Tue Nov 12 21:48:37 UTC 2024 I: starting to build mdtraj/unstable/amd64 on jenkins on '2024-11-12 21:48' Tue Nov 12 21:48:37 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_36/35622/console.log Tue Nov 12 21:48:37 UTC 2024 I: Downloading source for unstable/mdtraj=1.10.1-2 --2024-11-12 21:48:37-- http://deb.debian.org/debian/pool/main/m/mdtraj/mdtraj_1.10.1-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2702 (2.6K) [text/prs.lines.tag] Saving to: ‘mdtraj_1.10.1-2.dsc’ 0K .. 100% 377M=0s 2024-11-12 21:48:37 (377 MB/s) - ‘mdtraj_1.10.1-2.dsc’ saved [2702/2702] Tue Nov 12 21:48:37 UTC 2024 I: mdtraj_1.10.1-2.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: 1.10.1-2 Maintainer: Debichem Team Uploaders: Drew Parsons Homepage: https://mdtraj.org/ Standards-Version: 4.7.0 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-pandas, python3-pytest, python3-sklearn Build-Depends: debhelper-compat (= 13), dh-sequence-python3, cython3, pandoc, python3-setuptools, python3-all-dev, python3-gsd, python3-numpy, python3-scipy, python3-nbsphinx, python3-nbsphinx-link, python3-netcdf4, python3-networkx, python3-pandas, python3-pyparsing, python3-sphinx, python3-tables, python3-versioneer, libjs-mathjax Build-Depends-Indep: 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: 58cc5041ad0faf24b219b3678c09e4e9bafb2f7e 21864788 mdtraj_1.10.1.orig.tar.gz 39fb90255b9cf75cc91455052fc65153415f672b 295976 mdtraj_1.10.1-2.debian.tar.xz Checksums-Sha256: cd7d90e6b3abcf1d83f1236727d6aa9897f2ba197332728cea2810e1fa3b6856 21864788 mdtraj_1.10.1.orig.tar.gz 5c3eb5b8c68ea5ec2f132a21435436795555c818367aba242020393b79895b24 295976 mdtraj_1.10.1-2.debian.tar.xz Files: 24c5d345cf37f9b28ea2dfa9200894cf 21864788 mdtraj_1.10.1.orig.tar.gz ffe1b46a53ae7ad4411890b2265e614f 295976 mdtraj_1.10.1-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEE3lnVbvHK7ir4q61+p3sXeEcY/EFAmcyYfMSHGVhbWFudUBk ZWJpYW4ub3JnAAoJEPqd7F3hHGPxpycP/ivquqXqoja2kYgLHR28B0lgC4Hj+rMb RfRxU6Jhb5P97Pu5tzMVY/HgMI0JEz5dZc//vvowbtBZJ0vJqGlqV4NQKOl4oWPZ Yg1tbuV7TdaY/LaxFEWpFqCXrUhixNNPhbDCtCB/j5ei9yllIAxDAtDyYbMFT7TJ BWePW9n4sVXyAXs6lgmrE7vgqPivKLnAwKsZo7HuWHoozEBWnOqY5Pn8Z9ig6Txy SLYlDeUrunT2sT9A4pcOAj6he9YzS1RFvsA0WIO9NlIibE99XmQhbOTni8ug40Jn 6cmhhezUtvYz9uHz9EjPGPbllc5EpAByLnVygA3o47PzPuEvZd38ieN0dNWI5/Vj vbqsPuJLZ23LaDOopLm45r5ltPWUHDIlE5++TEFS6ivsLU41H+7TKnm4FrYGawCs XRZV7/vfroMAtBhbqTn3W78iPkiRxsy73N5YlFdUqcMNdNF2YQvHsu2gzh8wFHKT A7qew2pOtl6xC7op6W/9u+BnhC8/N48nJcSo346FRtovPxW7QuhDJUzDSqMRMTO5 3z0D138QvYttGU44CIJJVIJj+5s8Bvo6qdMnYTesLeUFF9wuRW+4g3DMYsh7zV0m +BHv8h1gMmkfM1hC6GA3wTJYbyr68pTgIWzXmzysEBDLB+WTRiceW86ss2puTdu9 WXtBxeaPt0Ep =I/kS -----END PGP SIGNATURE----- Tue Nov 12 21:48:37 UTC 2024 I: Checking whether the package is not for us Tue Nov 12 21:48:37 UTC 2024 I: Starting 1st build on remote node infom02-amd64.debian.net. Tue Nov 12 21:48:37 UTC 2024 I: Preparing to do remote build '1' on infom02-amd64.debian.net. Tue Nov 12 21:57:31 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Dec 15 16:11:39 -12 2025 I: pbuilder-time-stamp: 1765858299 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [mdtraj_1.10.1-2.dsc] I: copying [./mdtraj_1.10.1.orig.tar.gz] I: copying [./mdtraj_1.10.1-2.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Nov 11 19:58:43 2024 gpgv: using RSA key 13796755BBC72BB8ABE2AEB5FA9DEC5DE11C63F1 gpgv: issuer "eamanu@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.10.1-2.dsc: no acceptable signature found dpkg-source: info: extracting mdtraj in mdtraj-1.10.1 dpkg-source: info: unpacking mdtraj_1.10.1.orig.tar.gz dpkg-source: info: unpacking mdtraj_1.10.1-2.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2704318/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='1aa17826c35b409f9eaf1ff923e6ee06' 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='2704318' 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.OR2hRjOM/pbuilderrc_eout --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OR2hRjOM/b1 --logfile b1/build.log mdtraj_1.10.1-2.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom02-amd64 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2704318/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, cython3, pandoc, python3-setuptools, python3-all-dev, python3-gsd, python3-numpy, python3-scipy, python3-nbsphinx, python3-nbsphinx-link, python3-netcdf4, python3-networkx, python3-pandas, python3-pyparsing, python3-sphinx, python3-tables, python3-versioneer, libjs-mathjax, 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 ... 19969 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 cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on pandoc; however: Package pandoc 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; 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-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-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 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} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhdf5-103-1t64{a} libhdf5-hl-100t64{a} libicu72{a} libimagequant0{a} libipt2{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} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblua5.4-0{a} liblzo2-2{a} libmagic-mgc{a} libmagic1t64{a} libnetcdf19t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnorm1t64{a} libnsl2{a} libnuma1{a} libopenjp2-7{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} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsnappy1v5{a} libsodium23{a} libsource-highlight-common{a} libsource-highlight4t64{a} libssh2-1t64{a} libsz2{a} libtcl8.6{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} libzmq5{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-appdirs{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-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-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-prompt-toolkit{a} python3-psutil{a} python3-ptyprocess{a} python3-pure-eval{a} python3-py{a} python3-pygments{a} python3-pyparsing{a} python3-referencing{a} python3-requests{a} python3-roman{a} python3-rpds-py{a} python3-scipy{a} python3-setuptools{a} python3-six{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-tz{a} python3-ufolib2{a} python3-urllib3{a} python3-versioneer{a} python3-wcwidth{a} python3-webencodings{a} python3-zipp{a} python3-zmq{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} python3.12-tk{a} python3.13-tk{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} tk8.6-blt2.5{a} tzdata{a} 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 libc6-dbg libglib2.0-data 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-gdal python3-json-pointer python3-numba python3-odf python3-olefile python3-openpyxl python3-pydot python3-pygraphviz python3-pytest python3-rfc3987 python3-simplejson python3-sphinxcontrib.bibtex python3-uritemplate python3-webcolors python3-yaml shared-mime-info wget xdg-user-dirs 0 packages upgraded, 292 newly installed, 0 to remove and 0 not upgraded. Need to get 200 MB of archives. After unpacking 980 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libdebuginfod-common all 0.192-4 [23.7 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-3 [255 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 16 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 26 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-10 [97.2 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b5 [307 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b2 [24.4 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get: 67 http://deb.debian.org/debian unstable/main amd64 cython3 amd64 3.0.11+dfsg-1 [2449 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 74 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2 [699 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 88 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.2.0-1 [731 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20241024 [109 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.2.1-1 [190 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libdw1t64 amd64 0.192-4 [255 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libbabeltrace1 amd64 1.5.11-4 [176 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.4.0-1+b1 [63.6 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.11.0-1 [359 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libjson-c5 amd64 0.18+ds-1 [46.0 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libdebuginfod1t64 amd64 0.192-4 [32.4 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libipt2 amd64 2.1.1-1 [47.8 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.7-3 [2153 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libsource-highlight-common all 3.1.9-4.3 [77.5 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libsource-highlight4t64 amd64 3.1.9-4.3+b1 [335 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 gdb amd64 15.2-1 [4380 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3+b1 [152 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libsnappy1v5 amd64 1.2.1-1+b1 [29.6 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libblosc1 amd64 1.21.5+ds-1+b2 [49.5 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libblosc2-4 amd64 2.15.1+ds-1 [192 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get: 133 http://deb.debian.org/debian unstable/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4 [1253 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-4 [63.9 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3+b1 [2450 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 liblua5.4-0 amd64 5.4.6-3+b2 [147 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 liblzo2-2 amd64 2.10-3+b1 [55.1 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libnetcdf19t64 amd64 1:4.9.2-7 [477 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libnorm1t64 amd64 1.5.9+dfsg-3.1+b1 [221 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libpgm-5.3-0t64 amd64 5.3.128~dfsg-2.1+b1 [162 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.7-3 [5124 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.12.6-1 [9952 B] Get: 158 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.12.6-1 [1064 B] Get: 159 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.1-1+b2 [14.1 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libsodium23 amd64 1.0.18-1+b2 [165 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.4.0-0.1+b1 [111 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.4.0-0.1+b1 [123 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b2 [52.7 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libzmq5 amd64 4.3.5-1+b3 [283 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 pandoc-data all 3.1.11.1-3 [459 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 pandoc amd64 3.1.11.1+ds-2 [26.4 MB] Get: 172 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 python-tables-data all 3.10.1-1 [49.5 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 python-tinycss2-common all 1.3.0-1 [31.9 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.12.6-1 [1040 B] Get: 178 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.7-3 [505 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.12.6-1 [26.1 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.12.6-1 [1068 B] Get: 181 http://deb.debian.org/debian unstable/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 python3-asttokens all 2.4.1-2 [20.5 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 python3-attr all 24.2.0-1 [68.4 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.14.0-1 [111 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 python3-webencodings all 0.5.1-5 [11.1 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 python3-html5lib all 1.2-1 [92.2 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 python3-bleach all 6.2.0-1 [51.2 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b5 [318 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 python3-soupsieve all 2.6-1 [38.3 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 python3-bs4 all 4.12.3-3 [133 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 193 http://deb.debian.org/debian unstable/main amd64 python3-cffi-backend amd64 1.17.1-2 [87.5 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-11 [4236 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 python3-cftime amd64 1.6.4-1+b1 [205 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.0-1 [118 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 python3-comm all 0.2.1-1 [8104 B] Get: 200 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.3.0-2 [215 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 python3-coverage amd64 7.6.0+dfsg1-2 [175 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 python3-cpuinfo all 9.0.0+git20221119-2 [23.4 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get: 204 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 python3-debugpy amd64 1.8.8+ds-1 [898 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 python3-roman all 4.2-1 [10.4 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 python3-executing all 2.1.0-0.1 [23.9 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 python3-fastjsonschema all 2.20.0-1 [21.8 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 python3-six all 1.16.0-7 [16.4 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-4 [95.4 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 5.3.0-1 [1251 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b4 [25.2 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.13.1-5 [16.7 MB] Get: 217 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.13.3-1 [4147 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [32.9 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.54.1-4 [1429 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 python3-gsd amd64 3.3.0-1+b1 [200 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.8-2 [41.6 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 225 http://deb.debian.org/debian unstable/main amd64 python3-parso all 0.8.3-1 [67.4 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 python3-typeshed all 0.0~git20231111.6764465-3 [1258 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 python3-jedi all 0.19.1+ds1-1 [691 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib-inline all 0.1.6-2 [8652 B] Get: 229 http://deb.debian.org/debian unstable/main amd64 python3-wcwidth all 0.2.13+dfsg1-1 [24.9 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 python3-prompt-toolkit all 3.0.48-1 [277 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 python3-pure-eval all 0.2.3-1 [11.2 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 python3-stack-data all 0.6.3-1 [21.6 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 python3-ptyprocess all 0.7.0-6 [14.5 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 python3-pexpect all 4.9-3 [55.6 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 python3-ipython all 8.29.0-1 [567 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-core all 5.7.2-4 [35.1 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 python3-psutil amd64 5.9.8-2 [225 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 python3-tornado amd64 6.4.1-3 [349 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 python3-py all 1.11.0-2 [88.7 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 python3-zmq amd64 24.0.1-5+b2 [269 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-client all 8.6.2-3 [91.5 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 python3-nest-asyncio all 1.5.4-1 [6248 B] Get: 245 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.1-1 [45.8 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 python3-ipykernel all 6.29.5-1 [102 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b1 [13.6 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 python3-joblib all 1.3.2-5 [216 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 python3-rpds-py amd64 0.21.0-1 [251 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 python3-referencing all 0.35.1-1 [23.5 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B] Get: 253 http://deb.debian.org/debian unstable/main amd64 python3-jsonschema all 4.19.2-5 [71.4 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 python3-jupyterlab-pygments all 0.2.2-3 [6096 B] Get: 255 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.7-2 [60.9 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 10.4.0-1 [502 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 python3.12-tk amd64 3.12.7-3 [112 kB] Get: 258 http://deb.debian.org/debian unstable/main amd64 python3.13-tk amd64 3.13.0-2 [103 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.12.7-1 [9444 B] Get: 260 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 10.4.0-1 [79.4 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.8.3-3 [5560 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 python3-mistune all 3.0.2-2 [33.2 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1022 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 7.4.7-4 [731 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.0.7-2 [111 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 7.4.7-4 [588 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 271 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [29.5 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 python3-msmb-theme all 1.2.0-4 [33.8 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 python3-nbformat all 5.9.1-1 [45.1 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 python3-nbclient all 0.8.0-1 [64.0 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 python3-pandocfilters all 1.5.1-1 [23.7 kB] Get: 276 http://deb.debian.org/debian unstable/main amd64 python3-tinycss2 all 1.3.0-1 [22.1 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 python3-nbconvert all 7.16.4-2 [158 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 python3-nbsphinx all 0.9.4+ds-1.1 [39.6 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 python3-nbsphinx-link all 1.3.0-4 [6264 B] Get: 280 http://deb.debian.org/debian unstable/main amd64 python3-netcdf4 amd64 1.7.2-1 [609 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 python3-networkx all 3.2.1-4 [14.2 MB] Get: 282 http://deb.debian.org/debian unstable/main amd64 python3-numexpr amd64 2.10.1-2+b1 [125 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 python3-numpydoc all 1.6.0-2 [49.6 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [4389 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 python3-sklearn-lib amd64 1.4.2+dfsg-6 [3657 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 python3-sklearn all 1.4.2+dfsg-6 [2248 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 python3-tables-lib amd64 3.10.1-1 [512 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 python3-tables all 3.10.1-1 [355 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 python3-versioneer all 0.29-1 [43.0 kB] Fetched 200 MB in 2s (84.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package fonts-lato. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19969 files and directories currently installed.) Preparing to unpack .../0-fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../1-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package ucf. Preparing to unpack .../2-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package libdebuginfod-common. Preparing to unpack .../3-libdebuginfod-common_0.192-4_all.deb ... Unpacking libdebuginfod-common (0.192-4) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../4-libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../5-libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../6-python3.12-minimal_3.12.7-3_amd64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:amd64 (3.12.7-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20401 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_amd64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21463 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-6_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-6) ... 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Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libqhull-r8.0:amd64 (2020.2-6+b2) ... Setting up liblzo2-2:amd64 (2.10-3+b1) ... Setting up libcom-err2:amd64 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libaec0:amd64 (1.1.3-1+b1) ... Setting up libsource-highlight-common (3.1.9-4.3) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up python-babel-localedata (2.14.0-1) ... Setting up libsnappy1v5:amd64 (1.2.1-1+b1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libdw1t64:amd64 (0.192-4) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Dec 16 04:14:35 UTC 2025. Universal Time is now: Tue Dec 16 04:14:35 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:amd64 (5.3.128~dfsg-2.1+b1) ... Setting up libblosc2-4:amd64 (2.15.1+ds-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:amd64 (2.82.2-2) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libexpat1-dev:amd64 (2.6.4-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libfribidi0:amd64 (1.0.15-1) ... Setting up libimagequant0:amd64 (2.18.0-1+b2) ... 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Setting up libblosc1:amd64 (1.21.5+ds-1+b2) ... Setting up liblua5.4-0:amd64 (5.4.6-3+b2) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b4) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:amd64 (1.6.0-1) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (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 (3.8.3-3) ... Setting up openssl (3.3.2-2) ... Setting up libwebpmux3:amd64 (1.4.0-0.1+b1) ... Setting up libjson-c5:amd64 (0.18+ds-1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2) ... Setting up python-tables-data (3.10.1-1) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (3.0.1+dfsg-1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up libsz2:amd64 (1.1.3-1+b1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:amd64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b2) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libwebpdemux2:amd64 (1.4.0-0.1+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libsource-highlight4t64:amd64 (3.1.9-4.3+b1) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up pandoc (3.1.11.1+ds-2) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up ucf (3.0043+nmu1) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1.1+b1) ... Setting up libharfbuzz0b:amd64 (10.0.1-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b2) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Setting up libxft2:amd64 (2.3.6-1+b2) ... Setting up libzmq5:amd64 (4.3.5-1+b3) ... Setting up libdebuginfod-common (0.192-4) ... Setting up libcurl4t64:amd64 (8.11.0-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:amd64 (8.6.15-1) ... Setting up python3.12-tk (3.12.7-3) ... Setting up libcurl3t64-gnutls:amd64 (8.11.0-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3.13-tk (3.13.0-2) ... Setting up libraqm0:amd64 (0.10.1-1+b2) ... Setting up sphinx-common (7.4.7-4) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-4) ... Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-4) ... Setting up libdebuginfod1t64:amd64 (0.192-4) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up libnetcdf19t64:amd64 (1:4.9.2-7) ... Setting up libpython3.12-stdlib:amd64 (3.12.7-3) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up libpython3.12t64:amd64 (3.12.7-3) ... Setting up gdb (15.2-1) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up libpython3.12-dev:amd64 (3.12.7-3) ... 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 python3-markupsafe (2.1.5-1+b1) ... Setting up python3-webencodings (0.5.1-5) ... Setting up python3-platformdirs (4.3.6-1) ... Setting up python3-psutil (5.9.8-2) ... Setting up python3-tz (2024.1-2) ... Setting up python3-six (1.16.0-7) ... Setting up python3-pil:amd64 (10.4.0-1) ... Setting up python3-roman (4.2-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.1-1) ... Setting up python3-wcwidth (0.2.13+dfsg1-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-certifi (2024.8.30+dfsg-1) ... Setting up python3-typeshed (0.0~git20231111.6764465-3) ... 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+b5) ... 