Wed Sep 11 05:27:32 UTC 2024 I: starting to build mdtraj/unstable/i386 on jenkins on '2024-09-11 05:27' Wed Sep 11 05:27:32 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_16/38928/console.log Wed Sep 11 05:27:32 UTC 2024 I: Downloading source for unstable/mdtraj=1.10.0-3 --2024-09-11 05:27:33-- http://deb.debian.org/debian/pool/main/m/mdtraj/mdtraj_1.10.0-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2635 (2.6K) [text/prs.lines.tag] Saving to: ‘mdtraj_1.10.0-3.dsc’ 0K .. 100% 352M=0s 2024-09-11 05:27:33 (352 MB/s) - ‘mdtraj_1.10.0-3.dsc’ saved [2635/2635] Wed Sep 11 05:27:33 UTC 2024 I: mdtraj_1.10.0-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: mdtraj Binary: python3-mdtraj, python-mdtraj-doc Architecture: any-amd64 arm64 i386 all Version: 1.10.0-3 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-legacy, python3-setuptools, python3-all-dev, python3-gsd, python3-numpy, python3-scipy, python3-astunparse, python3-netcdf4, python3-networkx, python3-pandas, python3-pyparsing, python3-sphinx, python3-tables, 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: 426934bc5dff6d1bba19236bcc1f2c9dc86b2816 21485622 mdtraj_1.10.0.orig.tar.gz 4b546334338f9452a56b7588acbc2209d962edc5 301160 mdtraj_1.10.0-3.debian.tar.xz Checksums-Sha256: 3ea76dc813b947c451b5eba0fd7d665c1386f06b291f09ebe48a8c21e88d5531 21485622 mdtraj_1.10.0.orig.tar.gz 0ec2d61c7655b0af25ffd3315e94077a369817fff6b147bfdd05f9a98cabb461 301160 mdtraj_1.10.0-3.debian.tar.xz Files: 6c955dc294f21e4f0a0b6ab826c9a2aa 21485622 mdtraj_1.10.0.orig.tar.gz 5b68dd90c3b67950a3316dc8526658c8 301160 mdtraj_1.10.0-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAmaTys0ACgkQVz7x5L1a AfoFuRAAljx/WAeOAbY8rgHk1BulMB1uugfSt+fCC5En9ANvpkWb90cQZMUBtyPM 10zi3rjyKyBughVzkqofkZlIhVGcz1aV+1fQS0dvp8m9hlCHsgd4DTRMqPaJKxjb Tj6ObXvF4ig5SnYwg5eNHKLBLAVzswoQXZZKjllAoQ8mUXP1U0sTEtVLuPjmAbRW D8P/re3tMJQYc9uvhmz8uwzETdohnxkUF5uGGLyZ7bBK2jDeByA9fwrrtk+9XtX+ 7/huz+T2aH8jZZoV6xHYvzbKsZMftd3n37/QtvleqHKrezvs+LvjmT8ArQ3GLQ7K 2dpVIi8aSbCePsVCM5VlZ4D4OiHdAEK94YhupGLmtz/WxFNdKYhXf288jEQWOt2K XMpFsSozFsrVdidKHkiZ+a3HknRd55l+Gb5wfO0d9XvyDOx4loxVTlg8XRNfGGY5 aK1islXHJ323Fw8wLps11643ecQgRCjUuZSkuFr3NBAmnfJiRyUqFM1WNj+iqnhh hWH+bYpIvjCBK10eQSD5b9LUsXN9mo3a1ChhEcDnk2UUYehLCGHwDmrmtBgPQghc V1dPW115RdcgUqCld2w9KU5PLOPKLLGzPQQycpWZX8YFpv4p4qa3hS7G4sECnctJ HdUVmlVKw5EvpDXNpoIHxqYbLBB2POvbJWvSWq2y+OPZoR3SB60= =f3XE -----END PGP SIGNATURE----- Wed Sep 11 05:27:33 UTC 2024 I: Checking whether the package is not for us Wed Sep 11 05:27:33 UTC 2024 I: Starting 1st build on remote node infom08-i386.debian.net. Wed Sep 11 05:27:33 UTC 2024 I: Preparing to do remote build '1' on infom08-i386.debian.net. Wed Sep 11 05:32:32 UTC 2024 I: Deleting $TMPDIR on infom08-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Oct 13 23:50:33 -12 2025 I: pbuilder-time-stamp: 1760442633 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: using eatmydata during job I: Copying source file I: copying [mdtraj_1.10.0-3.dsc] I: copying [./mdtraj_1.10.0.orig.tar.gz] I: copying [./mdtraj_1.10.0-3.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Jul 14 12:55:41 2024 gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.10.0-3.dsc: no acceptable signature found dpkg-source: info: extracting mdtraj in mdtraj-1.10.0 dpkg-source: info: unpacking mdtraj_1.10.0.orig.tar.gz dpkg-source: info: unpacking mdtraj_1.10.0-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying docs_use_local_mathjax.patch dpkg-source: info: applying build_dir_pybuild.patch dpkg-source: info: applying python_hashbang.patch dpkg-source: info: applying 32bit_skip_image_molecule.patch dpkg-source: info: applying test_relax_tol.patch dpkg-source: info: applying rename-mdconvert-mdtraj.patch dpkg-source: info: applying drop_notebook_in_docs.patch dpkg-source: info: applying test_increase_timeout.patch dpkg-source: warning: diff 'mdtraj-1.10.0/debian/patches/fix_netcdf_PR1894.patch' patches file mdtraj-1.10.0/mdtraj/testing/testing.py more than once dpkg-source: info: applying fix_netcdf_PR1894.patch dpkg-source: info: applying remove_six_PR1908.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/30204/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='54a9049740a54f7b9be3798e087e9e4a' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='30204' 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.mvAe80M4/pbuilderrc_pDPV --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.mvAe80M4/b1 --logfile b1/build.log mdtraj_1.10.0-3.dsc' SUDO_GID='111' 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 infom08-i386 6.10.6+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.6-1~bpo12+1 (2024-08-26) 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/30204/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: i386 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-legacy, python3-setuptools, python3-all-dev, python3-gsd, python3-numpy, python3-scipy, python3-astunparse, python3-netcdf4, python3-networkx, python3-pandas, python3-pyparsing, python3-sphinx, python3-tables, 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 ... 19768 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-legacy; however: Package cython3-legacy 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-astunparse; however: Package python3-astunparse 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 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-legacy{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-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} 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} 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} libzmq5{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{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-astunparse{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-hatch-vcs{a} python3-hatchling{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-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-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-pathspec{a} python3-pexpect{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pluggy{a} python3-prompt-toolkit{a} python3-psutil{a} python3-ptyprocess{a} python3-pure-eval{a} python3-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-setuptools-scm{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-trove-classifiers{a} python3-typeguard{a} python3-typeshed{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-urllib3{a} python3-wcwidth{a} python3-webencodings{a} python3-zipp{a} python3-zmq{a} python3-zombie-imp{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 pandoc psmisc publicsuffix python3-bottleneck python3-cssselect python3-gdal python3-json-pointer python3-odf python3-olefile python3-openpyxl python3-pydot python3-pygraphviz python3-pytest python3-rfc3987 python3-simplejson python3-uritemplate python3-webcolors python3-yaml shared-mime-info wget xdg-user-dirs 0 packages upgraded, 290 newly installed, 0 to remove and 0 not upgraded. Need to get 173 MB of archives. After unpacking 770 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 ucf all 3.0043+nmu1 [55.2 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 libdebuginfod-common all 0.191-2 [22.9 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 libpython3.12-minimal i386 3.12.6-1 [813 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.3-1 [107 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 python3.12-minimal i386 3.12.6-1 [2242 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.12.5-1 [26.7 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 tzdata all 2024a-4 [255 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.1-1 [23.1 