...) [ 71%] tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] XFAIL (These...) [ 71%] tests/test_trajectory.py::test_read_write[ncrst-ncrst] XFAIL (These ...) [ 71%] tests/test_trajectory.py::test_read_write[ncrst-rst7] XFAIL (These r...) [ 71%] tests/test_trajectory.py::test_read_write[ncrst-gro] XFAIL (These re...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-nc] XFAIL (These refe...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-h5] XFAIL (These refe...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-xtc] XFAIL (These ref...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-trr] XFAIL (These ref...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 71%] tests/test_trajectory.py::test_read_write[rst7-xyz] XFAIL (These ref...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-xyz.gz] XFAIL (These ...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-lammpstrj] XFAIL (The...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-lh5] XFAIL (These ref...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-pdb] XFAIL (These ref...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-pdb.gz] XFAIL (These ...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-ncrst] XFAIL (These r...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-rst7] XFAIL (These re...) [ 72%] tests/test_trajectory.py::test_read_write[rst7-gro] XFAIL (These ref...) [ 72%] tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 72%] tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 72%] tests/test_trajectory.py::test_read_write[gro-xtc] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-trr] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-dcd] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-mdcrd] SKIPPED (mdcrd ...) [ 73%] tests/test_trajectory.py::test_read_write[gro-dtr] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-xyz] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-xyz.gz] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-lammpstrj] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-lh5] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 73%] tests/test_trajectory.py::test_read_write[gro-ncrst] SKIPPED (ncrst ...) [ 74%] tests/test_trajectory.py::test_read_write[gro-rst7] SKIPPED (rst7 ca...) [ 74%] tests/test_trajectory.py::test_read_write[gro-gro] PASSED [ 74%] tests/test_trajectory.py::test_load[nc] PASSED [ 74%] tests/test_trajectory.py::test_load[h5] PASSED [ 74%] tests/test_trajectory.py::test_load[xtc] PASSED [ 74%] tests/test_trajectory.py::test_load[trr] PASSED [ 74%] tests/test_trajectory.py::test_load[dcd] PASSED [ 74%] tests/test_trajectory.py::test_load[mdcrd] PASSED [ 74%] tests/test_trajectory.py::test_load[dtr] PASSED [ 74%] tests/test_trajectory.py::test_load[xyz] PASSED [ 74%] tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 74%] tests/test_trajectory.py::test_load[lammpstrj] PASSED [ 75%] tests/test_trajectory.py::test_load[lh5] PASSED [ 75%] tests/test_trajectory.py::test_load[pdb] PASSED [ 75%] tests/test_trajectory.py::test_load[pdb.gz] PASSED [ 75%] tests/test_trajectory.py::test_load[ncrst] XFAIL (These reference fi...) [ 75%] tests/test_trajectory.py::test_load[rst7] XFAIL (These reference fil...) [ 75%] tests/test_trajectory.py::test_load[gro] PASSED [ 75%] tests/test_trajectory.py::test_hdf5 PASSED [ 75%] tests/test_trajectory.py::test_center PASSED [ 75%] tests/test_trajectory.py::test_center_aind PASSED [ 75%] tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 75%] tests/test_trajectory.py::test_float_atom_indices_exception[h5] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[xtc] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[trr] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[dcd] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[mdcrd] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[dtr] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[xyz] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[xyz.gz] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[lammpstrj] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[lh5] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 76%] tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] XFAIL [ 77%] tests/test_trajectory.py::test_float_atom_indices_exception[rst7] XFAIL [ 77%] tests/test_trajectory.py::test_float_atom_indices_exception[gro] PASSED [ 77%] tests/test_trajectory.py::test_restrict_atoms PASSED [ 77%] tests/test_trajectory.py::test_restrict_atoms_not_inplace PASSED [ 77%] tests/test_trajectory.py::test_array_vs_matrix PASSED [ 77%] tests/test_trajectory.py::test_pdb_unitcell_loadsave PASSED [ 77%] tests/test_trajectory.py::test_load_combination[nc] PASSED [ 77%] tests/test_trajectory.py::test_load_combination[h5] PASSED [ 77%] tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 77%] tests/test_trajectory.py::test_load_combination[trr] PASSED [ 77%] tests/test_trajectory.py::test_load_combination[dcd] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[mdcrd] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[dtr] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[xyz] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[xyz.gz] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[lammpstrj] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[lh5] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[pdb] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[pdb.gz] PASSED [ 78%] tests/test_trajectory.py::test_load_combination[ncrst] XFAIL (These ...) [ 78%] tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 78%] tests/test_trajectory.py::test_load_combination[gro] PASSED [ 79%] tests/test_trajectory.py::test_no_topology PASSED [ 79%] tests/test_trajectory.py::test_join PASSED [ 79%] tests/test_trajectory.py::test_md_join PASSED [ 79%] tests/test_trajectory.py::test_stack_1 PASSED [ 79%] tests/test_trajectory.py::test_stack_2 PASSED [ 79%] tests/test_trajectory.py::test_seek_read_mode[nc] PASSED [ 79%] tests/test_trajectory.py::test_seek_read_mode[h5] PASSED [ 79%] tests/test_trajectory.py::test_seek_read_mode[xtc] PASSED [ 79%] tests/test_trajectory.py::test_seek_read_mode[trr] PASSED [ 79%] tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 79%] tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 79%] tests/test_trajectory.py::test_seek_read_mode[dtr] PASSED [ 80%] tests/test_trajectory.py::test_seek_read_mode[xyz] PASSED [ 80%] tests/test_trajectory.py::test_seek_read_mode[xyz.gz] XFAIL (This is...) [ 80%] tests/test_trajectory.py::test_seek_read_mode[lammpstrj] PASSED [ 80%] tests/test_trajectory.py::test_seek_read_mode[lh5] PASSED [ 80%] tests/test_trajectory.py::test_seek_read_mode[pdb] XFAIL (PDB Files ...) [ 80%] tests/test_trajectory.py::test_seek_read_mode[pdb.gz] XFAIL (PDB Fil...) [ 80%] tests/test_trajectory.py::test_seek_read_mode[ncrst] XFAIL (These re...) [ 80%] tests/test_trajectory.py::test_seek_read_mode[rst7] XFAIL (These ref...) [ 80%] tests/test_trajectory.py::test_seek_read_mode[gro] XFAIL (This is br...) [ 80%] tests/test_trajectory.py::test_load_frame[nc] PASSED [ 80%] tests/test_trajectory.py::test_load_frame[h5] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[xtc] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[trr] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[dcd] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[mdcrd] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[dtr] XFAIL (DTR doesn't lo...) [ 81%] tests/test_trajectory.py::test_load_frame[xyz] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[xyz.gz] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[lammpstrj] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[lh5] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 81%] tests/test_trajectory.py::test_load_frame[pdb.gz] PASSED [ 82%] tests/test_trajectory.py::test_load_frame[ncrst] XFAIL (These refere...) [ 82%] tests/test_trajectory.py::test_load_frame[rst7] XFAIL (These referen...) [ 82%] tests/test_trajectory.py::test_load_frame[gro] XFAIL (Gro doesn't im...) [ 82%] tests/test_trajectory.py::test_load_frame_2eqq PASSED [ 82%] tests/test_trajectory.py::test_iterload[nc] PASSED [ 82%] tests/test_trajectory.py::test_iterload[h5] PASSED [ 82%] tests/test_trajectory.py::test_iterload[xtc] PASSED [ 82%] tests/test_trajectory.py::test_iterload[trr] PASSED [ 82%] tests/test_trajectory.py::test_iterload[dcd] PASSED [ 82%] tests/test_trajectory.py::test_iterload[mdcrd] PASSED [ 82%] tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 82%] tests/test_trajectory.py::test_iterload[xyz] PASSED [ 83%] tests/test_trajectory.py::test_iterload[xyz.gz] PASSED [ 83%] tests/test_trajectory.py::test_iterload[lammpstrj] PASSED [ 83%] tests/test_trajectory.py::test_iterload[lh5] PASSED [ 83%] tests/test_trajectory.py::test_iterload[pdb] PASSED [ 83%] tests/test_trajectory.py::test_iterload[pdb.gz] PASSED [ 83%] tests/test_trajectory.py::test_iterload[ncrst] SKIPPED (Only 1 frame...) [ 83%] tests/test_trajectory.py::test_iterload[rst7] SKIPPED (Only 1 frame ...) [ 83%] tests/test_trajectory.py::test_iterload[gro] PASSED [ 83%] tests/test_trajectory.py::test_iterload_skip[nc] PASSED [ 83%] tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 83%] tests/test_trajectory.py::test_iterload_skip[xtc] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[trr] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[dcd] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[mdcrd] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[dtr] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[xyz] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[xyz.gz] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[lammpstrj] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[lh5] PASSED [ 84%] tests/test_trajectory.py::test_iterload_skip[pdb] XFAIL (PDB Iterloa...) [ 84%] tests/test_trajectory.py::test_iterload_skip[pdb.gz] XFAIL (PDB Iter...) [ 84%] tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 84%] tests/test_trajectory.py::test_iterload_skip[rst7] XFAIL (These refe...) [ 85%] tests/test_trajectory.py::test_iterload_skip[gro] XFAIL (Not impleme...) [ 85%] tests/test_trajectory.py::test_iterload_chunk_dcd PASSED [ 85%] tests/test_trajectory.py::test_save_load[nc] PASSED [ 85%] tests/test_trajectory.py::test_save_load[h5] PASSED [ 85%] tests/test_trajectory.py::test_save_load[xtc] PASSED [ 85%] tests/test_trajectory.py::test_save_load[trr] PASSED [ 85%] tests/test_trajectory.py::test_save_load[dcd] PASSED [ 85%] tests/test_trajectory.py::test_save_load[mdcrd] PASSED [ 85%] tests/test_trajectory.py::test_save_load[dtr] PASSED [ 85%] tests/test_trajectory.py::test_save_load[xyz] PASSED [ 85%] tests/test_trajectory.py::test_save_load[xyz.gz] PASSED [ 86%] tests/test_trajectory.py::test_save_load[lammpstrj] PASSED [ 86%] tests/test_trajectory.py::test_save_load[lh5] PASSED [ 86%] tests/test_trajectory.py::test_save_load[pdb] PASSED [ 86%] tests/test_trajectory.py::test_save_load[pdb.gz] PASSED [ 86%] tests/test_trajectory.py::test_save_load[ncrst] PASSED [ 86%] tests/test_trajectory.py::test_save_load[rst7] PASSED [ 86%] tests/test_trajectory.py::test_save_load[gro] PASSED [ 86%] tests/test_trajectory.py::test_force_overwrite[nc] PASSED [ 86%] tests/test_trajectory.py::test_force_overwrite[h5] PASSED [ 86%] tests/test_trajectory.py::test_force_overwrite[xtc] PASSED [ 86%] tests/test_trajectory.py::test_force_overwrite[trr] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[dcd] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[mdcrd] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[dtr] XFAIL (This is b...) [ 