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Setting up python3-tk:amd64 (3.12.7-1) ... Setting up python3-debugpy (1.8.8+ds-1) ... Setting up python3-bs4 (4.12.3-3) ... Setting up python3-bleach (6.2.0-1) ... Setting up python3-matplotlib-inline (0.1.6-2) ... Setting up python3-comm (0.2.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pil.imagetk:amd64 (10.4.0-1) ... Setting up python3-executing (2.1.0-0.1) ... Setting up libpython3-all-dev:amd64 (3.12.6-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pexpect (4.9-3) ... Setting up python3-dev (3.12.6-1) ... Setting up python3-stack-data (0.6.3-1) ... Setting up python3-referencing (0.35.1-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-all-dev (3.12.6-1) ... Setting up python3-setuptools (75.2.0-1) ... Setting up python3-py (1.11.0-2) ... Setting up python3-jedi (0.19.1+ds1-1) ... Setting up python3-joblib (1.3.2-5) ... Setting up python3-babel (2.14.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-networkx (3.2.1-4) ... Setting up python3-fs (2.4.16-4) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-ipython (8.29.0-1) ... Setting up python3-zmq (24.0.1-5+b2) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up python3-jupyter-client (8.6.2-3) ... Setting up python3-contourpy (1.3.0-2) ... Setting up python3-jsonschema-specifications (2023.12.1-2) ... Setting up dh-python (6.20241024) ... Setting up python3-scipy (1.13.1-5) ... Setting up python3-tables-lib (3.10.1-1) ... Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-6) ... Setting up python3-gsd (3.3.0-1+b1) ... Setting up python3-jupyterlab-pygments (0.2.2-3) ... Setting up python3-pandas (2.2.3+dfsg-5) ... Setting up python3-jsonschema (4.19.2-5) ... Setting up python3-ipykernel (6.29.5-1) ... Setting up python3-sklearn (1.4.2+dfsg-6) ... Setting up python3-cftime (1.6.4-1+b1) ... Setting up python3-numexpr (2.10.1-2+b1) ... Setting up python3-netcdf4 (1.7.2-1) ... Setting up python3-nbformat (5.9.1-1) ... Setting up python3-tables (3.10.1-1) ... Setting up python3-nbclient (0.8.0-1) ... Setting up python3-nbconvert (7.16.4-2) ... Setting up python3-fonttools (4.54.1-4) ... Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... Setting up python3-matplotlib (3.8.3-3) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (7.4.7-4) ... Setting up python3-nbsphinx (0.9.4+ds-1.1) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-numpydoc (1.6.0-2) ... Setting up python3-nbsphinx-link (1.3.0-4) ... Setting up python3-sphinx-rtd-theme (3.0.1+dfsg-1) ... Setting up python3-msmb-theme (1.2.0-4) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/mdtraj-1.10.1/ && 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_1.10.1-2_source.changes dpkg-buildpackage: info: source package mdtraj dpkg-buildpackage: info: source version 1.10.1-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Emmanuel Arias dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from mdtraj-1.10.1/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 3.12 I: pybuild base:311: python3.12 setup.py clean Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-linux-gnu/14/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --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=x86_64-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-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) /build/reproducible-path/mdtraj-1.10.1/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... Compiler supports SSE2 Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support [ 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 running clean removing '/build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.12' 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-1.10.1' 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-1.10.1' 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 3.12 I: pybuild base:311: python3.12 setup.py config Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-linux-gnu/14/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --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=x86_64-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-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) /build/reproducible-path/mdtraj-1.10.1/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... Compiler supports SSE2 Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support [ 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 running config dh_auto_build -O--buildsystem=pybuild pybuild --build -i python{version} -p 3.12 I: pybuild base:311: /usr/bin/python3 setup.py build Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-linux-gnu/14/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --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=x86_64-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-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) 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... Compiler supports SSE2 Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support [ 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 running build running build_py creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj copying mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj copying mdtraj/io.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj copying mdtraj/_version.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data UPDATING /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py set /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py to '1.10.1' running build_ext building 'mdtraj.formats.xtc' extension creating build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord': mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes': mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 119 | if (NULL == xd) | ^~ mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 122 | do { | ^~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/xtc.c:1263: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write' at mdtraj/formats/xtc/xtc.c:13728:16, inlined from '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write' at mdtraj/formats/xtc/xtc.c:13424:13: mdtraj/formats/xtc/xtc.c:1165:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 1165 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/xtc.c:25481:20: note: in expansion of macro 'PyInt_FromLong' 25481 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write': mdtraj/formats/xtc/xtc.c:13444:7: note: '__pyx_v_status' was declared here 13444 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:11491:10: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11491 | if (unlikely(__pyx_t_5 != -1)) { | ^ mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 10279 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11490:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11490 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 10279 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11856:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11856 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11860:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11860 | } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11864:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 11864 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11902:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11902 | } else if (unlikely(__pyx_t_41 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10283:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 10283 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11826:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11826 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10287:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 10287 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11844:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11844 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10291:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 10291 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11884:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11884 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11888:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11888 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11892:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 11892 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-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-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/xtc.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-x86_64-linux-gnu.so building 'mdtraj.formats.trr' extension x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/trr.c:1265: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write' at mdtraj/formats/xtc/trr.c:15643:16, inlined from '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write' at mdtraj/formats/xtc/trr.c:15083:13: mdtraj/formats/xtc/trr.c:1167:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 1167 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/trr.c:27476:20: note: in expansion of macro 'PyInt_FromLong' 27476 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write': mdtraj/formats/xtc/trr.c:15111:7: note: '__pyx_v_status' was declared here 15111 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:12632:12: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12632 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 10939 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12631:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12631 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 10939 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12580:12: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12580 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 10955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12579:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12579 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 10955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12739:10: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12739 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 10959 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12738:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12738 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 10959 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12341:19: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12341 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_4 = 0; | ^ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:2533:90: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:12354:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 12354 | __pyx_v_frame_vel = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_vel.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_vel.diminfo[0].strides, __pyx_t_30, __pyx_pybuffernd_vel.diminfo[1].strides, __pyx_t_31, __pyx_pybuffernd_vel.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12345:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12345 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12349:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 12349 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_4 = 2; | ^ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12398:19: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12398 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_4 = 0; | ^ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:2533:90: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:12411:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 12411 | __pyx_v_frame_forces = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_forces.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_forces.diminfo[0].strides, __pyx_t_31, __pyx_pybuffernd_forces.diminfo[1].strides, __pyx_t_30, __pyx_pybuffernd_forces.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12402:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12402 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12406:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 12406 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_4 = 2; | ^ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-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-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/trr.