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-3 [9432 B] Get: 16 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libtirpc3t64 i386 1.3.4+ds-1.3 [90.2 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 libnsl2 i386 1.3.0-3+b2 [42.4 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-5 [69.3 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-5 [173 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 libpython3.12-stdlib i386 3.12.6-1 [1961 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 python3.12 i386 3.12.6-1 [669 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.12.5-1 [9588 B] Get: 26 http://deb.debian.org/debian unstable/main i386 python3 i386 3.12.5-1 [27.6 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 sgml-base all 1.31 [15.4 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 libproc2-0 i386 2:4.0.4-5 [65.6 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 procps i386 2:4.0.4-5 [875 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 openssl i386 3.3.2-1 [1386 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 ca-certificates all 20240203 [158 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3 [42.9 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.2-8 [102 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-2 [723 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 libtcl8.6 i386 8.6.14+dfsg-1 [1095 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b4 [309 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 libpng16-16t64 i386 1.6.43-5 [286 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 libfreetype6 i386 2.13.3+dfsg-1 [464 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 fontconfig-config i386 2.15.0-1.1 [317 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 libfontconfig1 i386 2.15.0-1.1 [401 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 libxau6 i386 1:1.0.9-1+b1 [18.5 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 libxdmcp6 i386 1:1.1.2-3+b1 [24.8 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 libxcb1 i386 1.17.0-2 [148 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 libx11-6 i386 2:1.8.7-1+b1 [822 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 libxrender1 i386 1:0.9.10-1.1+b1 [28.8 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 libxft2 i386 2.3.6-1+b1 [55.3 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 x11-common all 1:7.7+23.1 [216 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 libxss1 i386 1:1.2.3-1+b1 [17.3 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 libtk8.6 i386 8.6.14-1 [826 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 tk8.6-blt2.5 i386 2.5.3+dfsg-7 [616 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 blt i386 2.5.3+dfsg-7 [6024 B] Get: 67 http://deb.debian.org/debian unstable/main i386 python3-zombie-imp all 0.0.2-2 [11.7 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 cython3-legacy i386 0.29.37-2+b1 [1910 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-7 [517 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 75 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.191-2 [194 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-5 [9550 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg-3+b1 [704 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 debhelper all 13.20 [915 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 python3-more-itertools all 10.4.0-1 [63.7 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 python3-inflect all 7.3.1-1 [42.2 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 89 http://deb.debian.org/debian unstable/main i386 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 python3-zipp all 3.20.1-1 [10.2 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 python3-setuptools all 74.1.2-2 [736 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 dh-python all 6.20240824 [109 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 xml-core all 0.19 [20.1 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 fonts-lyx all 2.4.1-2 [189 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 libdw1t64 i386 0.191-2 [276 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 libglib2.0-0t64 i386 2.82.0-1 [1568 kB] Get: 101 http://deb.debian.org/debian unstable/main i386 libbabeltrace1 i386 1.5.11-4 [195 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB] Get: 103 http://deb.debian.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB] Get: 104 http://deb.debian.org/debian unstable/main i386 libldap-2.5-0 i386 2.5.18+dfsg-3 [200 kB] Get: 105 http://deb.debian.org/debian unstable/main i386 libnghttp2-14 i386 1.63.0-1 [82.7 kB] Get: 106 http://deb.debian.org/debian unstable/main i386 libnghttp3-9 i386 1.4.0-1 [74.3 kB] Get: 107 http://deb.debian.org/debian unstable/main i386 libngtcp2-16 i386 1.6.0-1 [154 kB] Get: 108 http://deb.debian.org/debian unstable/main i386 libngtcp2-crypto-gnutls8 i386 1.6.0-1 [20.2 kB] Get: 109 http://deb.debian.org/debian unstable/main i386 libpsl5t64 i386 0.21.2-1.1 [57.4 kB] Get: 110 http://deb.debian.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b4 [62.0 kB] Get: 111 http://deb.debian.org/debian unstable/main i386 libssh2-1t64 i386 1.11.0-7 [226 kB] Get: 112 http://deb.debian.org/debian unstable/main i386 libcurl3t64-gnutls i386 8.9.1-2 [511 kB] Get: 113 http://deb.debian.org/debian unstable/main i386 libdebuginfod1t64 i386 0.191-2 [29.4 kB] Get: 114 http://deb.debian.org/debian unstable/main i386 libipt2 i386 2.0.6-1 [52.6 kB] Get: 115 http://deb.debian.org/debian unstable/main i386 libpython3.12t64 i386 3.12.6-1 [2168 kB] Get: 116 http://deb.debian.org/debian unstable/main i386 libsource-highlight-common all 3.1.9-4.3 [77.5 kB] Get: 117 http://deb.debian.org/debian unstable/main i386 libsource-highlight4t64 i386 3.1.9-4.3 [349 kB] Get: 118 http://deb.debian.org/debian unstable/main i386 gdb i386 15.1-1 [4537 kB] Get: 119 http://deb.debian.org/debian unstable/main i386 libaec0 i386 1.1.3-1 [24.5 kB] Get: 120 http://deb.debian.org/debian unstable/main i386 libblas3 i386 3.12.0-3 [140 kB] Get: 121 http://deb.debian.org/debian unstable/main i386 libsnappy1v5 i386 1.2.1-1 [31.3 kB] Get: 122 http://deb.debian.org/debian unstable/main i386 libblosc1 i386 1.21.5+ds-1+b1 [51.4 kB] Get: 123 http://deb.debian.org/debian unstable/main i386 libblosc2-4 i386 2.15.1+ds-1 [217 kB] Get: 124 http://deb.debian.org/debian unstable/main i386 libcurl4t64 i386 8.9.1-2 [502 kB] Get: 125 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.21-1 [48.0 kB] Get: 126 http://deb.debian.org/debian unstable/main i386 libexpat1-dev i386 2.6.3-1 [164 kB] Get: 127 http://deb.debian.org/debian unstable/main i386 libfribidi0 i386 1.0.15-1 [72.4 kB] Get: 128 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14.2.0-4 [735 kB] Get: 129 http://deb.debian.org/debian unstable/main i386 libgraphite2-3 i386 1.3.14-2 [77.7 kB] Get: 130 http://deb.debian.org/debian unstable/main i386 libharfbuzz0b i386 9.0.0-1 [500 kB] Get: 131 http://deb.debian.org/debian unstable/main i386 libsz2 i386 1.1.3-1 [7824 B] Get: 132 http://deb.debian.org/debian unstable/main i386 libhdf5-103-1t64 i386 1.10.10+repack-4 [1186 kB] Get: 133 http://deb.debian.org/debian unstable/main i386 libhdf5-hl-100t64 i386 1.10.10+repack-4 [76.0 kB] Get: 134 http://deb.debian.org/debian unstable/main i386 libimagequant0 i386 2.18.0-1+b1 [35.9 kB] Get: 135 http://deb.debian.org/debian unstable/main i386 libjbig0 i386 2.1-6.1+b1 [31.8 kB] Get: 136 http://deb.debian.org/debian unstable/main i386 libjpeg62-turbo i386 1:2.1.5-3 [169 kB] Get: 137 http://deb.debian.org/debian unstable/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 138 