87%] tests/test_trajectory.py::test_force_overwrite[xyz] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[xyz.gz] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[lammpstrj] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[lh5] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[pdb] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[pdb.gz] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[ncrst] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 87%] tests/test_trajectory.py::test_force_overwrite[gro] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[nc] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[h5] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[xtc] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[trr] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[dcd] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[mdcrd] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[dtr] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[xyz] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[xyz.gz] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[lammpstrj] PASSED [ 88%] tests/test_trajectory.py::test_force_noverwrite[lh5] PASSED [ 89%] tests/test_trajectory.py::test_force_noverwrite[pdb] PASSED [ 89%] tests/test_trajectory.py::test_force_noverwrite[pdb.gz] PASSED [ 89%] tests/test_trajectory.py::test_force_noverwrite[ncrst] PASSED [ 89%] tests/test_trajectory.py::test_force_noverwrite[rst7] PASSED [ 89%] tests/test_trajectory.py::test_force_noverwrite[gro] PASSED [ 89%] tests/test_trajectory.py::test_open_and_load PASSED [ 89%] tests/test_trajectory.py::test_length PASSED [ 89%] tests/test_trajectory.py::test_unitcell[nc] PASSED [ 89%] tests/test_trajectory.py::test_unitcell[h5] PASSED [ 89%] tests/test_trajectory.py::test_unitcell[xtc] PASSED [ 89%] tests/test_trajectory.py::test_unitcell[trr] PASSED [ 89%] tests/test_trajectory.py::test_unitcell[dcd] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[mdcrd] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[dtr] XFAIL (dtr seems to nee...) [ 90%] tests/test_trajectory.py::test_unitcell[xyz] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[xyz.gz] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[lammpstrj] XFAIL (lammpstrj ...) [ 90%] tests/test_trajectory.py::test_unitcell[lh5] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[pdb] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[pdb.gz] PASSED [ 90%] tests/test_trajectory.py::test_unitcell[ncrst] XFAIL (ncrst seems to...) [ 90%] tests/test_trajectory.py::test_unitcell[rst7] XFAIL (rst7 seems to n...) [ 90%] tests/test_trajectory.py::test_unitcell[gro] PASSED [ 91%] tests/test_trajectory.py::test_chunk0_iterload PASSED [ 91%] tests/test_trajectory.py::test_hashing PASSED [ 91%] tests/test_trajectory.py::test_smooth PASSED [ 91%] tests/test_trajectory.py::test_make_whole PASSED [ 91%] tests/test_trajectory.py::test_load_pdb_no_standard_names PASSED [ 91%] tests/test_trajectory.py::test_load_with_atom_indices PASSED [ 91%] tests/test_trajectory.py::test_atom_slicing PASSED [ 91%] tests/test_trajectory.py::test_load_with_frame PASSED [ 91%] tests/test_trajectory.py::test_add_remove_atoms PASSED [ 91%] tests/test_trr.py::test_1 PASSED [ 91%] tests/test_trr.py::test_read_stride PASSED [ 92%] tests/test_trr.py::test_read_stride_n_frames PASSED [ 92%] tests/test_trr.py::test_read_stride_offsets PASSED [ 92%] tests/test_trr.py::test_read_stride_n_frames_offsets PASSED [ 92%] tests/test_trr.py::test_read_stride_switching PASSED [ 92%] tests/test_trr.py::test_write_read PASSED [ 92%] tests/test_trr.py::test_read_atomindices_1 PASSED [ 92%] tests/test_trr.py::test_read_atomindices_2 PASSED [ 92%] tests/test_trr.py::test_deficient_shape PASSED [ 92%] tests/test_trr.py::test_ragged_1 PASSED [ 92%] tests/test_trr.py::test_ragged_2 PASSED [ 92%] tests/test_trr.py::test_malformed PASSED [ 92%] tests/test_trr.py::test_tell PASSED [ 93%] tests/test_trr.py::test_seek PASSED [ 93%] tests/test_trr.py::test_get_velocities PASSED [ 93%] tests/test_trr.py::test_get_forces PASSED [ 93%] tests/test_trr.py::test_get_velocities_and_forces PASSED [ 93%] tests/test_trr.py::test_get_velocities_forces_atom_indices_1 PASSED [ 93%] tests/test_trr.py::test_get_velocities_forces_atom_indices_2 PASSED [ 93%] tests/test_trr.py::test_read_velocities_do_not_exist PASSED [ 93%] tests/test_trr.py::test_read_forces_do_not_exist PASSED [ 93%] tests/test_unitcell.py::Test_Unitcell::test_valid[orthogonal] PASSED [ 93%] tests/test_unitcell.py::Test_Unitcell::test_valid[triclinic] PASSED [ 93%] tests/test_unitcell.py::Test_Unitcell::test_invalid_over360[over360] PASSED [ 94%] tests/test_unitcell.py::Test_Unitcell::test_invalid_over360[close] PASSED [ 94%] tests/test_unitcell.py::Test_Unitcell::test_valid_array PASSED [ 94%] tests/test_unitcell.py::Test_Unitcell::test_invalid_over360_array PASSED [ 94%] tests/test_unitcell.py::Test_Unitcell::test_invalid_angles_close_array PASSED [ 94%] tests/test_utils.py::test_unitcell_0 PASSED [ 94%] tests/test_utils.py::test_unitcell_1 PASSED [ 94%] tests/test_utils.py::test_ensure_type_1 PASSED [ 94%] tests/test_utils.py::test_ensure_type_2 PASSED [ 94%] tests/test_utils.py::test_ensure_type_25 PASSED [ 94%] tests/test_utils.py::test_ensure_type_3 PASSED [ 94%] tests/test_utils.py::test_ensure_type_4 PASSED [ 94%] tests/test_utils.py::test_ensure_type_5 PASSED [ 95%] tests/test_utils.py::test_ensure_type_6 PASSED [ 95%] tests/test_utils.py::test_ensure_type_7 PASSED [ 95%] tests/test_utils.py::test_ensure_type_8 PASSED [ 95%] tests/test_utils.py::test_ensure_type_9 PASSED [ 95%] tests/test_utils.py::test_ensure_type_10 PASSED [ 95%] tests/test_utils.py::test_ensure_type_11 PASSED [ 95%] tests/test_utils.py::test_ensure_type_12 PASSED [ 95%] tests/test_utils.py::test_ensure_type_13 PASSED [ 95%] tests/test_utils.py::test_ensure_type_14 PASSED [ 95%] tests/test_utils.py::test_ensure_type_15 PASSED [ 95%] tests/test_utils.py::test_delay_import_fail_1 PASSED [ 96%] tests/test_utils.py::test_delay_import PASSED [ 96%] tests/test_utils.py::test_unit_0 PASSED [ 96%] tests/test_utils.py::test_unit_1 PASSED [ 96%] tests/test_utils.py::test_unit_2 PASSED [ 96%] tests/test_utils.py::test_unit_3 PASSED [ 96%] tests/test_xml.py::test_xml PASSED [ 96%] tests/test_xtc.py::test_read_chunk1 PASSED [ 96%] tests/test_xtc.py::test_read_stride PASSED [ 96%] tests/test_xtc.py::test_read_stride_n_frames PASSED [ 96%] tests/test_xtc.py::test_read_stride_offsets PASSED [ 96%] tests/test_xtc.py::test_read_stride_n_frames_offsets PASSED [ 97%] tests/test_xtc.py::test_read_stride_switching_offsets PASSED [ 97%] tests/test_xtc.py::test_read_atomindices_1 PASSED [ 97%] tests/test_xtc.py::test_read_atomindices_w_stride PASSED [ 97%] tests/test_xtc.py::test_read_atomindices_2 PASSED [ 97%] tests/test_xtc.py::test_read_chunk2 PASSED [ 97%] tests/test_xtc.py::test_read_chunk3 PASSED [ 97%] tests/test_xtc.py::test_write_0 PASSED [ 97%] tests/test_xtc.py::test_write_1 PASSED [ 97%] tests/test_xtc.py::test_write_2 PASSED [ 97%] tests/test_xtc.py::test_read_error_0 PASSED [ 97%] tests/test_xtc.py::test_write_error_0 PASSED [ 97%] tests/test_xtc.py::test_read_error_1 PASSED [ 98%] tests/test_xtc.py::test_read_error_2 PASSED [ 98%] tests/test_xtc.py::test_xtc_write_wierd_0 PASSED [ 98%] tests/test_xtc.py::test_tell PASSED [ 98%] tests/test_xtc.py::test_seek PASSED [ 98%] tests/test_xtc.py::test_seek_natoms9 PASSED [ 98%] tests/test_xtc.py::test_seek_out_of_bounds PASSED [ 98%] tests/test_xtc.py::test_ragged_1 PASSED [ 98%] tests/test_xtc.py::test_ragged_2 PASSED [ 98%] tests/test_xtc.py::test_short_traj PASSED [ 98%] tests/test_xtc.py::test_flush PASSED [ 98%] tests/test_xyz.py::test_read_0 PASSED [ 99%] tests/test_xyz.py::test_read_1 PASSED [ 99%] tests/test_xyz.py::test_read_gz PASSED [ 99%] tests/test_xyz.py::test_read_write PASSED [ 99%] tests/test_xyz.py::test_mdwrite PASSED [ 99%] tests/test_xyz.py::test_multiread PASSED [ 99%] tests/test_xyz.py::test_seek PASSED [ 99%] tests/test_xyz.py::test_len PASSED [ 99%] tests/test_zipped.py::test_read_gz PASSED [ 99%] tests/test_zipped.py::test_write_gz PASSED [ 99%] tests/test_zipped.py::test_read_bz2 PASSED [ 99%] tests/test_zipped.py::test_write_bz2 PASSED [100%] =============================== warnings summary =============================== tests/test_distance.py::Test_Distance::test_6 :488: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ SKIPPED [1] tests/test_dihedral.py:56: pymol executable not found SKIPPED [1] tests/test_dihedral.py:181: pymol executable not found SKIPPED [15] tests/test_docstrings.py:38: Skip checking certain modules' docstrings SKIPPED [1] tests/test_geometry.py:300: Not doing performance testing SKIPPED [1] tests/test_geometry.py:322: Not doing performance testing SKIPPED [1] tests/test_hdf5.py:105: requires openmm.units SKIPPED [1] tests/test_hdf5.py:156: requires openmm.units SKIPPED [1] tests/test_hdf5.py:223: requires openmm.units SKIPPED [1] tests/test_mol2.py:59: Requires obabel SKIPPED [1] tests/test_netcdf.py:274: This test requires cpptraj from AmberTools to be installed (http://ambermd.org) SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found SKIPPED [1] tests/test_nmr.py:26: PPM binary not found SKIPPED [1] tests/test_nmr.py:42: SHIFTX2 binary not found or running on travis. SKIPPED [2] tests/test_psf.py:93: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/ SKIPPED [1] tests/test_rdf.py:64: Binning does not match up with gromacs currently. SKIPPED [1] tests/test_rdf.py:200: Binning does not match up with gromacs currently. SKIPPED [1] tests/test_reporter.py:58: test_reporter.py needs OpenMM. SKIPPED [1] tests/test_reporter.py:145: test_reporter.py needs OpenMM. SKIPPED [1] tests/test_reporter.py:245: test_reporter.py needs OpenMM. SKIPPED [1] tests/test_selection.py:267: failed to parse selection SKIPPED [1] tests/test_thermodynamic_properties.py:161: Thermal expansion test doesn't work. SKIPPED [1] tests/test_topology.py:49: needs OpenMM SKIPPED [1] tests/test_topology.py:66: needs OpenMM SKIPPED [1] tests/test_topology.py:76: needs OpenMM SKIPPED [1] tests/test_topology.py:85: needs OpenMM SKIPPED [1] tests/test_topology.py:95: needs OpenMM SKIPPED [1] tests/test_topology.py:102: requires openmm >= 8.2 SKIPPED [1] tests/test_topology.py:284: needs OpenMM SKIPPED [1] tests/test_trajectory.py:129: xyz does not store box information SKIPPED [1] tests/test_trajectory.py:129: xyz.gz does not store box information SKIPPED [1] tests/test_trajectory.py:129: lh5 does not store box information SKIPPED [1] tests/test_trajectory.py:129: pdb does not store box information SKIPPED [1] tests/test_trajectory.py:129: pdb.gz does not store box information SKIPPED [1] tests/test_trajectory.py:225: mdcrd can only store rectilinear boxes SKIPPED [1] tests/test_trajectory.py:223: ncrst can only store 1 frame per file SKIPPED [1] tests/test_trajectory.py:223: rst7 can only store 1 frame per file SKIPPED [14] tests/test_trajectory.py:247: mdcrd can only store rectilinear boxes SKIPPED [14] tests/test_trajectory.py:245: ncrst can only store 1 frame per file SKIPPED [14] tests/test_trajectory.py:245: rst7 can only store 1 frame per file SKIPPED [4] tests/test_trajectory.py:255: dtr needs to write unitcells SKIPPED [4] tests/test_trajectory.py:255: lammpstrj needs to write unitcells SKIPPED [2] tests/test_trajectory.py:641: Only 1 frame per file format XFAIL tests/test_trajectory.py::test_read_path[ncrst] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_path[rst7] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_load[ncrst] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_load[rst7] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_load_combination[rst7] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - reason: This is broken XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - reason: PDB Files don't support seeking XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - reason: PDB Files don't support seeking XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - reason: This is broken XFAIL tests/test_trajectory.py::test_load_frame[dtr] - reason: DTR doesn't load a single frame properly XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_load_frame[rst7] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_load_frame[gro] - reason: Gro doesn't implement seek XFAIL tests/test_trajectory.py::test_iterload[dtr] - reason: This is broken with dtr XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - reason: PDB Iterloads an extra frame!! XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - reason: PDB Iterloads an extra frame!! XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - reason: These reference files don't exist yet XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - reason: Not implemented for some reason XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - reason: This is broken with dtr XFAIL tests/test_trajectory.py::test_unitcell[dtr] - reason: dtr seems to need unit vectors XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - reason: lammpstrj seems to need unit vectors XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - reason: ncrst seems to need unit vectors XFAIL tests/test_trajectory.py::test_unitcell[rst7] - reason: rst7 seems to need unit vectors = 975 passed, 103 skipped, 22 deselected, 61 xfailed, 1 warning in 324.03s (0:05:24) = lugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) rm -fr -- /tmp/dh-xdg-rundir-u1FCp9IG create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild rm -f -- debian/python3-mdtraj.substvars debian/python-mdtraj-doc.substvars rm -fr -- debian/.debhelper/generated/python3-mdtraj/ debian/python3-mdtraj/ debian/tmp/ debian/.debhelper/generated/python-mdtraj-doc/ debian/python-mdtraj-doc/ dh_installdirs -O--buildsystem=pybuild install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples/data dh_auto_install -O--buildsystem=pybuild install -m0755 -d /build/reproducible-path/mdtraj-1.11.0/debian/tmp pybuild --install -i python{version} -p 3.13 --dest-dir=/build/reproducible-path/mdtraj-1.11.0/debian/tmp I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj Using built-in specs. COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/14/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-19) warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired. Possible solutions: 1. Declare 'make_whole' 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 'make_whole' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired. Possible solutions: 1. Declare 'anchor_dists' 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 'anchor_dists' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired. Possible solutions: 1. Declare 'wrap_mols' 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 'wrap_mols' to allow an error code to be returned. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE2 support... Did not detect SSE2 support Attempting to autodetect SSE3 support... Did not detect SSE3 support Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support Attempting to autodetect NEON support... Compiler supports NEON [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx [ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 5/10] Cythonizing mdtraj/geometry/drid.pyx [ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx /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 v2 or later (LGPLv2+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py UPDATING /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_version.py set /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_version.py to '1.11.0' running build_ext building 'mdtraj.formats.xtc' extension aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/xtc.c:1263: /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/xtc.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so building 'mdtraj.formats.trr' extension aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/trr.c:1265: /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/trr.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so building 'mdtraj.formats.dcd' extension aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from mdtraj/formats/dcd/dcd.c:1260: /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/dcd.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so building 'mdtraj.formats.dtr' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from mdtraj/formats/dtr/dtr.cpp:1279: /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/dtr/src/dtrplugin.cxx: In member function 'bool desres::molfile::Timekeys::init(const std::string&)': mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format '%d' expects argument of type 'int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %ld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 706 | sprintf(sub, "%03x/", i); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 706 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:970, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(subsub, "%03x", j); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 714 | sprintf(subsub, "%03x", j); | ^~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 4 and 9 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 667 | sprintf(answer, "%03x/", d1); | ^ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:667:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: '%03x' directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ In function 'std::string DDreldir(const std::string&, int, int)', inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:665:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 9 and 19 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr/dtr.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so building 'mdtraj._rmsd' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from mdtraj/rmsd/_rmsd.cpp:1298: /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/_rmsd.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so building 'mdtraj._lprmsd' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from mdtraj/rmsd/_lprmsd.cpp:1305: /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/_lprmsd.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/Munkres.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/fancy_index.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so building 'mdtraj.geometry._geometry' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from mdtraj/geometry/src/_geometry.cpp:1287: /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/_geometry.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/dssp.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/geometry.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/sasa.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so building 'mdtraj.geometry.drid' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/drid.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/geometry/drid.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/dridkernels.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/moments.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so building 'mdtraj.geometry.neighbors' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/geometry/neighbors.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/neighbors.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.11.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/geometry/neighborlist.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/neighborlist.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so running install_lib creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/.pytest_cache creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/.pytest_cache/v creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/.pytest_cache/v/cache copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/.pytest_cache/v/cache/stepwise -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/.pytest_cache/v/cache copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/.pytest_cache/v/cache/nodeids -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/.pytest_cache/v/cache copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/.pytest_cache/CACHEDIR.TAG -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/.pytest_cache copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/.pytest_cache/.gitignore -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/.pytest_cache copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/.pytest_cache/README.md -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/.pytest_cache creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/__pycache__/io.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/__pycache__/_version.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/__pycache__ creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__pycache__/trajectory.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__pycache__/selection.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__pycache__/residue_names.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__pycache__/topology.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__pycache__/element.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__ creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/lib/center.h -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/lib/theobald_rmsd.h -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/lib/libtheobald.a -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/openmmxml.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/psf.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/prmtop.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/mol2.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/hoomdxml.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/gsd.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/xyzfile.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/netcdf.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/mdcrd.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/lh5.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/lammpstrj.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/hdf5.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/gro.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/arc.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/registry.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/amberrst.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbstructure.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbfile.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/__pycache__ creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdbx/__pycache__/pdbxfile.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdbx/__pycache__/PdbxReader.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdbx/__pycache__/PdbxContainers.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdbx/__pycache__/pdbx.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdbx/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdbx/PdbxContainers.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdbx/PdbxReader.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdbx/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdbx/pdbx.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdbx/pdbxfile.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/internal.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/alignment.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/thermodynamic_properties.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/shape.