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-x86_64-linux-gnu.so building 'mdtraj.formats.dcd' extension creating build/temp.linux-x86_64-cpython-312/mdtraj/formats/dcd creating build/temp.linux-x86_64-cpython-312/mdtraj/formats/dcd/src x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dcd/dcd.c:1260: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read' at mdtraj/formats/dcd/dcd.c:10190:17: mdtraj/formats/dcd/dcd.c:1162:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 1162 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/dcd/dcd.c:18997:20: note: in expansion of macro 'PyInt_FromLong' 18997 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:8994:7: note: '__pyx_v_i' was declared here 8994 | int __pyx_v_i; | ^~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-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-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/mdtraj/formats/dcd/dcd.o build/temp.linux-x86_64-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-x86_64-linux-gnu.so building 'mdtraj.formats.dtr' extension creating build/temp.linux-x86_64-cpython-312/mdtraj/formats/dtr creating build/temp.linux-x86_64-cpython-312/mdtraj/formats/dtr/src x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dtr/dtr.cpp:1279: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-x86_64-cpython-312/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/x86_64-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/x86_64-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/x86_64-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/x86_64-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 ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/mdtraj/formats/dtr/dtr.o build/temp.linux-x86_64-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-x86_64-linux-gnu.so building 'mdtraj._rmsd' extension creating build/temp.linux-x86_64-cpython-312/mdtraj/rmsd creating build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/_rmsd.o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-x86_64-linux-gnu.so building 'mdtraj._lprmsd' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/_lprmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/rmsd/_lprmsd.cpp:1307: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/Munkres.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/fancy_index.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/_lprmsd.o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/Munkres.o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/fancy_index.o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-x86_64-linux-gnu.so building 'mdtraj.core.lib.libtheobald' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -msse2 -mssse3 -O3 -funroll-loops --std=c++11 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/center.o -msse2 -mssse3 -O3 -funroll-loops --std=c++11 x86_64-linux-gnu-gcc-ar rcs /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/libtheobald.a build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/center.o building 'mdtraj.geometry._geometry' extension creating build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/_geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/geometry/src/_geometry.cpp:1289: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/dssp.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/sasa.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/_geometry.o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/dssp.o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/geometry.o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/sasa.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-x86_64-linux-gnu.so building 'mdtraj.geometry.drid' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/drid.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/drid.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/dridkernels.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/moments.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/mdtraj/geometry/drid.o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/dridkernels.o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/moments.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-x86_64-linux-gnu.so building 'mdtraj.geometry.neighbors' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/mdtraj/geometry/neighbors.o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/neighbors.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-x86_64-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/mdtraj/geometry/neighborlist.o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/neighborlist.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-x86_64-linux-gnu.so dh_auto_test -O--buildsystem=pybuild pybuild --test -i python{version} -p 3.12 I: pybuild base:311: cd /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build; python3.12 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN rm -fr -- /tmp/dh-xdg-rundir-U_ncE_bp 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-1.10.1/debian/tmp pybuild --install -i python{version} -p 3.12 --dest-dir /build/reproducible-path/mdtraj-1.10.1/debian/tmp I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj Using built-in specs. COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-linux-gnu/14/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --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=x86_64-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-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) 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... Compiler supports SSE2 Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support [ 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 running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: 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-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py set /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py to '1.10.1' running build_ext building 'mdtraj.formats.xtc' extension x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord': mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes': mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 119 | if (NULL == xd) | ^~ mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 122 | do { | ^~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/xtc.c:1263: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write' at mdtraj/formats/xtc/xtc.c:13728:16, inlined from '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write' at mdtraj/formats/xtc/xtc.c:13424:13: mdtraj/formats/xtc/xtc.c:1165:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 1165 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/xtc.c:25481:20: note: in expansion of macro 'PyInt_FromLong' 25481 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write': mdtraj/formats/xtc/xtc.c:13444:7: note: '__pyx_v_status' was declared here 13444 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:11491:10: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11491 | if (unlikely(__pyx_t_5 != -1)) { | ^ mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 10279 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11490:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11490 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 10279 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11856:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11856 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11860:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11860 | } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11864:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 11864 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11902:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11902 | } else if (unlikely(__pyx_t_41 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10283:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 10283 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11826:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11826 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10287:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 10287 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11844:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11844 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10291:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 10291 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11884:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11884 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11888:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11888 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11892:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 11892 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-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-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/xtc.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-x86_64-linux-gnu.so building 'mdtraj.formats.trr' extension x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/trr.c:1265: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write' at mdtraj/formats/xtc/trr.c:15643:16, inlined from '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write' at mdtraj/formats/xtc/trr.c:15083:13: mdtraj/formats/xtc/trr.c:1167:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 1167 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/trr.c:27476:20: note: in expansion of macro 'PyInt_FromLong' 27476 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write': mdtraj/formats/xtc/trr.c:15111:7: note: '__pyx_v_status' was declared here 15111 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:12632:12: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12632 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 10939 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12631:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12631 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 10939 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12580:12: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12580 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 10955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12579:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12579 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 10955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12739:10: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12739 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 10959 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12738:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12738 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 10959 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12341:19: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12341 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_4 = 0; | ^ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:2533:90: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:12354:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 12354 | __pyx_v_frame_vel = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_vel.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_vel.diminfo[0].strides, __pyx_t_30, __pyx_pybuffernd_vel.diminfo[1].strides, __pyx_t_31, __pyx_pybuffernd_vel.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12345:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12345 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12349:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 12349 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_4 = 2; | ^ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12398:19: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12398 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_4 = 0; | ^ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:2533:90: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:12411:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 12411 | __pyx_v_frame_forces = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_forces.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_forces.diminfo[0].strides, __pyx_t_31, __pyx_pybuffernd_forces.diminfo[1].strides, __pyx_t_30, __pyx_pybuffernd_forces.