http://deb.debian.org/debian unstable/main i386 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 139 http://deb.debian.org/debian unstable/main i386 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 140 http://deb.debian.org/debian unstable/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 141 http://deb.debian.org/debian unstable/main i386 libjs-sphinxdoc all 7.4.7-3 [158 kB] Get: 142 http://deb.debian.org/debian unstable/main i386 libjson-perl all 4.10000-1 [87.5 kB] Get: 143 http://deb.debian.org/debian unstable/main i386 liblapack3 i386 3.12.0-3 [2167 kB] Get: 144 http://deb.debian.org/debian unstable/main i386 liblbfgsb0 i386 3.0+dfsg.4-1+b1 [29.1 kB] Get: 145 http://deb.debian.org/debian unstable/main i386 liblcms2-2 i386 2.14-2+b1 [165 kB] Get: 146 http://deb.debian.org/debian unstable/main i386 liblerc4 i386 4.0.0+ds-4+b1 [180 kB] Get: 147 http://deb.debian.org/debian unstable/main i386 liblzo2-2 i386 2.10-3 [57.6 kB] Get: 148 http://deb.debian.org/debian unstable/main i386 libnetcdf19t64 i386 1:4.9.2-7 [528 kB] Get: 149 http://deb.debian.org/debian unstable/main i386 libnorm1t64 i386 1.5.9+dfsg-3.1 [237 kB] Get: 150 http://deb.debian.org/debian unstable/main i386 libopenjp2-7 i386 2.5.0-2+b3 [197 kB] Get: 151 http://deb.debian.org/debian unstable/main i386 libpgm-5.3-0t64 i386 5.3.128~dfsg-2.1 [167 kB] Get: 152 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1 [915 kB] Get: 153 http://deb.debian.org/debian unstable/main i386 libpython3.12-dev i386 3.12.6-1 [5284 kB] Get: 154 http://deb.debian.org/debian unstable/main i386 libpython3-dev i386 3.12.5-1 [9852 B] Get: 155 http://deb.debian.org/debian unstable/main i386 libpython3-all-dev i386 3.12.5-1 [1068 B] Get: 156 http://deb.debian.org/debian unstable/main i386 libqhull-r8.0 i386 2020.2-6+b1 [256 kB] Get: 157 http://deb.debian.org/debian unstable/main i386 libraqm0 i386 0.10.1-1+b1 [14.7 kB] Get: 158 http://deb.debian.org/debian unstable/main i386 libsharpyuv0 i386 1.4.0-0.1 [113 kB] Get: 159 http://deb.debian.org/debian unstable/main i386 libsodium23 i386 1.0.18-1+b1 [185 kB] Get: 160 http://deb.debian.org/debian unstable/main i386 libwebp7 i386 1.4.0-0.1 [318 kB] Get: 161 http://deb.debian.org/debian unstable/main i386 libtiff6 i386 4.5.1+git230720-5 [339 kB] Get: 162 http://deb.debian.org/debian unstable/main i386 libwebpdemux2 i386 1.4.0-0.1 [111 kB] Get: 163 http://deb.debian.org/debian unstable/main i386 libwebpmux3 i386 1.4.0-0.1 [125 kB] Get: 164 http://deb.debian.org/debian unstable/main i386 libxslt1.1 i386 1.1.35-1.1 [242 kB] Get: 165 http://deb.debian.org/debian unstable/main i386 libzmq5 i386 4.3.5-1+b2 [306 kB] Get: 166 http://deb.debian.org/debian unstable/main i386 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 167 http://deb.debian.org/debian unstable/main i386 python-matplotlib-data all 3.8.3-3 [2731 kB] Get: 168 http://deb.debian.org/debian unstable/main i386 python-tables-data all 3.10.1-1 [49.5 kB] Get: 169 http://deb.debian.org/debian unstable/main i386 python-tinycss2-common all 1.3.0-1 [31.9 kB] Get: 170 http://deb.debian.org/debian unstable/main i386 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 171 http://deb.debian.org/debian unstable/main i386 python3-all i386 3.12.5-1 [1044 B] Get: 172 http://deb.debian.org/debian unstable/main i386 python3.12-dev i386 3.12.6-1 [506 kB] Get: 173 http://deb.debian.org/debian unstable/main i386 python3-dev i386 3.12.5-1 [26.2 kB] Get: 174 http://deb.debian.org/debian unstable/main i386 python3-all-dev i386 3.12.5-1 [1068 B] Get: 175 http://deb.debian.org/debian unstable/main i386 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 176 http://deb.debian.org/debian unstable/main i386 python3-six all 1.16.0-7 [16.4 kB] Get: 177 http://deb.debian.org/debian unstable/main i386 python3-asttokens all 2.4.1-1 [20.6 kB] Get: 178 http://deb.debian.org/debian unstable/main i386 python3-astunparse all 1.6.3-2 [13.8 kB] Get: 179 http://deb.debian.org/debian unstable/main i386 python3-attr all 24.2.0-1 [68.4 kB] Get: 180 http://deb.debian.org/debian unstable/main i386 python3-tz all 2024.1-2 [30.9 kB] Get: 181 http://deb.debian.org/debian unstable/main i386 python3-babel all 2.14.0-1 [111 kB] Get: 182 http://deb.debian.org/debian unstable/main i386 python3-webencodings all 0.5.1-5 [11.1 kB] Get: 183 http://deb.debian.org/debian unstable/main i386 python3-html5lib all 1.1-6 [90.5 kB] Get: 184 http://deb.debian.org/debian unstable/main i386 python3-bleach all 6.1.0-2 [50.7 kB] Get: 185 http://deb.debian.org/debian unstable/main i386 python3-brotli i386 1.1.0-2+b4 [315 kB] Get: 186 http://deb.debian.org/debian unstable/main i386 python3-soupsieve all 2.6-1 [38.3 kB] Get: 187 http://deb.debian.org/debian unstable/main i386 python3-bs4 all 4.12.3-3 [133 kB] Get: 188 http://deb.debian.org/debian unstable/main i386 python3-certifi all 2024.6.2-1 [157 kB] Get: 189 http://deb.debian.org/debian unstable/main i386 python3-cffi-backend i386 1.17.1-1 [89.9 kB] Get: 190 http://deb.debian.org/debian unstable/main i386 python3-numpy i386 1:1.26.4+ds-11 [4299 kB] Get: 191 http://deb.debian.org/debian unstable/main i386 python3-cftime i386 1.6.4-1+b1 [205 kB] Get: 192 http://deb.debian.org/debian unstable/main i386 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 193 http://deb.debian.org/debian unstable/main i386 python3-charset-normalizer i386 3.3.2-2 [118 kB] Get: 194 http://deb.debian.org/debian unstable/main i386 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB] Get: 195 http://deb.debian.org/debian unstable/main i386 python3-comm all 0.2.1-1 [8104 B] Get: 196 http://deb.debian.org/debian unstable/main i386 python3-contourpy i386 1.3.0-1 [221 kB] Get: 197 http://deb.debian.org/debian unstable/main i386 python3-coverage i386 7.6.0+dfsg1-1 [175 kB] Get: 198 http://deb.debian.org/debian unstable/main i386 python3-cpuinfo all 9.0.0+git20221119-2 [23.4 kB] Get: 199 http://deb.debian.org/debian unstable/main i386 python3-cycler all 0.12.1-1 [9496 B] Get: 200 http://deb.debian.org/debian unstable/main i386 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 201 http://deb.debian.org/debian unstable/main i386 python3-debugpy i386 1.8.5+ds-1 [573 kB] Get: 202 http://deb.debian.org/debian unstable/main i386 python3-decorator all 5.1.1-5 [15.1 kB] Get: 203 http://deb.debian.org/debian unstable/main i386 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 204 http://deb.debian.org/debian unstable/main i386 python3-roman all 3.3-3 [9880 B] Get: 205 http://deb.debian.org/debian unstable/main i386 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 206 http://deb.debian.org/debian unstable/main i386 python3-executing all 2.0.1-0.1 [22.7 kB] Get: 207 http://deb.debian.org/debian unstable/main i386 python3-fastjsonschema all 2.20.0-1 [21.8 kB] Get: 208 http://deb.debian.org/debian unstable/main i386 python3-scipy i386 1.13.1-5 [16.6 MB] Get: 209 http://deb.debian.org/debian unstable/main i386 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get: 210 http://deb.debian.org/debian unstable/main i386 python3-mpmath all 1.3.0-1 [419 kB] Get: 211 http://deb.debian.org/debian unstable/main i386 python3-sympy all 1.13.2-1 [4147 kB] Get: 212 http://deb.debian.org/debian unstable/main i386 python3-fs all 2.4.16-4 [95.4 kB] Get: 213 http://deb.debian.org/debian unstable/main i386 python3-lxml i386 5.3.0-1 [1239 kB] Get: 214 http://deb.debian.org/debian unstable/main i386 python3-lz4 i386 4.0.2+dfsg-1+b4 [25.2 kB] Get: 215 http://deb.debian.org/debian unstable/main i386 unicode-data all 15.1.0-1 [8547 kB] Get: 216 http://deb.debian.org/debian unstable/main i386 python3-fonttools i386 4.46.0-1+b1 [1385 kB] Get: 217 