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/sasa.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/rg.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/rdf.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/pi_stacking.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/order.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/hbond.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/dssp.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/dihedral.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/contact.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/distance.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/angle.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/pi_stacking.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/__pycache__/shift_wrappers.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/__pycache__/scalar_couplings.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__pycache__/xtcreporter.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__pycache__/netcdfreporter.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__pycache__/hdf5reporter.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__pycache__/basereporter.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__pycache__/dcdreporter.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts/__pycache__/mdinspect.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts/__pycache__/mdconvert.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/__pycache__/testing.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/__pycache__/docscrape.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/__pycache__/docstrings.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/singleton.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/zipped.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/unitcell.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/validation.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/rotation.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/delay_import.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/contextmanagers.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__ creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_math.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/doctests.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/constants.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/quantity.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_operators.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/basedimension.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/standard_dimensions.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/mymatrix.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/unit.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/prefix.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/baseunit.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_definitions.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_version.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/io.py -> /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/element.py to element.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/residue_names.py to residue_names.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/selection.py to selection.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/topology.py to topology.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/trajectory.py to trajectory.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/pdbfile.py to pdbfile.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/pdbstructure.py to pdbstructure.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx/PdbxContainers.py to PdbxContainers.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx/PdbxReader.py to PdbxReader.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx/pdbx.py to pdbx.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx/pdbxfile.py to pdbxfile.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/amberrst.py to amberrst.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/arc.py to arc.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/gro.py to gro.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/gsd.py to gsd.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/hdf5.py to hdf5.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/lh5.py to lh5.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/mol2.py to mol2.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/netcdf.py to netcdf.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/prmtop.py to prmtop.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/psf.py to psf.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/registry.py to registry.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/alignment.py to alignment.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/angle.py to angle.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/contact.py to contact.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/distance.py to distance.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/dssp.py to dssp.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/hbond.py to hbond.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/internal.py to internal.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/order.py to order.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/pi_stacking.py to pi_stacking.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/rdf.py to rdf.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/rg.py to rg.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/sasa.py to sasa.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/shape.py to shape.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/thermodynamic_properties.py to thermodynamic_properties.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/scalar_couplings.py to scalar_couplings.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/shift_wrappers.py to shift_wrappers.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts/mdconvert.py to mdconvert.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/docscrape.py to docscrape.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/docstrings.py to docstrings.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/testing.py to testing.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/mymatrix.py to mymatrix.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/constants.py to constants.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/prefix.py to prefix.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/quantity.py to quantity.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/standard_dimensions.py to standard_dimensions.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/unit_definitions.py to unit_definitions.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/unit_math.py to unit_math.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/unit_operators.py to unit_operators.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/basedimension.py to basedimension.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/baseunit.py to baseunit.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/doctests.py to doctests.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/unit.py to unit.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/delay_import.py to delay_import.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/rotation.py to rotation.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/singleton.py to singleton.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unitcell.py to unitcell.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/validation.py to validation.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/zipped.py to zipped.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/_version.py to _version.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/io.py to io.cpython-313.pyc running install_egg_info running egg_info creating mdtraj.egg-info writing mdtraj.egg-info/PKG-INFO writing dependency_links to mdtraj.egg-info/dependency_links.txt writing entry points to mdtraj.egg-info/entry_points.txt writing requirements to mdtraj.egg-info/requires.txt writing top-level names to mdtraj.egg-info/top_level.txt writing manifest file 'mdtraj.egg-info/SOURCES.txt' dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative reading manifest file 'mdtraj.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching '__pycache__' no previously-included directories found matching '*.pyc' adding license file 'LICENSE' writing manifest file 'mdtraj.egg-info/SOURCES.txt' Copying mdtraj.egg-info to /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj-1.11.0.egg-info Skipping SOURCES.txt running install_scripts Installing mdconvert-mdtraj script to /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/bin Installing mdinspect script to /build/reproducible-path/mdtraj-1.11.0/debian/python3-mdtraj/usr/bin debian/rules execute_after_dh_auto_install-indep make[1]: Entering directory '/build/reproducible-path/mdtraj-1.11.0' cp -a /build/reproducible-path/mdtraj-1.11.0/examples /build/reproducible-path/mdtraj-1.11.0/examples.orig mkdir -p /build/reproducible-path/mdtraj-1.11.0/build/html/examples/iterload ln -s /build/reproducible-path/mdtraj-1.11.0/examples/data /build/reproducible-path/mdtraj-1.11.0/build/html/examples/iterload/data sed "s|http://www.rcsb.org/pdb/files|/build/reproducible-path/mdtraj-1.11.0/debian/external|g" -i /build/reproducible-path/mdtraj-1.11.0/examples/*.ipynb PYTHONPATH=/build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build \ MPLCONFIGDIR=/build/reproducible-path/mdtraj-1.11.0/build/matplotlib \ make -C docs BUILDDIR=/build/reproducible-path/mdtraj-1.11.0/build html make[2]: Entering directory '/build/reproducible-path/mdtraj-1.11.0/docs' sphinx-build -b html -d /build/reproducible-path/mdtraj-1.11.0/build/doctrees . /build/reproducible-path/mdtraj-1.11.0/build/html Running Sphinx v8.1.3 loading translations [en]... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. [autosummary] generating autosummary for: analysis.rst, api/reporters.rst, api/trajectory_files.rst, api/utils.rst, atom_selection.rst, building_docs.rst, examples/atom-selection.rst, examples/centroids.rst, examples/clustering.rst, examples/hbonds.rst, ..., notebook-examples/native-contact.nblink, notebook-examples/openmm.nblink, notebook-examples/pca.nblink, notebook-examples/pi_stacking.nblink, notebook-examples/ramachandran-plot.nblink, notebook-examples/rmsd-benchmark.nblink, notebook-examples/rmsd-drift.nblink, notebook-examples/solvent-accessible-surface-area.nblink, notebook-examples/two-pass-clustering.nblink, whatsnew.rst [autosummary] generating autosummary for: /build/reproducible-path/mdtraj-1.11.0/docs/api/generated/mdtraj.Topology.rst, /build/reproducible-path/mdtraj-1.11.0/docs/api/generated/mdtraj.Trajectory.rst, /build/reproducible-path/mdtraj-1.11.0/docs/api/generated/mdtraj.Trajectory.superpose.rst, /build/reproducible-path/mdtraj-1.11.0/docs/api/generated/mdtraj.acylindricity.rst, /build/reproducible-path/mdtraj-1.11.0/docs/api/generated/mdtraj.asphericity.rst, /build/reproducible-path/mdtraj-1.11.0/docs/api/generated/mdtraj.baker_hubbard.rst, /build/reproducible-path/mdtraj-1.11.0/docs/api/generated/mdtraj.chemical_shifts_ppm.rst, /build/reproducible-path/mdtraj-1.11.0/docs/api/generated/mdtraj.chemical_shifts_shiftx2.rst, /build/reproducible-path/mdtraj-1.11.0/docs/api/generated/mdtraj.chemical_shifts_spartaplus.rst, /build/reproducible-path/mdtraj-1.11.0/docs/api/generated/mdtraj.compute_J3_HN_C.rst, ..., /build/reproducible-path/mdtraj-1.11.0/docs/api/generated/mdtraj.utils.check_random_state.rst, /build/reproducible-path/mdtraj-1.11.0/docs/api/generated/mdtraj.utils.ensure_type.rst, /build/reproducible-path/mdtraj-1.11.0/docs/api/generated/mdtraj.utils.ilen.rst, /build/reproducible-path/mdtraj-1.11.0/docs/api/generated/mdtraj.utils.import_.rst, /build/reproducible-path/mdtraj-1.11.0/docs/api/generated/mdtraj.utils.in_units_of.rst, /build/reproducible-path/mdtraj-1.11.0/docs/api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors.rst, /build/reproducible-path/mdtraj-1.11.0/docs/api/generated/mdtraj.utils.rotation_matrix_from_quaternion.rst, /build/reproducible-path/mdtraj-1.11.0/docs/api/generated/mdtraj.utils.timing.rst, /build/reproducible-path/mdtraj-1.11.0/docs/api/generated/mdtraj.utils.uniform_quaternion.rst, /build/reproducible-path/mdtraj-1.11.0/docs/api/generated/mdtraj.wernet_nilsson.rst Writing evaluated template result to /build/reproducible-path/mdtraj-1.11.0/build/html/_static/nbsphinx-code-cells.css building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 46 source files that are out of date updating environment: [new config] 143 added, 0 changed, 0 removed reading sources... [ 1%] analysis reading sources... [ 1%] api/generated/mdtraj.Topology /usr/lib/python3/dist-packages/numpydoc/docscrape.py:203: UserWarning: potentially wrong underline length... Returns ---------- in Get the indices of biologically-relevant groups by name. ... in the docstring of select_atom_indices in /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/topology.py. while not self._is_at_section() and not self._doc.eof(): reading sources... [ 2%] api/generated/mdtraj.Trajectory reading sources... [ 3%] api/generated/mdtraj.Trajectory.superpose reading sources... [ 3%] api/generated/mdtraj.acylindricity reading sources... [ 4%] api/generated/mdtraj.asphericity reading sources... [ 5%] api/generated/mdtraj.baker_hubbard reading sources... [ 6%] api/generated/mdtraj.chemical_shifts_ppm reading sources... [ 6%] api/generated/mdtraj.chemical_shifts_shiftx2 reading sources... [ 7%] api/generated/mdtraj.chemical_shifts_spartaplus reading sources... [ 8%] api/generated/mdtraj.compute_J3_HN_C reading sources... [ 8%] api/generated/mdtraj.compute_J3_HN_CB reading sources... [ 9%] api/generated/mdtraj.compute_J3_HN_HA reading sources... [ 10%] api/generated/mdtraj.compute_angles reading sources... [ 10%] api/generated/mdtraj.compute_center_of_mass reading sources... [ 11%] api/generated/mdtraj.compute_chi1 reading sources... [ 12%] api/generated/mdtraj.compute_chi2 reading sources... [ 13%] api/generated/mdtraj.compute_chi3 reading sources... [ 13%] api/generated/mdtraj.compute_chi4 reading sources... [ 14%] api/generated/mdtraj.compute_contacts reading sources... [ 15%] api/generated/mdtraj.compute_dihedrals reading sources... [ 15%] api/generated/mdtraj.compute_directors reading sources... [ 16%] api/generated/mdtraj.compute_displacements reading sources... [ 17%] api/generated/mdtraj.compute_distances reading sources... [ 17%] api/generated/mdtraj.compute_drid reading sources... [ 18%] api/generated/mdtraj.compute_dssp reading sources... [ 19%] api/generated/mdtraj.compute_gyration_tensor reading sources... [ 20%] api/generated/mdtraj.compute_inertia_tensor reading sources... [ 20%] api/generated/mdtraj.compute_neighbors reading sources... [ 21%] api/generated/mdtraj.compute_nematic_order reading sources... [ 22%] api/generated/mdtraj.compute_omega reading sources... [ 22%] api/generated/mdtraj.compute_phi reading sources... [ 23%] api/generated/mdtraj.compute_psi reading sources... [ 24%] api/generated/mdtraj.compute_rdf reading sources... [ 24%] api/generated/mdtraj.compute_rg reading sources... [ 25%] api/generated/mdtraj.density reading sources... [ 26%] api/generated/mdtraj.dipole_moments reading sources... [ 27%] api/generated/mdtraj.formats.AmberNetCDFRestartFile reading sources... [ 27%] api/generated/mdtraj.formats.AmberRestartFile reading sources... [ 28%] api/generated/mdtraj.formats.ArcTrajectoryFile reading sources... [ 29%] api/generated/mdtraj.formats.DCDTrajectoryFile reading sources... [ 29%] api/generated/mdtraj.formats.DTRTrajectoryFile reading sources... [ 30%] api/generated/mdtraj.formats.GroTrajectoryFile reading sources... [ 31%] api/generated/mdtraj.formats.HDF5TrajectoryFile reading sources... [ 31%] api/generated/mdtraj.formats.LAMMPSTrajectoryFile reading sources... [ 32%] api/generated/mdtraj.formats.LH5TrajectoryFile reading sources... [ 33%] api/generated/mdtraj.formats.MDCRDTrajectoryFile reading sources... [ 34%] api/generated/mdtraj.formats.NetCDFTrajectoryFile reading sources... [ 34%] api/generated/mdtraj.formats.PDBTrajectoryFile reading sources... [ 35%] api/generated/mdtraj.formats.TRRTrajectoryFile reading sources... [ 36%] api/generated/mdtraj.formats.XTCTrajectoryFile reading sources... [ 36%] api/generated/mdtraj.formats.XYZTrajectoryFile reading sources... [ 37%] api/generated/mdtraj.geometry.squareform reading sources... [ 38%] api/generated/mdtraj.isothermal_compressability_kappa_T reading sources... [ 38%] api/generated/mdtraj.iterload reading sources... [ 39%] api/generated/mdtraj.join reading sources... [ 40%] api/generated/mdtraj.kabsch_sander reading sources... [ 41%] api/generated/mdtraj.load reading sources... [ 41%] api/generated/mdtraj.load_arc reading sources... [ 42%] api/generated/mdtraj.load_dcd reading sources... [ 43%] api/generated/mdtraj.load_dtr reading sources... [ 43%] api/generated/mdtraj.load_frame reading sources... [ 44%] api/generated/mdtraj.load_hdf5 reading sources... [ 45%] api/generated/mdtraj.load_hoomdxml reading sources... [ 45%] api/generated/mdtraj.load_lammpstrj reading sources... [ 46%] api/generated/mdtraj.load_lh5 reading sources... [ 47%] api/generated/mdtraj.load_netcdf reading sources... [ 48%] api/generated/mdtraj.load_pdb reading sources... [ 48%] api/generated/mdtraj.load_prmtop reading sources... [ 49%] api/generated/mdtraj.load_trr reading sources... 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[ 99%] notebook-examples/two-pass-clustering reading sources... [100%] whatsnew /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.asphericity:9: WARNING: Explicit markup ends without a blank line; unexpected unindent. [docutils] /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:33: ERROR: Unexpected indentation. [docutils] docstring of mdtraj.formats.dtr.load_dtr:7: ERROR: Unexpected indentation. [docutils] /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:9: WARNING: Explicit markup ends without a blank line; unexpected unindent. [docutils] /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:11: ERROR: Unexpected indentation. [docutils] /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:12: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:14: WARNING: Definition list ends without a blank line; unexpected unindent. [docutils] /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:15: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] /build/reproducible-path/mdtraj-1.11.0/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/rotation.py:docstring of mdtraj.utils.rotation.uniform_quaternion:39: ERROR: Error in "rubric" directive: no content permitted. .. rubric:: References .. [R17e8d31e726c-1] K. Shoemake. Uniform random rotations. In D. Kirk, editor, Graphics Gems III, pages 124-132. Academic, New York, 1992. .. [R17e8d31e726c-2] http://planning.cs.uiuc.edu/node198.html [docutils] /build/reproducible-path/mdtraj-1.11.0/docs/examples/atom-selection.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/atom-selection.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.11.0/docs/examples/centroids.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/centroids.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.11.0/docs/examples/clustering.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/clustering.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.11.0/docs/examples/hbonds.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/hbonds.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.11.0/docs/examples/iterload.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/iterload.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.11.0/docs/examples/native-contact.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/native-contact.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.11.0/docs/examples/nmr.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/nmr.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.11.0/docs/examples/openmm.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/simulation-with-openmm.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.11.0/docs/examples/pca.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/principal-components.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.11.0/docs/examples/pi_stacking.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/pi_stacking.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.11.0/docs/examples/ramachandran-plot.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/ramachandran-plot.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.11.0/docs/examples/rmsd-benchmark.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/rmsd-benchmark.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.11.0/docs/examples/solvent-accessible-surface-area.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/solvent-accessible-surface-area.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.11.0/docs/examples/two-pass-clustering.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/two-pass-clustering.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.11.0/docs/index.rst:26: WARNING: toctree contains reference to nonexisting document '.. examples/index' [toc.not_readable] /build/reproducible-path/mdtraj-1.11.0/docs/installation.rst:1: WARNING: malformed hyperlink target. 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[ 97%] notebook-examples/rmsd-benchmark writing output... [ 98%] notebook-examples/rmsd-drift writing output... [ 99%] notebook-examples/solvent-accessible-surface-area writing output... [ 99%] notebook-examples/two-pass-clustering writing output... [100%] whatsnew generating indices... genindex done copying linked files... copying notebooks ... [ 7%] notebook-examples/atom-selection.ipynb copying notebooks ... [ 14%] notebook-examples/centroids.ipynb copying notebooks ... [ 21%] notebook-examples/clustering.ipynb copying notebooks ... [ 29%] notebook-examples/hbonds.ipynb copying notebooks ... [ 36%] notebook-examples/iterload.ipynb copying notebooks ... [ 43%] notebook-examples/native-contact.ipynb copying notebooks ... [ 50%] notebook-examples/openmm.ipynb copying notebooks ... [ 57%] notebook-examples/pca.ipynb copying notebooks ... [ 64%] notebook-examples/pi_stacking.ipynb copying notebooks ... [ 71%] notebook-examples/ramachandran-plot.ipynb copying notebooks ... [ 79%] notebook-examples/rmsd-benchmark.ipynb copying notebooks ... [ 86%] notebook-examples/rmsd-drift.ipynb copying notebooks ... [ 93%] notebook-examples/solvent-accessible-surface-area.ipynb copying notebooks ... [100%] notebook-examples/two-pass-clustering.ipynb highlighting module code... [ 2%] mdtraj._lprmsd highlighting module code... [ 4%] mdtraj._rmsd highlighting module code... [ 6%] mdtraj.core.topology highlighting module code... [ 8%] mdtraj.core.trajectory highlighting module code... [ 10%] mdtraj.formats.amberrst highlighting module code... [ 12%] mdtraj.formats.arc highlighting module code... [ 15%] mdtraj.formats.dcd highlighting module code... [ 17%] mdtraj.formats.dtr highlighting module code... [ 19%] mdtraj.formats.gro highlighting module code... [ 21%] mdtraj.formats.hdf5 highlighting module code... [ 23%] mdtraj.formats.hoomdxml highlighting module code... [ 