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12402:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12402 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12406:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 12406 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_4 = 2; | ^ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-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-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-x86_64-cpython-312/mdtraj/formats/xtc/trr.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-x86_64-linux-gnu.so building 'mdtraj.formats.dcd' extension x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dcd/dcd.c:1260: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read' at mdtraj/formats/dcd/dcd.c:10190:17: mdtraj/formats/dcd/dcd.c:1162:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 1162 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/dcd/dcd.c:18997:20: note: in expansion of macro 'PyInt_FromLong' 18997 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:8994:7: note: '__pyx_v_i' was declared here 8994 | int __pyx_v_i; | ^~~~~~~~~ x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-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-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/mdtraj/formats/dcd/dcd.o build/temp.linux-x86_64-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-x86_64-linux-gnu.so building 'mdtraj.formats.dtr' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dtr/dtr.cpp:1279: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-x86_64-cpython-312/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/x86_64-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/x86_64-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/x86_64-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/x86_64-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 ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/mdtraj/formats/dtr/dtr.o build/temp.linux-x86_64-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-x86_64-linux-gnu.so building 'mdtraj._rmsd' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/_rmsd.o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-x86_64-linux-gnu.so building 'mdtraj._lprmsd' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/_lprmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/rmsd/_lprmsd.cpp:1307: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/Munkres.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/fancy_index.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/_lprmsd.o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/Munkres.o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/fancy_index.o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-x86_64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-x86_64-linux-gnu.so building 'mdtraj.geometry._geometry' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/_geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/geometry/src/_geometry.cpp:1289: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/dssp.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/sasa.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/_geometry.o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/dssp.o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/geometry.o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/sasa.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-x86_64-linux-gnu.so building 'mdtraj.geometry.drid' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/drid.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/drid.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/dridkernels.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/moments.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/mdtraj/geometry/drid.o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/dridkernels.o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/moments.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-x86_64-linux-gnu.so building 'mdtraj.geometry.neighbors' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/mdtraj/geometry/neighbors.o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/neighbors.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-x86_64-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.10.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/mdtraj/geometry/neighborlist.o build/temp.linux-x86_64-cpython-312/mdtraj/geometry/src/neighborlist.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-x86_64-linux-gnu.so running install_lib creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbfile.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbstructure.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/registry.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/prmtop.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/pdbx.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/gsd.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/mol2.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/mdcrd.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/hdf5.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/amberrst.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/psf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/arc.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/netcdf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/xyzfile.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/openmmxml.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/gro.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/hoomdxml.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/lammpstrj.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/lh5.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/netcdfreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/xtcreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/dcdreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/basereporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/hdf5reporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/docstrings.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/testing.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/docscrape.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/angle.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/thermodynamic_properties.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/sasa.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/order.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/hbond.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/dihedral.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/rg.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/contact.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/rdf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/dssp.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/distance.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/shape.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_operators.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/prefix.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/basedimension.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/standard_dimensions.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/mymatrix.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_definitions.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/quantity.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/baseunit.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/delay_import.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/validation.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/contextmanagers.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/singleton.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/zipped.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/unitcell.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/rotation.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/shift_wrappers.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/scalar_couplings.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/io.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/center.h -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/theobald_rmsd.h -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/libtheobald.a -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/topology.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/selection.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/element.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/residue_names.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/trajectory.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__pycache__/_version.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__ byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/psf.py to psf.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/mol2.py to mol2.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/netcdf.py to netcdf.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/gsd.py to gsd.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdbx.py to pdbx.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/amberrst.py to amberrst.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/arc.py to arc.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/prmtop.py to prmtop.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/hdf5.py to hdf5.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/registry.py to registry.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/gro.py to gro.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/pdbfile.py to pdbfile.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/pdbstructure.py to pdbstructure.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/lh5.py to lh5.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/docstrings.py to docstrings.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/testing.py to testing.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/docscrape.py to docscrape.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/mdconvert.py to mdconvert.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/dssp.py to dssp.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/order.py to order.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/distance.py to distance.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/shape.py to shape.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/alignment.py to alignment.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/rdf.py to rdf.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/internal.py to internal.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/angle.py to angle.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/sasa.py to sasa.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/thermodynamic_properties.py to thermodynamic_properties.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/hbond.py to hbond.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/contact.py to contact.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/rg.py to rg.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/singleton.py to singleton.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/rotation.py to rotation.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unitcell.py to unitcell.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/delay_import.py to delay_import.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/zipped.py to zipped.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/mymatrix.py to mymatrix.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/doctests.py to doctests.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/quantity.py to quantity.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/unit_math.py to unit_math.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/basedimension.py to basedimension.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/unit.py to unit.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/prefix.py to prefix.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/constants.py to constants.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/standard_dimensions.py to standard_dimensions.