http://deb.debian.org/debian unstable/main i386 python3-gsd i386 3.3.0-1+b1 [202 kB] Get: 218 http://deb.debian.org/debian unstable/main i386 python3-packaging all 24.1-1 [45.8 kB] Get: 219 http://deb.debian.org/debian unstable/main i386 python3-pathspec all 0.12.1-1 [28.1 kB] Get: 220 http://deb.debian.org/debian unstable/main i386 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 221 http://deb.debian.org/debian unstable/main i386 python3-trove-classifiers all 2024.4.10-1 [10.1 kB] Get: 222 http://deb.debian.org/debian unstable/main i386 python3-hatchling all 1.25.0-1 [53.8 kB] Get: 223 http://deb.debian.org/debian unstable/main i386 python3-setuptools-scm all 8.1.0-1 [40.5 kB] Get: 224 http://deb.debian.org/debian unstable/main i386 python3-hatch-vcs all 0.4.0-1 [8336 B] Get: 225 http://deb.debian.org/debian unstable/main i386 python3-idna all 3.6-2.1 [38.6 kB] Get: 226 http://deb.debian.org/debian unstable/main i386 python3-imagesize all 1.4.1-1 [6688 B] Get: 227 http://deb.debian.org/debian unstable/main i386 python3-parso all 0.8.3-1 [67.4 kB] Get: 228 http://deb.debian.org/debian unstable/main i386 python3-typeshed all 0.0~git20231111.6764465-3 [1258 kB] Get: 229 http://deb.debian.org/debian unstable/main i386 python3-jedi all 0.19.1+ds1-1 [691 kB] Get: 230 http://deb.debian.org/debian unstable/main i386 python3-matplotlib-inline all 0.1.6-2 [8652 B] Get: 231 http://deb.debian.org/debian unstable/main i386 python3-ptyprocess all 0.7.0-5 [14.7 kB] Get: 232 http://deb.debian.org/debian unstable/main i386 python3-pexpect all 4.9-2 [55.5 kB] Get: 233 http://deb.debian.org/debian unstable/main i386 python3-wcwidth all 0.2.13+dfsg1-1 [24.9 kB] Get: 234 http://deb.debian.org/debian unstable/main i386 python3-prompt-toolkit all 3.0.47-1 [277 kB] Get: 235 http://deb.debian.org/debian unstable/main i386 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 236 http://deb.debian.org/debian unstable/main i386 python3-pure-eval all 0.2.2-2 [11.0 kB] Get: 237 http://deb.debian.org/debian unstable/main i386 python3-stack-data all 0.6.3-1 [21.6 kB] Get: 238 http://deb.debian.org/debian unstable/main i386 python3-ipython all 8.20.0-1 [556 kB] Get: 239 http://deb.debian.org/debian unstable/main i386 python3-platformdirs all 4.2.2-1 [16.3 kB] Get: 240 http://deb.debian.org/debian unstable/main i386 python3-jupyter-core all 5.7.2-4 [35.1 kB] Get: 241 http://deb.debian.org/debian unstable/main i386 python3-psutil i386 5.9.8-2 [226 kB] Get: 242 http://deb.debian.org/debian unstable/main i386 python3-tornado i386 6.4.1-2 [349 kB] Get: 243 http://deb.debian.org/debian unstable/main i386 python3-py all 1.11.0-2 [88.7 kB] Get: 244 http://deb.debian.org/debian unstable/main i386 python3-zmq i386 24.0.1-5+b2 [276 kB] Get: 245 http://deb.debian.org/debian unstable/main i386 python3-jupyter-client all 8.6.2-3 [91.5 kB] Get: 246 http://deb.debian.org/debian unstable/main i386 python3-nest-asyncio all 1.5.4-1 [6248 B] Get: 247 http://deb.debian.org/debian unstable/main i386 python3-ipykernel all 6.29.5-1 [102 kB] Get: 248 http://deb.debian.org/debian unstable/main i386 python3-markupsafe i386 2.1.5-1+b1 [13.7 kB] Get: 249 http://deb.debian.org/debian unstable/main i386 python3-jinja2 all 3.1.3-1 [119 kB] Get: 250 http://deb.debian.org/debian unstable/main i386 python3-joblib all 1.3.2-2 [218 kB] Get: 251 http://deb.debian.org/debian unstable/main i386 python3-rpds-py i386 0.12.0-3+b1 [235 kB] Get: 252 http://deb.debian.org/debian unstable/main i386 python3-referencing all 0.35.1-1 [23.5 kB] Get: 253 http://deb.debian.org/debian unstable/main i386 python3-jsonschema-specifications all 2023.12.1-1 [8976 B] Get: 254 http://deb.debian.org/debian unstable/main i386 python3-jsonschema all 4.19.2-3 [71.3 kB] Get: 255 http://deb.debian.org/debian unstable/main i386 python3-jupyterlab-pygments all 0.2.2-3 [6096 B] Get: 256 http://deb.debian.org/debian unstable/main i386 python3-kiwisolver i386 1.4.5-1+b1 [65.4 kB] Get: 257 http://deb.debian.org/debian unstable/main i386 python3-pil i386 10.4.0-1 [503 kB] Get: 258 http://deb.debian.org/debian unstable/main i386 python3.12-tk i386 3.12.6-1 [113 kB] Get: 259 http://deb.debian.org/debian unstable/main i386 python3.13-tk i386 3.13.0~rc2-1 [103 kB] Get: 260 http://deb.debian.org/debian unstable/main i386 python3-tk i386 3.12.6-1 [9428 B] Get: 261 http://deb.debian.org/debian unstable/main i386 python3-pil.imagetk i386 10.4.0-1 [79.6 kB] Get: 262 http://deb.debian.org/debian unstable/main i386 python3-pyparsing all 3.1.2-1 [146 kB] Get: 263 http://deb.debian.org/debian unstable/main i386 python3-matplotlib i386 3.8.3-3 [5569 kB] Get: 264 http://deb.debian.org/debian unstable/main i386 python3-mistune all 3.0.2-1 [33.1 kB] Get: 265 http://deb.debian.org/debian unstable/main i386 sphinx-rtd-theme-common all 2.0.0+dfsg-2 [1021 kB] Get: 266 http://deb.debian.org/debian unstable/main i386 sphinx-common all 7.4.7-3 [731 kB] Get: 267 http://deb.debian.org/debian unstable/main i386 python3-urllib3 all 2.0.7-2 [111 kB] Get: 268 http://deb.debian.org/debian unstable/main i386 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 269 http://deb.debian.org/debian unstable/main i386 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 270 http://deb.debian.org/debian unstable/main i386 python3-sphinx all 7.4.7-3 [588 kB] Get: 271 http://deb.debian.org/debian unstable/main i386 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 272 http://deb.debian.org/debian unstable/main i386 python3-sphinx-rtd-theme all 2.0.0+dfsg-2 [28.5 kB] Get: 273 http://deb.debian.org/debian unstable/main i386 python3-msmb-theme all 1.2.0-4 [33.8 kB] Get: 274 http://deb.debian.org/debian unstable/main i386 python3-nbformat all 5.9.1-1 [45.1 kB] Get: 275 http://deb.debian.org/debian unstable/main i386 python3-nbclient all 0.8.0-1 [64.0 kB] Get: 276 http://deb.debian.org/debian unstable/main i386 python3-pandocfilters all 1.5.1-1 [23.7 kB] Get: 277 http://deb.debian.org/debian unstable/main i386 python3-tinycss2 all 1.3.0-1 [22.1 kB] Get: 278 http://deb.debian.org/debian unstable/main i386 python3-nbconvert all 7.16.4-1 [175 kB] Get: 279 http://deb.debian.org/debian unstable/main i386 python3-netcdf4 i386 1.7.1-1+b1 [570 kB] Get: 280 http://deb.debian.org/debian unstable/main i386 python3-networkx all 3.2.1-4 [14.2 MB] Get: 281 http://deb.debian.org/debian unstable/main i386 python3-numexpr i386 2.10.1-2+b1 [127 kB] Get: 282 http://deb.debian.org/debian unstable/main i386 python3-tabulate all 0.9.0-1 [45.9 kB] Get: 283 http://deb.debian.org/debian unstable/main i386 python3-numpydoc all 1.6.0-2 [49.6 kB] Get: 284 http://deb.debian.org/debian unstable/main i386 python3-pandas-lib i386 2.2.2+dfsg-4+b1 [3998 kB] Get: 285 http://deb.debian.org/debian unstable/main i386 python3-pandas all 2.2.2+dfsg-4 [3095 kB] Get: 286 http://deb.debian.org/debian unstable/main i386 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 287 http://deb.debian.org/debian unstable/main i386 python3-sklearn-lib i386 1.4.2+dfsg-6 [3400 kB] Get: 288 http://deb.debian.org/debian unstable/main i386 python3-sklearn all 1.4.2+dfsg-6 [2248 kB] Get: 289 http://deb.debian.org/debian unstable/main i386 python3-tables-lib i386 3.10.1-1 [526 kB] Get: 290 http://deb.debian.org/debian unstable/main i386 python3-tables all 3.10.1-1 [355 kB] Fetched 173 MB in 4s (41.4 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 ... 19768 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_0.191-2_all.deb ... Unpacking libdebuginfod-common (0.191-2) ... Selecting previously unselected package libpython3.12-minimal:i386. Preparing to unpack .../4-libpython3.12-minimal_3.12.6-1_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.6-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../5-libexpat1_2.6.3-1_i386.deb ... Unpacking libexpat1:i386 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../6-python3.12-minimal_3.12.6-1_i386.