25%] mdtraj.formats.lammpstrj highlighting module code... [ 27%] mdtraj.formats.lh5 highlighting module code... [ 29%] mdtraj.formats.mdcrd highlighting module code... [ 31%] mdtraj.formats.netcdf highlighting module code... [ 33%] mdtraj.formats.openmmxml highlighting module code... [ 35%] mdtraj.formats.pdb.pdbfile highlighting module code... [ 38%] mdtraj.formats.prmtop highlighting module code... [ 40%] mdtraj.formats.trr highlighting module code... [ 42%] mdtraj.formats.xtc highlighting module code... [ 44%] mdtraj.formats.xyzfile highlighting module code... [ 46%] mdtraj.geometry.angle highlighting module code... [ 48%] mdtraj.geometry.contact highlighting module code... [ 50%] mdtraj.geometry.dihedral highlighting module code... [ 52%] mdtraj.geometry.distance highlighting module code... [ 54%] mdtraj.geometry.drid highlighting module code... [ 56%] mdtraj.geometry.dssp highlighting module code... [ 58%] mdtraj.geometry.hbond highlighting module code... [ 60%] mdtraj.geometry.neighbors highlighting module code... [ 62%] mdtraj.geometry.order highlighting module code... [ 65%] mdtraj.geometry.pi_stacking highlighting module code... [ 67%] mdtraj.geometry.rdf highlighting module code... [ 69%] mdtraj.geometry.rg highlighting module code... [ 71%] mdtraj.geometry.sasa highlighting module code... [ 73%] mdtraj.geometry.shape highlighting module code... [ 75%] mdtraj.geometry.thermodynamic_properties highlighting module code... [ 77%] mdtraj.nmr.scalar_couplings highlighting module code... [ 79%] mdtraj.nmr.shift_wrappers highlighting module code... [ 81%] mdtraj.reporters.dcdreporter highlighting module code... [ 83%] mdtraj.reporters.hdf5reporter highlighting module code... [ 85%] mdtraj.reporters.netcdfreporter highlighting module code... [ 88%] mdtraj.utils highlighting module code... [ 90%] mdtraj.utils.contextmanagers highlighting module code... [ 92%] mdtraj.utils.delay_import highlighting module code... [ 94%] mdtraj.utils.rotation highlighting module code... [ 96%] mdtraj.utils.unit highlighting module code... [ 98%] mdtraj.utils.unitcell highlighting module code... [100%] mdtraj.utils.validation writing additional pages... search done copying images... [ 11%] ../build/doctrees/nbsphinx/notebook-examples_clustering_11_0.png copying images... [ 22%] ../build/doctrees/nbsphinx/notebook-examples_hbonds_9_1.png copying images... [ 33%] ../build/doctrees/nbsphinx/notebook-examples_native-contact_6_0.png copying images... [ 44%] ../build/doctrees/nbsphinx/notebook-examples_pca_9_0.png copying images... [ 56%] ../build/doctrees/nbsphinx/notebook-examples_pca_12_0.png copying images... [ 67%] ../build/doctrees/nbsphinx/notebook-examples_ramachandran-plot_7_1.png copying images... [ 78%] ../build/doctrees/nbsphinx/notebook-examples_rmsd-drift_7_1.png copying images... [ 89%] ../build/doctrees/nbsphinx/notebook-examples_solvent-accessible-surface-area_8_0.png copying images... [100%] ../build/doctrees/nbsphinx/notebook-examples_solvent-accessible-surface-area_10_0.png dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 54 warnings. The HTML pages are in ../build/html. Build finished. The HTML pages are in /build/reproducible-path/mdtraj-1.11.0/build/html. make[2]: Leaving directory '/build/reproducible-path/mdtraj-1.11.0/docs' for img in `find /build/reproducible-path/mdtraj-1.11.0/build/html/examples -name *.png`; do \ mv $img /build/reproducible-path/mdtraj-1.11.0/build/html/examples; \ done sed "s|/build/reproducible-path/mdtraj-1.11.0/build/html/examples/|./|g; s|.ipynb|.ipynb.gz|g" -i /build/reproducible-path/mdtraj-1.11.0/build/html/examples/*.html sed "s|/build/reproducible-path/mdtraj-1.11.0/debian/external|http://www.rcsb.org/pdb/files|g" -i /build/reproducible-path/mdtraj-1.11.0/build/html/examples/*.html rm /build/reproducible-path/mdtraj-1.11.0/build/html/examples/iterload/data rm -rf /build/reproducible-path/mdtraj-1.11.0/examples mv /build/reproducible-path/mdtraj-1.11.0/examples.orig /build/reproducible-path/mdtraj-1.11.0/examples make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.11.0' dh_install -O--buildsystem=pybuild install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples/data cp --reflink=auto -a ./debian/external/2EQQ.pdb ./debian/external/2MI7.pdb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples/data/ install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doi-10.1016_j.bpj.2015.08.015-blue.svg cp --reflink=auto -a ./debian/external/doi-10.1016_j.bpj.2015.08.015-blue.svg debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doi-10.1016_j.bpj.2015.08.015-blue.svg/ dh_installdocs -O--buildsystem=pybuild dh_installdocs: warning: Cannot auto-detect main package for python-mdtraj-doc. If the default is wrong, please use --doc-main-package install -m0755 -d debian/python3-mdtraj/usr/share/doc/python3-mdtraj install -p -m0644 debian/copyright debian/python3-mdtraj/usr/share/doc/python3-mdtraj/copyright install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc cd './build/html/..' && find 'html' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/mdtraj-1.11.0/debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc cp --reflink=auto -a ./README.md debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc chmod -R u\+rw,go=rX debian/python-mdtraj-doc/usr/share/doc install -p -m0644 debian/copyright debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/copyright install -m0755 -d debian/python-mdtraj-doc/usr/share/doc-base/ install -p -m0644 debian/python-mdtraj-doc.doc-base debian/python-mdtraj-doc/usr/share/doc-base/python-mdtraj-doc.mdtraj debian/rules override_dh_sphinxdoc-indep make[1]: Entering directory '/build/reproducible-path/mdtraj-1.11.0' dh_sphinxdoc -i ln -sf ../../../../../sphinx_rtd_theme/static/js/theme.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/theme.js ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.ttf ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.svg debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.svg ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.eot debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.eot ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.ttf ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.ttf ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.ttf ln -sf ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Regular.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Bold.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/css/theme.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css ln -sf ../../../../../sphinx_rtd_theme/static/css/badge_only.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css ln -sf ../../../../javascript/sphinxdoc/1.0/language_data.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/language_data.js ln -sf ../../../../javascript/sphinxdoc/1.0/doctools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js ln -sf ../../../../javascript/jquery/jquery.min.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/jquery.js ln -sf ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/sphinx_highlight.js ln -sf ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/searchtools.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/.buildinfo mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars sed "s|src=\"https://img.shields.io/badge/DOI-10.1016%2Fj.bpj.2015.08.015-blue.svg\"|src=\"_static/doi-10.1016_j.bpj.2015.08.015-blue.svg\"|g" -i debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/index.html make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.11.0' dh_sphinxdoc -O--buildsystem=pybuild -Npython-mdtraj-doc dh_sphinxdoc: warning: Sphinx documentation not found dh_installchangelogs -O--buildsystem=pybuild install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc install -p -m0644 debian/.debhelper/generated/python-mdtraj-doc/dh_installchangelogs.dch.trimmed debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/changelog.Debian install -m0755 -d debian/python3-mdtraj/usr/share/doc/python3-mdtraj install -p -m0644 debian/.debhelper/generated/python3-mdtraj/dh_installchangelogs.dch.trimmed debian/python3-mdtraj/usr/share/doc/python3-mdtraj/changelog.Debian dh_installexamples -O--buildsystem=pybuild dh_installexamples: warning: Cannot auto-detect main package for python-mdtraj-doc. If the default is wrong, please use --doc-main-package install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/1vii_3frames.pdb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/ala2.h5 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/atom-selection.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/centroids.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/clustering.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/data debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/hbonds.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/iterload.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/native-contact.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/nmr.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/pi_stacking.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/principal-components.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/ramachandran-plot.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/rmsd-benchmark.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/rmsd-drift.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/simulation-with-openmm.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/solvent-accessible-surface-area.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/test_examples.py debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/two-pass-clustering.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples dh_installman -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/usr/share/man/man1/ install -p -m0644 ./debian/mdconvert-mdtraj.1 debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1 install -m0755 -d debian/python3-mdtraj/usr/share/man/man1/ install -p -m0644 ./debian/mdinspect.1 debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 man-recode --to-code UTF-8 --suffix .dh-new debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 man-recode --to-code UTF-8 --suffix .dh-new debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1 mv debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1.dh-new debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1 chmod 0644 -- debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1 mv debian/python3-mdtraj/usr/share/man/man1/mdinspect.1.dh-new debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 chmod 0644 -- debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 dh_python3 -O--buildsystem=pybuild D: dh_python3 dh_python3:180: version: 6.20250414 D: dh_python3 dh_python3:181: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:182: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=['--buildsystem=pybuild']) D: dh_python3 dh_python3:183: supported Python versions: 3.13 (default=3.13) D: dh_python3 debhelper:166: skipping package python-mdtraj-doc (missing ${python3:Depends} in Depends/Recommends) D: dh_python3 debhelper:174: source=mdtraj, binary packages=['python3-mdtraj'] D: dh_python3 dh_python3:205: processing package python3-mdtraj... D: dh_python3 fs:50: moving files from debian/python3-mdtraj/usr/lib/python3.13/dist-packages to debian/python3-mdtraj/usr/lib/python3/dist-packages/ I: dh_python3 tools:114: replacing shebang in debian/python3-mdtraj/usr/bin/mdinspect I: dh_python3 tools:114: replacing shebang in debian/python3-mdtraj/usr/bin/mdconvert-mdtraj D: dh_python3 fs:249: removing dist-packages/.pytest_cache D: dh_python3 fs:338: package python3-mdtraj details = {'requires.txt': {'debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.11.0.egg-info/requires.txt'}, 'egg-info': {'debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.11.0.egg-info/PKG-INFO'}, 'dist-info': set(), 'nsp.txt': set(), 'shebangs': {/usr/bin/python3, /usr/bin/python3}, 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': {Version('3.13')}, 'ext_no_version': set()} D: dh_python3 depends:103: generating dependencies for package python3-mdtraj D: dh_python3 pydist:175: trying to find dependency for numpy<3,>=1.25.0 (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:277: dependency: included in build-deps with limits D: dh_python3 pydist:175: trying to find dependency for packaging (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:284: dependency: included in build-deps D: dh_python3 pydist:175: trying to find dependency for pyparsing (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:284: dependency: included in build-deps D: dh_python3 pydist:175: trying to find dependency for scipy (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:284: dependency: included in build-deps D: dh_python3 depends:253: D={'python3-numpy (>= 2.0.0~)', 'python3-scipy', 'python3 (>= 3.13~)', 'python3:any', 'python3-packaging', 'python3-pyparsing', 'python3 (<< 3.14)'}; R=[]; S=[]; E=[], B=[]; RT=[] rm -f debian/python-mdtraj-doc.debhelper.log debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/mdtraj-1.11.0' # setup.py builds the static lib libtheobald.a for each python version # but dh_python3 can't tell the difference between the different builds, # since py3.11 compiles libtheobald.o with -fwrapv, where py3.12 uses -fno-strict-overflow # So clean up manually (assume the binary difference is not an issue) rm -f debian/python3-mdtraj/usr/lib/python3.