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/unit_operators.py to unit_operators.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/unit_definitions.py to unit_definitions.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/baseunit.py to baseunit.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/validation.py to validation.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/shift_wrappers.py to shift_wrappers.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/scalar_couplings.py to scalar_couplings.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/io.py to io.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/selection.py to selection.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/topology.py to topology.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/residue_names.py to residue_names.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/element.py to element.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/trajectory.py to trajectory.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/_version.py to _version.cpython-312.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/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative reading manifest file '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-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj-1.10.1.egg-info Skipping SOURCES.txt running install_scripts Installing mdconvert-mdtraj script to /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/bin Installing mdinspect script to /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/bin debian/rules execute_after_dh_auto_install-indep make[1]: Entering directory '/build/reproducible-path/mdtraj-1.10.1' cp -a /build/reproducible-path/mdtraj-1.10.1/examples /build/reproducible-path/mdtraj-1.10.1/examples.orig mkdir -p /build/reproducible-path/mdtraj-1.10.1/build/html/examples/iterload ln -s /build/reproducible-path/mdtraj-1.10.1/examples/data /build/reproducible-path/mdtraj-1.10.1/build/html/examples/iterload/data sed "s|http://www.rcsb.org/pdb/files|/build/reproducible-path/mdtraj-1.10.1/debian/external|g" -i /build/reproducible-path/mdtraj-1.10.1/examples/*.ipynb PYTHONPATH=/build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build \ MPLCONFIGDIR=/build/reproducible-path/mdtraj-1.10.1/build/matplotlib \ make -C docs BUILDDIR=/build/reproducible-path/mdtraj-1.10.1/build html make[2]: Entering directory '/build/reproducible-path/mdtraj-1.10.1/docs' sphinx-build -b html -d /build/reproducible-path/mdtraj-1.10.1/build/doctrees . /build/reproducible-path/mdtraj-1.10.1/build/html Running Sphinx v7.4.7 WARNING: Calling get_html_theme_path is deprecated. If you are calling it to define html_theme_path, you are safe to remove that code. 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/iterload.nblink, notebook-examples/native-contact.nblink, notebook-examples/openmm.nblink, notebook-examples/pca.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-1.10.1/docs/api/generated/mdtraj.Topology.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.Trajectory.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.Trajectory.superpose.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.acylindricity.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.asphericity.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.baker_hubbard.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.chemical_shifts_ppm.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.chemical_shifts_shiftx2.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.chemical_shifts_spartaplus.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_J3_HN_C.rst, ..., /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.check_random_state.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.ensure_type.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.ilen.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.import_.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.in_units_of.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.rotation_matrix_from_quaternion.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.timing.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.uniform_quaternion.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.wernet_nilsson.rst building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 44 source files that are out of date updating environment: [new config] 140 added, 0 changed, 0 removed reading sources... [ 1%] analysis reading sources... [ 1%] api/generated/mdtraj.Topology /usr/lib/python3/dist-packages/numpydoc/docscrape.py:455: 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-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/topology.py. warn(msg) reading sources... [ 2%] api/generated/mdtraj.Trajectory reading sources... [ 3%] api/generated/mdtraj.Trajectory.superpose reading sources... [ 4%] 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... [ 9%] 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... [ 11%] 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... [ 14%] api/generated/mdtraj.compute_chi4 reading sources... [ 14%] api/generated/mdtraj.compute_contacts reading sources... [ 15%] api/generated/mdtraj.compute_dihedrals reading sources... [ 16%] api/generated/mdtraj.compute_directors reading sources... [ 16%] api/generated/mdtraj.compute_displacements reading sources... [ 17%] api/generated/mdtraj.compute_distances reading sources... [ 18%] api/generated/mdtraj.compute_drid reading sources... [ 19%] 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... [ 21%] api/generated/mdtraj.compute_neighbors reading sources... [ 21%] api/generated/mdtraj.compute_nematic_order reading sources... [ 22%] api/generated/mdtraj.compute_omega reading sources... [ 23%] api/generated/mdtraj.compute_phi reading sources... [ 24%] api/generated/mdtraj.compute_psi reading sources... [ 24%] api/generated/mdtraj.compute_rdf reading sources... [ 25%] api/generated/mdtraj.compute_rg reading sources... [ 26%] api/generated/mdtraj.density reading sources... [ 26%] api/generated/mdtraj.dipole_moments reading sources... [ 27%] api/generated/mdtraj.formats.AmberNetCDFRestartFile reading sources... [ 28%] api/generated/mdtraj.formats.AmberRestartFile reading sources... [ 29%] api/generated/mdtraj.formats.ArcTrajectoryFile reading sources... [ 29%] api/generated/mdtraj.formats.DCDTrajectoryFile reading sources... [ 30%] api/generated/mdtraj.formats.DTRTrajectoryFile reading sources... [ 31%] api/generated/mdtraj.formats.GroTrajectoryFile reading sources... [ 31%] api/generated/mdtraj.formats.HDF5TrajectoryFile reading sources... [ 32%] api/generated/mdtraj.formats.LAMMPSTrajectoryFile reading sources... [ 33%] api/generated/mdtraj.formats.LH5TrajectoryFile reading sources... [ 34%] api/generated/mdtraj.formats.MDCRDTrajectoryFile reading sources... [ 34%] api/generated/mdtraj.formats.NetCDFTrajectoryFile reading sources... [ 35%] api/generated/mdtraj.formats.PDBTrajectoryFile reading sources... [ 36%] api/generated/mdtraj.formats.TRRTrajectoryFile reading sources... [ 36%] api/generated/mdtraj.formats.XTCTrajectoryFile reading sources... [ 37%] api/generated/mdtraj.formats.XYZTrajectoryFile reading sources... [ 38%] api/generated/mdtraj.geometry.squareform reading sources... [ 39%] api/generated/mdtraj.isothermal_compressability_kappa_T reading sources... [ 39%] api/generated/mdtraj.iterload reading sources... [ 40%] api/generated/mdtraj.join reading sources... [ 41%] api/generated/mdtraj.kabsch_sander reading sources... [ 41%] api/generated/mdtraj.load reading sources... [ 42%] api/generated/mdtraj.load_arc reading sources... [ 43%] api/generated/mdtraj.load_dcd reading sources... [ 44%] api/generated/mdtraj.load_dtr reading sources... [ 44%] api/generated/mdtraj.load_frame reading sources... [ 45%] api/generated/mdtraj.load_hdf5 reading sources... [ 46%] api/generated/mdtraj.load_hoomdxml reading sources... [ 46%] api/generated/mdtraj.load_lammpstrj reading sources... [ 47%] api/generated/mdtraj.load_lh5 reading sources... [ 48%] api/generated/mdtraj.load_netcdf reading sources... [ 49%] api/generated/mdtraj.load_pdb reading sources... [ 49%] api/generated/mdtraj.load_prmtop reading sources... [ 50%] api/generated/mdtraj.load_trr reading sources... [ 51%] api/generated/mdtraj.load_xml reading sources... [ 51%] api/generated/mdtraj.load_xtc reading sources... [ 52%] api/generated/mdtraj.load_xyz reading sources... [ 53%] api/generated/mdtraj.lprmsd reading sources... [ 54%] api/generated/mdtraj.open reading sources... [ 54%] api/generated/mdtraj.principal_moments reading sources... [ 55%] api/generated/mdtraj.reindex_dataframe_by_atoms reading sources... [ 56%] api/generated/mdtraj.relative_shape_antisotropy reading sources... [ 56%] api/generated/mdtraj.reporters.DCDReporter reading sources... [ 57%] api/generated/mdtraj.reporters.HDF5Reporter reading sources... [ 58%] api/generated/mdtraj.reporters.NetCDFReporter reading sources... [ 59%] api/generated/mdtraj.rmsd reading sources... [ 59%] api/generated/mdtraj.rmsf reading sources... [ 60%] api/generated/mdtraj.shrake_rupley reading sources... [ 61%] api/generated/mdtraj.static_dielectric reading sources... [ 61%] api/generated/mdtraj.thermal_expansion_alpha_P reading sources... [ 62%] api/generated/mdtraj.utils.box_vectors_to_lengths_and_angles reading sources... [ 63%] api/generated/mdtraj.utils.check_random_state reading sources... [ 64%] api/generated/mdtraj.utils.ensure_type reading sources... [ 64%] api/generated/mdtraj.utils.ilen reading sources... [ 65%] api/generated/mdtraj.utils.import_ reading sources... [ 66%] api/generated/mdtraj.utils.in_units_of reading sources... [ 66%] api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors reading sources... [ 67%] api/generated/mdtraj.utils.rotation_matrix_from_quaternion reading sources... [ 68%] api/generated/mdtraj.utils.timing reading sources... [ 69%] api/generated/mdtraj.utils.uniform_quaternion reading sources... [ 69%] api/generated/mdtraj.wernet_nilsson reading sources... [ 70%] api/reporters reading sources... [ 71%] api/trajectory_files reading sources... [ 71%] api/utils reading sources... [ 72%] atom_selection reading sources... [ 73%] building_docs reading sources... [ 74%] examples/atom-selection reading sources... [ 74%] examples/centroids reading sources... [ 75%] examples/clustering reading sources... [ 76%] examples/hbonds reading sources... [ 76%] examples/index reading sources... [ 77%] examples/introduction reading sources... [ 78%] examples/iterload reading sources... [ 79%] examples/native-contact reading sources... [ 79%] examples/nmr reading sources... [ 80%] examples/openmm reading sources... [ 81%] examples/pca reading sources... [ 81%] examples/ramachandran-plot reading sources... [ 82%] examples/rmsd-benchmark reading sources... [ 83%] examples/solvent-accessible-surface-area reading sources... [ 84%] examples/two-pass-clustering reading sources... [ 84%] faq reading sources... [ 85%] hdf5_format reading sources... [ 86%] index reading sources... [ 86%] installation reading sources... [ 87%] load_functions reading sources... [ 88%] mdconvert reading sources... [ 89%] new_to_python reading sources... [ 89%] notebook-examples/atom-selection reading sources... [ 90%] notebook-examples/centroids reading sources... [ 91%] notebook-examples/clustering reading sources... [ 91%] notebook-examples/hbonds reading sources... [ 92%] notebook-examples/index reading sources... [ 93%] notebook-examples/introduction reading sources... [ 94%] notebook-examples/iterload reading sources... [ 94%] notebook-examples/native-contact reading sources... [ 95%] notebook-examples/openmm reading sources... [ 96%] notebook-examples/pca reading sources... [ 96%] notebook-examples/ramachandran-plot reading sources... [ 97%] notebook-examples/rmsd-benchmark reading sources... [ 98%] notebook-examples/rmsd-drift reading sources... [ 99%] notebook-examples/solvent-accessible-surface-area reading sources... [ 99%] notebook-examples/two-pass-clustering reading sources... [100%] whatsnew /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.asphericity:9: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:9: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:36: ERROR: Unexpected indentation. /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:45: WARNING: Block quote ends without a blank line; unexpected unindent. docstring of mdtraj.formats.dtr.load_dtr:7: ERROR: Unexpected indentation. /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:9: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:11: ERROR: Unexpected indentation. /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_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. /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_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. /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_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. /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/rotation.py:docstring of mdtraj.utils.rotation.uniform_quaternion:37: 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 /build/reproducible-path/mdtraj-1.10.1/docs/examples/atom-selection.