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:i386 (3.12.6-1) ... Setting up libexpat1:i386 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20200 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.5-1_i386.deb ... Unpacking python3-minimal (3.12.5-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:i386. Preparing to unpack .../04-libkrb5support0_1.21.3-3_i386.deb ... Unpacking libkrb5support0:i386 (1.21.3-3) ... Selecting previously unselected package libcom-err2:i386. Preparing to unpack .../05-libcom-err2_1.47.1-1_i386.deb ... Unpacking libcom-err2:i386 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:i386. Preparing to unpack .../06-libk5crypto3_1.21.3-3_i386.deb ... Unpacking libk5crypto3:i386 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:i386. Preparing to unpack .../07-libkeyutils1_1.6.3-3_i386.deb ... Unpacking libkeyutils1:i386 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:i386. Preparing to unpack .../08-libkrb5-3_1.21.3-3_i386.deb ... Unpacking libkrb5-3:i386 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:i386. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_i386.deb ... Unpacking libgssapi-krb5-2:i386 (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:i386. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3 to /lib/i386-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3.0.0 to /lib/i386-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:i386 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:i386. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_i386.deb ... Unpacking libnsl2:i386 (1.3.0-3+b2) ... 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:i386. Preparing to unpack .../14-libreadline8t64_8.2-5_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:i386. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_i386.deb ... Unpacking libpython3.12-stdlib:i386 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_i386.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../17-libpython3-stdlib_3.12.5-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.12.5-1) ... Setting up python3-minimal (3.12.5-1) ... 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 ... 21272 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.5-1_i386.deb ... Unpacking python3 (3.12.5-1) ... 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:i386. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-5_i386.deb ... Unpacking libproc2-0:i386 (2:4.0.4-5) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-5_i386.deb ... Unpacking procps (2:4.0.4-5) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.3.2-1_i386.deb ... Unpacking openssl (3.3.2-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.45-3_i386.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../007-libmagic1t64_1%3a5.45-3_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.45-3_i386.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.22.5-2_i386.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../010-libuchardet0_0.0.8-1+b1_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.23.0-5_i386.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../012-bsdextrautils_2.40.2-8_i386.deb ... Unpacking bsdextrautils (2.40.2-8) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../013-libpipeline1_1.5.8-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../014-man-db_2.13.0-1_i386.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../015-m4_1.4.19-4_i386.deb ... 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Setting up libngtcp2-crypto-gnutls8:i386 (1.6.0-1) ... Setting up libsz2:i386 (1.1.3-1) ... 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:i386 (3.12.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libxrender1:i386 (1:0.9.10-1.1+b1) ... Setting up libtool (2.4.7-7) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:i386 (1.4.0-0.1) ... Setting up libxext6:i386 (2:1.3.4-1+b1) ... Setting up libsource-highlight4t64:i386 (3.1.9-4.3) ... Setting up libldap-2.5-0:i386 (2.5.18+dfsg-3) ... 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 libfreetype6:i386 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:i386 (1.21.3-3) ... Setting up ucf (3.0043+nmu1) ... Setting up libjs-sphinxdoc (7.4.7-3) ... Setting up libreadline8t64:i386 (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:i386 (1.1.35-1.1) ... Setting up libharfbuzz0b:i386 (9.0.0-1) ... Setting up libxss1:i386 (1:1.2.3-1+b1) ... Setting up libfontconfig1:i386 (2.15.0-1.1) ... Setting up liblbfgsb0:i386 (3.0+dfsg.4-1+b1) ... Setting up libxft2:i386 (2.3.6-1+b1) ... Setting up libzmq5:i386 (4.3.5-1+b2) ... Setting up libdebuginfod-common (0.191-2) ... Setting up libcurl4t64:i386 (8.9.1-2) ... Setting up libtirpc3t64:i386 (1.3.4+ds-1.3) ... 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Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (7.4.7-3) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-numpydoc (1.6.0-2) ... Setting up python3-sphinx-rtd-theme (2.0.0+dfsg-2) ... 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-1.10.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../mdtraj_1.10.0-3_source.changes dpkg-buildpackage: info: source package mdtraj dpkg-buildpackage: info: source version 1.10.0-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Drew Parsons dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 dpkg-source: info: using options from mdtraj-1.10.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild pybuild --clean -i python{version} -p 3.12 I: pybuild base:311: python3.12 setup.py clean Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-linux-gnu/14/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-4' --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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-4) /build/reproducible-path/mdtraj-1.10.0/basesetup.py:518: 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. 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-1.10.0/.pybuild/cpython3_3.12_mdtraj/build' (and everything under it) 'build/bdist.linux-i686' 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-1.10.0' for f in mdtraj/formats/binpos/binpos.c \ mdtraj/formats/dcd/dcd.c \ mdtraj/formats/dtr/dtr.cpp \ mdtraj/formats/tng/tng.c \ mdtraj/formats/xtc/trr.c \ mdtraj/formats/xtc/xtc.c \ mdtraj/geometry/drid.cpp \ mdtraj/geometry/neighborlist.cpp \ mdtraj/geometry/neighbors.cpp \ mdtraj/geometry/src/_geometry.cpp \ mdtraj/rmsd/_lprmsd.cpp \ mdtraj/rmsd/_rmsd.cpp \ mdtraj/version.py; \ do rm -f $f; done rm -rf mdtraj/core/lib rm -rf docs/api/generated rm -rf __pycache__ .pybuild find . -name "lib*.a" -delete make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.10.0' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/python3-mdtraj.substvars debian/python-mdtraj-doc.substvars debian/files rm -fr -- debian/python3-mdtraj/ debian/tmp/ debian/python-mdtraj-doc/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --with sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild pybuild --configure -i python{version} -p 3.12 I: pybuild base:311: python3.12 setup.py config Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-linux-gnu/14/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-4' --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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-4) /build/reproducible-path/mdtraj-1.10.0/basesetup.py:518: 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. 