*/dist-packages/mdtraj/core/lib/libtheobald.a for d in debian/python3-mdtraj/usr/lib/python3.*/dist-packages/mdtraj/core/lib; do if [-d $d]; then rmdir -p --ignore-fail-on-non-empty $d; fi; done /bin/sh: 1: [-d: not found make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.11.0' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css ln -s ../../../../../sphinx_rtd_theme/static/css/theme.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css ln -s ../../../../../sphinx_rtd_theme/static/css/badge_only.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.svg ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.svg debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.svg rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.eot ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.eot debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.eot rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Regular.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Regular.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Bold.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Bold.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/theme.js ln -s ../../../../../sphinx_rtd_theme/static/js/theme.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/theme.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/language_data.js ln -s ../../../../javascript/sphinxdoc/1.0/language_data.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/language_data.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js ln -s ../../../../javascript/sphinxdoc/1.0/doctools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/jquery.js ln -s ../../../../javascript/jquery/jquery.min.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/jquery.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/sphinx_highlight.js ln -s ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/sphinx_highlight.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/searchtools.js ln -s ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/searchtools.js dh_strip_nondeterminism -O--buildsystem=pybuild Using 1754933451 as canonical time Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_solvent-accessible-surface-area_8_0.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_solvent-accessible-surface-area_10_0.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_pca_9_0.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_pca_12_0.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_rmsd-drift_7_1.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_ramachandran-plot_7_1.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_clustering_11_0.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/plus.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/file.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_native-contact_6_0.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_hbonds_9_1.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/minus.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/mdtraj_logo-small.png using File::StripNondeterminism::handlers::png dh_compress -O--buildsystem=pybuild cd debian/python3-mdtraj cd debian/python-mdtraj-doc chmod a-x usr/share/doc/python3-mdtraj/changelog.Debian usr/share/man/man1/mdconvert-mdtraj.1 usr/share/man/man1/mdinspect.1 gzip -9nf usr/share/doc/python3-mdtraj/changelog.Debian usr/share/man/man1/mdconvert-mdtraj.1 usr/share/man/man1/mdinspect.1 chmod a-x usr/share/doc/python-mdtraj-doc/changelog.Debian usr/share/doc/python-mdtraj-doc/html/_static/example-trajectoryview-data.json usr/share/doc/python-mdtraj-doc/html/_static/mdtraj_logo.xcf usr/share/doc/python-mdtraj-doc/html/notebook-examples/atom-selection.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/clustering.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/hbonds.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/iterload.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/native-contact.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/pca.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/pi_stacking.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/ramachandran-plot.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/rmsd-benchmark.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/rmsd-drift.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/solvent-accessible-surface-area.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/two-pass-clustering.ipynb gzip -9nf usr/share/doc/python-mdtraj-doc/changelog.Debian usr/share/doc/python-mdtraj-doc/html/_static/example-trajectoryview-data.json usr/share/doc/python-mdtraj-doc/html/_static/mdtraj_logo.xcf usr/share/doc/python-mdtraj-doc/html/notebook-examples/atom-selection.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/clustering.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/hbonds.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/iterload.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/native-contact.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/pca.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/pi_stacking.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/ramachandran-plot.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/rmsd-benchmark.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/rmsd-drift.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/solvent-accessible-surface-area.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/two-pass-clustering.ipynb cd '/build/reproducible-path/mdtraj-1.11.0' cd '/build/reproducible-path/mdtraj-1.11.0' dh_fixperms -O--buildsystem=pybuild find debian/python3-mdtraj ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python-mdtraj-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python3-mdtraj/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-mdtraj/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-mdtraj/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/python3-mdtraj/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python-mdtraj-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/python-mdtraj-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-mdtraj -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python-mdtraj-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/python3-mdtraj/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/python-mdtraj-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-mdtraj/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-linux-gnu dwz -mdebian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-linux-gnu/python3-mdtraj.debug -M/usr/lib/debug/.dwz/aarch64-linux-gnu/python3-mdtraj.debug -- debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so objcopy --compress-debug-sections debian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-linux-gnu/python3-mdtraj.debug chmod 0644 -- debian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-linux-gnu/python3-mdtraj.debug dh_strip -a -O--buildsystem=pybuild install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/42 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/42/62309eab38eedaa4aaa8c1c65946414478be26.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/42/62309eab38eedaa4aaa8c1c65946414478be26.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/42/62309eab38eedaa4aaa8c1c65946414478be26.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/77 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/77/25e3e1ac994cd4bb6d7251272afa998aa92046.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/77/25e3e1ac994cd4bb6d7251272afa998aa92046.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/77/25e3e1ac994cd4bb6d7251272afa998aa92046.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/79 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/79/a61fa8c8e41faf6adf24236580390c690382dd.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/79/a61fa8c8e41faf6adf24236580390c690382dd.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/79/a61fa8c8e41faf6adf24236580390c690382dd.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/bf objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/bf/0ce051b5ab01f99bc0272c7e6a478a98f1e2dc.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/bf/0ce051b5ab01f99bc0272c7e6a478a98f1e2dc.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/bf/0ce051b5ab01f99bc0272c7e6a478a98f1e2dc.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/5d objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/5d/13f9119605f75ec6a358762622dfda4ad0e5b7.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/5d/13f9119605f75ec6a358762622dfda4ad0e5b7.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/5d/13f9119605f75ec6a358762622dfda4ad0e5b7.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/03 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/03/d4cb6392c72843f79d3ce8ee5254b124f39095.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/03/d4cb6392c72843f79d3ce8ee5254b124f39095.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/03/d4cb6392c72843f79d3ce8ee5254b124f39095.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/11 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/11/e90292f7e2aa0380e034af5404e5095516df67.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/11/e90292f7e2aa0380e034af5404e5095516df67.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/11/e90292f7e2aa0380e034af5404e5095516df67.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/3c objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/3c/d19ddf7c4885869b2d8c42d2be5ff5413d44ca.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/3c/d19ddf7c4885869b2d8c42d2be5ff5413d44ca.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/3c/d19ddf7c4885869b2d8c42d2be5ff5413d44ca.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/ee objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/ee/7f2b180cd645639b566c2548f1ef741bf3d485.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/ee/7f2b180cd645639b566c2548f1ef741bf3d485.