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/atom-selection.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/centroids.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/centroids.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/clustering.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/clustering.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/hbonds.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/hbonds.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/iterload.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/iterload.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/native-contact.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/native-contact.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/nmr.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/nmr.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/openmm.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/simulation-with-openmm.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/pca.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/principal-components.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/ramachandran-plot.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/ramachandran-plot.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/rmsd-benchmark.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/rmsd-benchmark.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/solvent-accessible-surface-area.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/solvent-accessible-surface-area.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/examples/two-pass-clustering.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/two-pass-clustering.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.1/docs/index.rst:26: WARNING: toctree contains reference to nonexisting document '.. examples/index' /build/reproducible-path/mdtraj-1.10.1/docs/installation.rst:1: WARNING: malformed hyperlink target. /build/reproducible-path/mdtraj-1.10.1/docs/mdconvert.rst:2: WARNING: Title underline too short. ``mdconvert`` (``mdconvert-mdtraj``) ============= /build/reproducible-path/mdtraj-1.10.1/docs/whatsnew.rst:60: WARNING: Title underline too short. v1.9.9 (July 22, 2023) --------------------- /build/reproducible-path/mdtraj-1.10.1/docs/whatsnew.rst:60: WARNING: Title underline too short. v1.9.9 (July 22, 2023) --------------------- /build/reproducible-path/mdtraj-1.10.1/docs/whatsnew.rst:115: WARNING: Title underline too short. v1.9.7 (November 12, 2021) ----------------------- /build/reproducible-path/mdtraj-1.10.1/docs/whatsnew.rst:115: WARNING: Title underline too short. v1.9.7 (November 12, 2021) ----------------------- looking for now-outdated files... none found pickling environment... WARNING: cannot cache unpickable configuration value: 'nbsphinx_custom_formats' (because it contains a function, class, or module object) done checking consistency... /build/reproducible-path/mdtraj-1.10.1/docs/building_docs.rst: WARNING: document isn't included in any toctree /build/reproducible-path/mdtraj-1.10.1/docs/examples/index.rst: WARNING: document isn't included in any toctree /build/reproducible-path/mdtraj-1.10.1/docs/faq.rst: WARNING: document isn't included in any toctree /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.chemical_shifts_ppm.rst:24: WARNING: Citation [R580094b12b10-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.chemical_shifts_shiftx2.rst:27: WARNING: Citation [R32f229ae9dd9-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.chemical_shifts_spartaplus.rst:30: WARNING: Citation [R85224fbb9dbc-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_J3_HN_C.rst:24: WARNING: Citation [R44e9b977b917-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_J3_HN_CB.rst:24: WARNING: Citation [Red2371ebcd94-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_J3_HN_HA.rst:25: WARNING: Citation [Rcea8e821fb69-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_J3_HN_HA.rst:30: WARNING: Citation [Rcea8e821fb69-2] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_J3_HN_HA.rst:35: WARNING: Citation [Rcea8e821fb69-3] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_directors.rst:33: WARNING: Citation [R476bbf639532-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_drid.rst:19: WARNING: Citation [Rb9f983981da1-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_dssp.rst:43: WARNING: Citation [Rb487c1f2550c-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_gyration_tensor.rst:18: WARNING: Citation [Rc72b27c79197-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_nematic_order.rst:25: WARNING: Citation [R38e8a5b92b1b-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_nematic_order.rst:27: WARNING: Citation [R38e8a5b92b1b-2] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_nematic_order.rst:28: WARNING: Citation [R38e8a5b92b1b-3] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.kabsch_sander.rst:33: WARNING: Citation [Rd51ca7d055fd-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.shrake_rupley.rst:68: WARNING: Citation [Re2ba905e251a-1] is not referenced. /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.rotation_matrix_from_quaternion.rst:20: WARNING: Citation [R7dd18c0d2619-1] is not referenced. done preparing documents... done copying assets... copying static files... done copying extra files... done copying assets: done writing output... 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[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-1.10.1/build/html. make[2]: Leaving directory '/build/reproducible-path/mdtraj-1.10.1/docs' for img in `find /build/reproducible-path/mdtraj-1.10.1/build/html/examples -name *.png`; do \ mv $img /build/reproducible-path/mdtraj-1.10.1/build/html/examples; \ done sed "s|/build/reproducible-path/mdtraj-1.10.1/build/html/examples/|./|g; s|.ipynb|.ipynb.gz|g" -i /build/reproducible-path/mdtraj-1.10.1/build/html/examples/*.html sed "s|/build/reproducible-path/mdtraj-1.10.1/debian/external|http://www.rcsb.org/pdb/files|g" -i /build/reproducible-path/mdtraj-1.10.1/build/html/examples/*.html rm /build/reproducible-path/mdtraj-1.10.1/build/html/examples/iterload/data rm -rf /build/reproducible-path/mdtraj-1.10.1/examples mv /build/reproducible-path/mdtraj-1.10.1/examples.orig /build/reproducible-path/mdtraj-1.10.1/examples make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.10.1' 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-1.10.1/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-1.10.1' dh_sphinxdoc -i 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 ../../../../../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/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/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/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/Lato-BoldItalic.woff2 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../../../../../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/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/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/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/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/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/js/theme.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/theme.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/language_data.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/language_data.js ln -sf ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/searchtools.js ln -sf ../../../../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/.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 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-1.10.1' dh_sphinxdoc -O--buildsystem=pybuild -Npython-mdtraj-doc dh_sphinxdoc: warning: Sphinx documentation not found dh_installchangelogs -O--buildsystem=pybuild 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 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 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/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/mdconvert-mdtraj.1 man-recode --to-code UTF-8 --suffix .dh-new debian/python3-mdtraj/usr/share/man/man1/mdinspect.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: 6.20241024 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: 3.12 (default=3.12) 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/python3.12/dist-packages to debian/python3-mdtraj/usr/lib/python3/dist-packages/ D: dh_python3 fs:338: package python3-mdtraj details = {'requires.txt': {'debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.10.1.egg-info/requires.txt'}, 'egg-info': {'debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.10.1.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('3.12')}, '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<2.0.0a0,>=1.23 (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 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-packaging', 'python3:any', 'python3-scipy', 'python3 (<< 3.13)', 'python3 (>= 3.12~)', 'python3-pyparsing', 'python3-numpy'}; 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-1.10.1' dh_numpy3 mv debian/python3-mdtraj.substvars.new debian/python3-mdtraj.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars # 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-1.10.1' 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/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/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/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/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/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/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/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-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/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/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/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/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.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/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/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/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/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/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/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 1731351154 as canonical time 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_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_hbonds_9_1.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_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_clustering_11_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_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/_static/file.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/plus.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/_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/openmm.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/pca.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-1.10.1' 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/openmm.