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/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-linux-gnu/14/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-4' --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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-4) 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. 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-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj copying mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj copying mdtraj/io.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj copying mdtraj/version.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj creating /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core creating /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing creating /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats creating /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils creating /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data running build_ext building 'mdtraj.formats.xtc' extension creating build creating build/temp.linux-i686-cpython-312 creating build/temp.linux-i686-cpython-312/mdtraj creating build/temp.linux-i686-cpython-312/mdtraj/formats creating build/temp.linux-i686-cpython-312/mdtraj/formats/xtc creating build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-i686-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-i686-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; | ^~~~~~ i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-i686-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 { | ^~ i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-i686-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:784: /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:9825:16: mdtraj/formats/xtc/xtc.c:696:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 696 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/xtc.c:19308:20: note: in expansion of macro 'PyInt_FromLong' 19308 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write': mdtraj/formats/xtc/xtc.c:9545:7: note: '__pyx_v_status' was declared here 9545 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:7652:10: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7652 | if (unlikely(__pyx_t_6 != -1)) { | ^ mdtraj/formats/xtc/xtc.c:6451:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 6451 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7651:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 7651 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6451:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 6451 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8028:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8028 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6449:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 6449 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8032:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8032 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6449:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 6449 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8036:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8036 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6449:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 6449 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8074:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8074 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6455:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 6455 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7998:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7998 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6459:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 6459 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8016:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8016 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6463:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 6463 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8056:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8056 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6467:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 6467 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8060:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8060 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6467:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 6467 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8064:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8064 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6467:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 6467 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/xtc.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-i386-linux-gnu.so building 'mdtraj.formats.trr' extension i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-i686-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-i686-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; | ^~~~~~ i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-i686-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:784: /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:11598:16: mdtraj/formats/xtc/trr.c:696:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 696 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/trr.c:21006:20: note: in expansion of macro 'PyInt_FromLong' 21006 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write': mdtraj/formats/xtc/trr.c:11071:7: note: '__pyx_v_status' was declared here 11071 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:8651:12: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8651 | if (unlikely(__pyx_t_5 != -1)) { | ^ mdtraj/formats/xtc/trr.c:6963:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 6963 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8650:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8650 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6963:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 6963 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8599:12: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8599 | if (unlikely(__pyx_t_5 != -1)) { | ^ mdtraj/formats/xtc/trr.c:6979:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 6979 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8598:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8598 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6979:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 6979 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8758:10: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8758 | if (unlikely(__pyx_t_5 != -1)) { | ^ mdtraj/formats/xtc/trr.c:6983:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 6983 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8757:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8757 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6983:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 6983 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8357:56: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8357 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:6977:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 6977 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1917:95: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1917 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8372:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8372 | __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:6977:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 6977 