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/ee/7f2b180cd645639b566c2548f1ef741bf3d485.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/33 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/33/4910e9d07d72a0155930512d1ce93cb7d10698.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/33/4910e9d07d72a0155930512d1ce93cb7d10698.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/33/4910e9d07d72a0155930512d1ce93cb7d10698.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives -R .gnu.lto_\* -R .gnu.debuglto_\* -N __gnu_lto_slim -N __gnu_lto_v1 debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/core/lib/libtheobald.a install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-linux-gnu debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/python3-mdtraj/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/python3-mdtraj/usr/lib/debug install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/share/doc ln -s python3-mdtraj debian/.debhelper/python3-mdtraj/dbgsym-root/usr/share/doc/python3-mdtraj-dbgsym install -m0755 -d debian/.debhelper/python3-mdtraj dh_makeshlibs -a -O--buildsystem=pybuild rm -f debian/python3-mdtraj/DEBIAN/shlibs dh_shlibdeps -a -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/DEBIAN dpkg-shlibdeps -Tdebian/python3-mdtraj.substvars debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/DEBIAN printf '#!/bin/sh\nset -e\n' > debian/python3-mdtraj/DEBIAN/postinst cat debian/python3-mdtraj.postinst.debhelper >> debian/python3-mdtraj/DEBIAN/postinst chmod 0755 -- debian/python3-mdtraj/DEBIAN/postinst printf '#!/bin/sh\nset -e\n' > debian/python3-mdtraj/DEBIAN/prerm cat debian/python3-mdtraj.prerm.debhelper >> debian/python3-mdtraj/DEBIAN/prerm chmod 0755 -- debian/python3-mdtraj/DEBIAN/prerm install -m0755 -d debian/python-mdtraj-doc/DEBIAN dh_numpy3 -O--buildsystem=pybuild Possible precedence issue with control flow operator (return) at /usr/bin/dh_numpy3 line 57. mv debian/python3-mdtraj.substvars.new debian/python3-mdtraj.substvars dh_gencontrol -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/DEBIAN echo misc:Depends= >> debian/python3-mdtraj.substvars echo misc:Pre-Depends= >> debian/python3-mdtraj.substvars install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN dpkg-gencontrol -ppython3-mdtraj -ldebian/changelog -Tdebian/python3-mdtraj.substvars -cdebian/control -Pdebian/.debhelper/python3-mdtraj/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=python3-mdtraj-dbgsym "-DDepends=python3-mdtraj (= \${binary:Version})" "-DDescription=debug symbols for python3-mdtraj" "-DBuild-Ids=03d4cb6392c72843f79d3ce8ee5254b124f39095 11e90292f7e2aa0380e034af5404e5095516df67 334910e9d07d72a0155930512d1ce93cb7d10698 3cd19ddf7c4885869b2d8c42d2be5ff5413d44ca 4262309eab38eedaa4aaa8c1c65946414478be26 5d13f9119605f75ec6a358762622dfda4ad0e5b7 7725e3e1ac994cd4bb6d7251272afa998aa92046 79a61fa8c8e41faf6adf24236580390c690382dd bf0ce051b5ab01f99bc0272c7e6a478a98f1e2dc ee7f2b180cd645639b566c2548f1ef741bf3d485" -DSection=debug -UMulti-Arch -UReplaces -UBreaks install -m0755 -d debian/python-mdtraj-doc/DEBIAN echo misc:Depends= >> debian/python-mdtraj-doc.substvars echo misc:Pre-Depends= >> debian/python-mdtraj-doc.substvars dpkg-gencontrol -ppython-mdtraj-doc -ldebian/changelog -Tdebian/python-mdtraj-doc.substvars -cdebian/control -Pdebian/python-mdtraj-doc chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN/control dpkg-gencontrol -ppython3-mdtraj -ldebian/changelog -Tdebian/python3-mdtraj.substvars -cdebian/control -Pdebian/python3-mdtraj dpkg-gencontrol: warning: package python-mdtraj-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined chmod 0644 -- debian/python-mdtraj-doc/DEBIAN/control chmod 0644 -- debian/python3-mdtraj/DEBIAN/control dh_md5sums -O--buildsystem=pybuild install -m0755 -d debian/python-mdtraj-doc/DEBIAN install -m0755 -d debian/python3-mdtraj/DEBIAN cd debian/python3-mdtraj >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/python-mdtraj-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/python3-mdtraj/DEBIAN/md5sums install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN cd debian/.debhelper/python3-mdtraj/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/python-mdtraj-doc/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN/md5sums dh_builddeb -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/python-mdtraj-doc .. dpkg-deb --root-owner-group --build debian/.debhelper/python3-mdtraj/dbgsym-root .. dpkg-deb --root-owner-group --build debian/python3-mdtraj .. dpkg-deb: building package 'python3-mdtraj-dbgsym' in '../python3-mdtraj-dbgsym_1.11.0-1_arm64.deb'. dpkg-deb: building package 'python-mdtraj-doc' in '../python-mdtraj-doc_1.11.0-1_all.deb'. dpkg-deb: building package 'python3-mdtraj' in '../python3-mdtraj_1.11.0-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../mdtraj_1.11.0-1_arm64.buildinfo dpkg-genchanges --build=binary -O../mdtraj_1.11.0-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from mdtraj-1.11.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3339124 and its subdirectories I: Current time: Sat Aug 16 01:55:04 -12 2025 I: pbuilder-time-stamp: 1755352504 Sat Aug 16 13:55:06 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Sat Aug 16 13:55:06 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Sat Aug 16 14:09:01 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Sat Aug 16 14:09:01 UTC 2025 I: mdtraj_1.11.0-1_arm64.changes: Format: 1.8 Date: Mon, 11 Aug 2025 19:30:51 +0200 Source: mdtraj Binary: python-mdtraj-doc python3-mdtraj python3-mdtraj-dbgsym Architecture: all arm64 Version: 1.11.0-1 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Drew Parsons Description: python-mdtraj-doc - Read, write and analyze MD trajectories in Python (documentation) python3-mdtraj - Read, write and analyze MD trajectories in Python Changes: mdtraj (1.11.0-1) unstable; urgency=medium . * New upstream release - versioned Build-Depends: python3-numpy (>= 2.0.0~) * drop debian patch revert_flaky_PR1972.patch for new upstream release * Build-Depends: dh-sequence-numpy3 and remove dh_numpy3 from execute_after_dh_python3 * Standards-Version: 4.7.2 * Depends: python3-pytest-rerunfailures (for rerun option in pytest.mark.flaky). Run build-time tests . * debian/tests: skip example pi_stacking.ipynb (needs py3Dmol) * apply test skips from debian/tests to PYBUILD_TEST_ARGS in debian/rules (skip tests needing internet or 3rd party packages) * skip mdconvert in build tests (binary not yet accessible) * debian patch openmm_version_skip.patch skips test_topology_openmm_formal_charges in test_topology if openmm 8.2 or later is not available (introducing the formal_charges API). See also upstream #1956, PR#1967. Build-Depends: python3-packaging Checksums-Sha1: eb1043a3435972dc3f1db961a5f976f2e9fbd1d2 13883 mdtraj_1.11.0-1_arm64.buildinfo 7fea2c3221bca06f3bd4377e820c8f8b254d93a8 1897332 python-mdtraj-doc_1.11.0-1_all.deb bd0287f9b78edc72181eba005e1f78c5012bcbb5 5526864 python3-mdtraj-dbgsym_1.11.0-1_arm64.deb f97a880793a41acc9afe2b88d5fe5845d6ef47d4 956980 python3-mdtraj_1.11.0-1_arm64.deb Checksums-Sha256: 24a3f1353d22c87ecf83009a22bb140f48ac6f522b3266b3347e56fb34b9890e 13883 mdtraj_1.11.0-1_arm64.buildinfo 06547d1f5a5b400ee3010a440a496f807f58e02135efcf0b55321789b2d7f6b9 1897332 python-mdtraj-doc_1.11.0-1_all.deb 7e49eb775c439ea2c2664dd77e5eed76ddc0d6a3966bb24ce7c1c4a6b1beb2df 5526864 python3-mdtraj-dbgsym_1.11.0-1_arm64.deb 15a5be2ec2f080330ccf270ada4a3804f91598b30d7ef108f9e47aa517919c5e 956980 python3-mdtraj_1.11.0-1_arm64.deb Files: e90785c7d639ed4e266f5df6f185ecb6 13883 python optional mdtraj_1.11.0-1_arm64.buildinfo b3f987a93661393d5b48909ea5865e16 1897332 doc optional python-mdtraj-doc_1.11.0-1_all.deb 670db734e89807e956474e456ddc9d00 5526864 debug optional python3-mdtraj-dbgsym_1.11.0-1_arm64.deb 958d7d1e779974af2685ff288b2bf809 956980 python optional python3-mdtraj_1.11.0-1_arm64.deb Sat Aug 16 14:09:02 UTC 2025 I: diffoscope 303 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_11-118222.service; invocation ID: e92154b9ecf84a0b81c6da626dbe1411 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.GWNZtOSj/mdtraj_1.11.0-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.GWNZtOSj/mdtraj_1.11.0-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.GWNZtOSj/mdtraj_1.11.0-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.GWNZtOSj/b1/mdtraj_1.11.0-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.GWNZtOSj/b2/mdtraj_1.11.0-1_arm64.changes ## close_archive (total time: 0.000s) 0.000s 20 calls diffoscope.comparators.xz.XzContainer 0.000s 14 calls diffoscope.comparators.tar.TarContainer 0.000s 8 calls diffoscope.comparators.deb.DebContainer 0.000s 6 calls diffoscope.comparators.deb.DebTarContainer ## command (total time: 23.810s) 9.680s 117 calls diff 9.424s 992 calls readelf 3.901s 176 calls objdump 0.419s 20 calls xz 0.311s 2 calls objcopy 0.059s 22 calls strings 0.008s 3 calls cmp 0.008s 3 calls cmp (external) 0.001s 21 calls cmp (internal) ## compare_files (cumulative) (total time: 74.729s) 14.151s 1 call abc.DotChangesFile 14.129s 2 calls abc.DebFile 14.081s 4 calls abc.XzFile 13.749s 2 calls abc.DebDataTarFile 13.482s 2 calls abc.ElfFile 4.706s 8 calls diffoscope.comparators.elf.ElfCodeSection 0.331s 33 calls diffoscope.comparators.elf.ElfSection 0.049s 2 calls abc.TarFile 0.026s 3 calls diffoscope.comparators.elf.ElfStringSection 0.010s 1 call abc.TextFile 0.008s 2 calls abc.Md5sumsFile 0.006s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection ## container_extract (total time: 0.538s) 0.419s 20 calls diffoscope.comparators.xz.XzContainer 0.073s 252 calls diffoscope.comparators.deb.DebTarContainer 0.038s 24 calls diffoscope.comparators.deb.DebContainer 0.008s 22 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 0.045s) 0.045s 65 calls linediff ## has_same_content_as (total time: 0.011s) 0.006s 2 calls abc.DebDataTarFile 0.002s 3 calls abc.DebFile 0.000s 6 calls abc.TextFile 0.000s 4 calls abc.Md5sumsFile 0.000s 4 calls abc.XzFile 0.000s 2 calls abc.TarFile 0.000s 2 calls abc.ElfFile 0.000s 33 calls diffoscope.comparators.elf.ElfSection 0.000s 1 call diffoscope.comparators.binary.FilesystemFile 0.000s 1 call abc.DotChangesFile 0.000s 1 call diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 8 calls diffoscope.comparators.elf.ElfCodeSection 0.000s 3 calls diffoscope.comparators.elf.ElfStringSection 0.000s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection ## main (total time: 14.778s) 14.775s 2 calls outputs 0.003s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 20 calls diffoscope.comparators.xz.XzContainer 0.000s 14 calls diffoscope.comparators.tar.TarContainer 0.000s 10 calls diffoscope.comparators.deb.DebContainer 0.000s 6 calls diffoscope.comparators.deb.DebTarContainer ## output (total time: 0.340s) 0.206s 1 call html 0.079s 1 call text 0.054s 1 call json ## recognizes (total time: 0.382s) 0.180s 914 calls diffoscope.comparators.utils.archive.ArchiveMember 0.115s 1924 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.062s 12 calls diffoscope.comparators.binary.FilesystemFile 0.026s 324 calls diffoscope.comparators.debian.DebControlMember ## specialize (total time: 0.350s) 0.350s 70 calls specialize Finished with result: success Main processes terminated with: code=exited, status=1/FAILURE Service runtime: 15.023s CPU time consumed: 20.106s Memory peak: 214M (swap: 0B) Sat Aug 16 14:09:17 UTC 2025 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Sat Aug 16 14:09:17 UTC 2025 E: mdtraj failed to build reproducibly in forky on arm64. Sat Aug 16 14:09:20 UTC 2025 I: Removing signed mdtraj_1.11.0-1_arm64.buildinfo.asc files: removed './b1/mdtraj_1.11.0-1_arm64.buildinfo.asc' removed './b2/mdtraj_1.11.0-1_arm64.buildinfo.asc'