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/pca.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-1.10.1' 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/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/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 d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 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 -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/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x 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/x86_64-linux-gnu dwz -mdebian/python3-mdtraj/usr/lib/debug/.dwz/x86_64-linux-gnu/python3-mdtraj.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/python3-mdtraj.debug -- debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-x86_64-linux-gnu.so objcopy --compress-debug-sections debian/python3-mdtraj/usr/lib/debug/.dwz/x86_64-linux-gnu/python3-mdtraj.debug chmod 0644 -- debian/python3-mdtraj/usr/lib/debug/.dwz/x86_64-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/1e objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/1e/894f26d8e411b8df20d90e2691a7d8ebb3a241.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/1e/894f26d8e411b8df20d90e2691a7d8ebb3a241.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/1e/894f26d8e411b8df20d90e2691a7d8ebb3a241.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c6 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c6/4baef871f959a8fa7b717207c34977778036b8.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c6/4baef871f959a8fa7b717207c34977778036b8.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c6/4baef871f959a8fa7b717207c34977778036b8.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d6 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d6/51389665fccb8eaf821a1e53970336fb8c665e.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d6/51389665fccb8eaf821a1e53970336fb8c665e.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d6/51389665fccb8eaf821a1e53970336fb8c665e.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/88 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/88/a01fe5fb275cf4026fdc99e6d10ccbe327ed89.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/88/a01fe5fb275cf4026fdc99e6d10ccbe327ed89.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/88/a01fe5fb275cf4026fdc99e6d10ccbe327ed89.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/90 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/90/bf189a89045523f28daadf7f2188c1809f551c.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/90/bf189a89045523f28daadf7f2188c1809f551c.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/90/bf189a89045523f28daadf7f2188c1809f551c.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f8 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f8/e198edb42d9401018169c30b642e76275f7ff9.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f8/e198edb42d9401018169c30b642e76275f7ff9.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f8/e198edb42d9401018169c30b642e76275f7ff9.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/88 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/88/1f02f113217d175632b30d5a12ece95f49413d.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/88/1f02f113217d175632b30d5a12ece95f49413d.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/88/1f02f113217d175632b30d5a12ece95f49413d.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/93 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/93/002be6ac27e88fb5b917ffc1c74a08f9f7b1cc.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/93/002be6ac27e88fb5b917ffc1c74a08f9f7b1cc.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/93/002be6ac27e88fb5b917ffc1c74a08f9f7b1cc.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/bd objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/bd/8d485000accc080144485f9bd8863c2140c371.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/bd/8d485000accc080144485f9bd8863c2140c371.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/bd/8d485000accc080144485f9bd8863c2140c371.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-x86_64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/61 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/61/98dfc110dc8d1829bb416a9219b9a41b2ab7cf.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/61/98dfc110dc8d1829bb416a9219b9a41b2ab7cf.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/61/98dfc110dc8d1829bb416a9219b9a41b2ab7cf.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-x86_64-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/x86_64-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/_rmsd.cpython-312-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-x86_64-linux-gnu.so 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_gencontrol -O--buildsystem=pybuild 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 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=1e894f26d8e411b8df20d90e2691a7d8ebb3a241 6198dfc110dc8d1829bb416a9219b9a41b2ab7cf 881f02f113217d175632b30d5a12ece95f49413d 88a01fe5fb275cf4026fdc99e6d10ccbe327ed89 90bf189a89045523f28daadf7f2188c1809f551c 93002be6ac27e88fb5b917ffc1c74a08f9f7b1cc bd8d485000accc080144485f9bd8863c2140c371 c64baef871f959a8fa7b717207c34977778036b8 d651389665fccb8eaf821a1e53970336fb8c665e f8e198edb42d9401018169c30b642e76275f7ff9" -DSection=debug -UMulti-Arch -UReplaces -UBreaks 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 ${python3:Depends} unused, but is defined 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/python3-mdtraj/DEBIAN install -m0755 -d debian/python-mdtraj-doc/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/python3-mdtraj .. dpkg-deb --root-owner-group --build debian/.debhelper/python3-mdtraj/dbgsym-root .. dpkg-deb --root-owner-group --build debian/python-mdtraj-doc .. dpkg-deb: building package 'python3-mdtraj-dbgsym' in '../python3-mdtraj-dbgsym_1.10.1-2_amd64.deb'. dpkg-deb: building package 'python3-mdtraj' in '../python3-mdtraj_1.10.1-2_amd64.deb'. dpkg-deb: building package 'python-mdtraj-doc' in '../python-mdtraj-doc_1.10.1-2_all.deb'. dpkg-genbuildinfo --build=binary -O../mdtraj_1.10.1-2_amd64.buildinfo dpkg-genchanges --build=binary -O../mdtraj_1.10.1-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from mdtraj-1.10.1/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2704318 and its subdirectories I: Current time: Mon Dec 15 16:20:30 -12 2025 I: pbuilder-time-stamp: 1765858830 Tue Nov 12 21:57:31 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom01-amd64.debian.net. Tue Nov 12 21:57:31 UTC 2024 I: Preparing to do remote build '2' on infom01-amd64.debian.net. Tue Nov 12 22:07:04 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. Tue Nov 12 22:07:05 UTC 2024 I: mdtraj_1.10.1-2_amd64.changes: Format: 1.8 Date: Mon, 11 Nov 2024 15:52:34 -0300 Source: mdtraj Binary: python-mdtraj-doc python3-mdtraj python3-mdtraj-dbgsym Architecture: all amd64 Version: 1.10.1-2 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Emmanuel Arias 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 (1.10.1-2) unstable; urgency=medium . * Team upload. * d/control: Remove python3-astunparse from depedencies. It is not longer needed. Checksums-Sha1: 7b6e74e035759ab5f1e6023646fcb8117320bcca 14037 mdtraj_1.10.1-2_amd64.buildinfo 92971b1bcf562a67d7d7103a61319d3b2bd1a772 1869904 python-mdtraj-doc_1.10.1-2_all.deb 8f9e2f529495ed10296ef43ff069040389dcebe4 5979520 python3-mdtraj-dbgsym_1.10.1-2_amd64.deb 1e8b76e9a55ea97f363cde2ed029ac7c4f0218ab 1025260 python3-mdtraj_1.10.1-2_amd64.deb Checksums-Sha256: 20569d4021794827f59e66a588075481e2c60f8e539bf1f68fa8d7febc6d397c 14037 mdtraj_1.10.1-2_amd64.buildinfo 4373874f4c227769c3aa3893342669e2cb7ab3fe2b4cb8b211fd5f12adda65e2 1869904 python-mdtraj-doc_1.10.1-2_all.deb ba61c35ccc5a05f97f905d560176d80a5ad7030a901ca11d4d1db7b4a90c89c3 5979520 python3-mdtraj-dbgsym_1.10.1-2_amd64.deb c8e66f4005ea03c8bbe36e1bcfe218ff8945a0020bd4f042c28a9514bc1aef4b 1025260 python3-mdtraj_1.10.1-2_amd64.deb Files: 1c2e63fd672b3cfd40d7afd99e770a3b 14037 python optional mdtraj_1.10.1-2_amd64.buildinfo 4bfd5b368a968eeafcb5ff074bdf6f93 1869904 doc optional python-mdtraj-doc_1.10.1-2_all.deb 21e4f5a44c1897a20257e5ecea6ff62f 5979520 debug optional python3-mdtraj-dbgsym_1.10.1-2_amd64.deb e1e3c3b1bdb1a5e0d1ee1bc5168cd072 1025260 python optional python3-mdtraj_1.10.1-2_amd64.deb Tue Nov 12 22:07:06 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_36-35622.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.OR2hRjOM/mdtraj_1.10.1-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.OR2hRjOM/mdtraj_1.10.1-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.OR2hRjOM/mdtraj_1.10.1-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.OR2hRjOM/b1/mdtraj_1.10.1-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.OR2hRjOM/b2/mdtraj_1.10.1-2_amd64.changes ## close_archive (total time: 0.000s) 0.000s 20 calls diffoscope.comparators.xz.XzContainer 0.000s 10 calls diffoscope.comparators.deb.DebContainer 0.000s 14 calls diffoscope.comparators.tar.TarContainer 0.000s 6 calls diffoscope.comparators.deb.DebTarContainer ## command (total time: 48.525s) 20.338s 1014 calls readelf 19.289s 123 calls diff 7.614s 220 calls objdump 0.613s 20 calls xz 0.534s 2 calls objcopy 0.113s 22 calls strings 0.011s 2 calls cmp 0.011s 2 calls cmp (external) 0.001s 19 calls cmp (internal) ## compare_files (cumulative) (total time: 143.524s) 27.021s 1 call abc.DotChangesFile 26.971s 2 calls abc.DebFile 26.875s 4 calls abc.XzFile 26.390s 2 calls abc.DebDataTarFile 26.033s 2 calls abc.ElfFile 9.552s 10 calls diffoscope.comparators.elf.ElfCodeSection 0.515s 33 calls diffoscope.comparators.elf.ElfSection 0.082s 2 calls abc.TarFile 0.046s 3 calls diffoscope.comparators.elf.ElfStringSection 0.015s 1 call abc.TextFile 0.013s 2 calls abc.Md5sumsFile 0.011s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection ## container_extract (total time: 0.837s) 0.614s 20 calls diffoscope.comparators.xz.XzContainer 0.133s 242 calls diffoscope.comparators.deb.DebTarContainer 0.078s 24 calls diffoscope.comparators.deb.DebContainer 0.012s 22 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 0.472s) 0.472s 65 calls linediff ## has_same_content_as (total time: 0.014s) 0.007s 3 calls abc.DebFile 0.005s 2 calls abc.DebDataTarFile 0.001s 6 calls abc.TextFile 0.000s 4 calls abc.Md5sumsFile 0.000s 4 calls abc.XzFile 0.000s 33 calls diffoscope.comparators.elf.ElfSection 0.000s 2 calls abc.TarFile 0.000s 2 calls abc.ElfFile 0.000s 1 call abc.DotChangesFile 0.000s 1 call diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 10 calls diffoscope.comparators.elf.ElfCodeSection 0.000s 3 calls diffoscope.comparators.elf.ElfStringSection 0.000s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection ## main (total time: 28.641s) 28.640s 2 calls outputs 0.001s 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: 1.153s) 0.807s 1 call html 0.228s 1 call text 0.118s 1 call json ## recognizes (total time: 0.691s) 0.290s 900 calls diffoscope.comparators.utils.archive.ArchiveMember 0.234s 1904 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.107s 12 calls diffoscope.comparators.binary.FilesystemFile 0.060s 324 calls diffoscope.comparators.debian.DebControlMember ## specialize (total time: 0.145s) 0.145s 72 calls specialize Finished with result: success Main processes terminated with: code=exited/status=1 Service runtime: 28.989s CPU time consumed: 37.353s Tue Nov 12 22:07:35 UTC 2024 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Tue Nov 12 22:07:35 UTC 2024 E: mdtraj failed to build reproducibly in unstable on amd64. Tue Nov 12 22:07:40 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Nov 12 22:07:40 UTC 2024 I: Submitting 16K b1/mdtraj_1.10.1-2_amd64.buildinfo.asc Tue Nov 12 22:07:41 UTC 2024 I: Submitting 16K b2/mdtraj_1.10.1-2_amd64.buildinfo.asc Tue Nov 12 22:07:42 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Nov 12 22:07:42 UTC 2024 I: Done submitting .buildinfo files. Tue Nov 12 22:07:42 UTC 2024 I: Removing signed mdtraj_1.10.1-2_amd64.buildinfo.asc files: removed './b1/mdtraj_1.10.1-2_amd64.buildinfo.asc' removed './b2/mdtraj_1.10.1-2_amd64.buildinfo.asc'