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8363:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8363 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6977:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 6977 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8367:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8367 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6977:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 6977 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8414:59: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8414 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:6961:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 6961 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1917:95: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1917 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8429:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8429 | __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:6961:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 6961 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8420:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8420 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6961:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 6961 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8424:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8424 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6961:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 6961 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/trr.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so building 'mdtraj.formats.dcd' extension creating build/temp.linux-i686-cpython-312/mdtraj/formats/dcd creating build/temp.linux-i686-cpython-312/mdtraj/formats/dcd/src i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-i686-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:782: /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:6621:17: mdtraj/formats/dcd/dcd.c:694:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 694 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/dcd/dcd.c:13637:20: note: in expansion of macro 'PyInt_FromLong' 13637 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:5440:7: note: '__pyx_v_i' was declared here 5440 | int __pyx_v_i; | ^~~~~~~~~ i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-i686-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/dcd/dcd.o build/temp.linux-i686-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so building 'mdtraj.formats.dtr' extension creating build/temp.linux-i686-cpython-312/mdtraj/formats/dtr creating build/temp.linux-i686-cpython-312/mdtraj/formats/dtr/src i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -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-i686-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:803: /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 " \ | ^~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -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-i686-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:486:64: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d 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 long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %lld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long 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 long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %lld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:494:60: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 494 | "non-constant time interval at frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d mdtraj/formats/dtr/src/dtrplugin.cxx:499:60: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)': mdtraj/formats/dtr/src/dtrplugin.cxx:1301:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", | ~~^ | | | long int | %lld 1302 | 3*natoms, pos.count); | ~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:1310:71: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", | ~~^ | | | long int | %lld 1311 | 3*natoms, vel.count); | ~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)': mdtraj/formats/dtr/src/dtrplugin.cxx:1572:45: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", | ~~^ | | | long int | %lld 1573 | velblob.count, 3*natoms); | ~~~~~~~~~~~~~ | | | uint64_t {aka long 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/i386-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/i386-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/i386-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/i386-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 ()); | ~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/dtr/dtr.o build/temp.linux-i686-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-i386-linux-gnu.so building 'mdtraj._rmsd' extension creating build/temp.linux-i686-cpython-312/mdtraj/rmsd creating build/temp.linux-i686-cpython-312/mdtraj/rmsd/src i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-cpython-312/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/rmsd/_rmsd.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so building 'mdtraj._lprmsd' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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:814: /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 " \ | ^~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/rmsd/_lprmsd.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/Munkres.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/fancy_index.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so building 'mdtraj.core.lib.libtheobald' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -msse2 -mssse3 -O3 -funroll-loops --std=c++11 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-cpython-312/mdtraj/rmsd/src/center.o -msse2 -mssse3 -O3 -funroll-loops --std=c++11 i686-linux-gnu-gcc-ar rcs /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/libtheobald.a build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/center.o building 'mdtraj.geometry._geometry' extension creating build/temp.linux-i686-cpython-312/mdtraj/geometry creating build/temp.linux-i686-cpython-312/mdtraj/geometry/src i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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:816: /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 " \ | ^~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/geometry/src/_geometry.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/dssp.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/geometry.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/sasa.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.drid' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-cpython-312/mdtraj/geometry/drid.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/geometry/drid.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/dridkernels.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/moments.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.neighbors' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-cpython-312/mdtraj/geometry/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/geometry/neighbors.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/neighbors.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-cpython-312/mdtraj/geometry/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/geometry/neighborlist.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/neighborlist.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-i386-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-1.10.0/.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-JrjGAgFu 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-1.10.0/debian/tmp pybuild --install -i python{version} -p 3.12 --dest-dir /build/reproducible-path/mdtraj-1.10.0/debian/tmp I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-linux-gnu/14/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-4' --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=i686-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-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-4) 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. 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 copying mdtraj/version.py -> /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj running build_ext building 'mdtraj.formats.xtc' extension i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-i686-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-i686-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; | ^~~~~~ i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-i686-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 { | ^~ i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-i686-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:784: /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:9825:16: mdtraj/formats/xtc/xtc.c:696:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 696 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/xtc.c:19308:20: note: in expansion of macro 'PyInt_FromLong' 19308 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write': mdtraj/formats/xtc/xtc.c:9545:7: note: '__pyx_v_status' was declared here 9545 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:7652:10: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7652 | if (unlikely(__pyx_t_6 != -1)) { | ^ mdtraj/formats/xtc/xtc.c:6451:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 6451 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7651:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 7651 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6451:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 6451 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8028:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8028 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6449:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 6449 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8032:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8032 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6449:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 6449 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8036:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8036 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6449:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 6449 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8074:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8074 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6455:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 6455 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7998:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7998 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6459:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 6459 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8016:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8016 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6463:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 6463 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8056:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8056 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6467:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 6467 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8060:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8060 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6467:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 6467 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8064:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8064 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6467:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 6467 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/xtc.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-i386-linux-gnu.so building 'mdtraj.formats.trr' extension i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-i686-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-i686-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; | ^~~~~~ i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-i686-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:784: /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:11598:16: mdtraj/formats/xtc/trr.c:696:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 696 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/trr.c:21006:20: note: in expansion of macro 'PyInt_FromLong' 21006 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write': mdtraj/formats/xtc/trr.c:11071:7: note: '__pyx_v_status' was declared here 11071 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:8651:12: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8651 | if (unlikely(__pyx_t_5 != -1)) { | ^ mdtraj/formats/xtc/trr.c:6963:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 6963 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8650:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8650 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6963:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 6963 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8599:12: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8599 | if (unlikely(__pyx_t_5 != -1)) { | ^ mdtraj/formats/xtc/trr.c:6979:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 6979 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8598:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8598 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6979:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 6979 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8758:10: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8758 | if (unlikely(__pyx_t_5 != -1)) { | ^ mdtraj/formats/xtc/trr.c:6983:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 6983 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8757:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8757 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6983:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 6983 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8357:56: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8357 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:6977:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 6977 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1917:95: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1917 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8372:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8372 | __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:6977:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 6977 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8363:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8363 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6977:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 6977 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8367:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8367 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6977:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 6977 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8414:59: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8414 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:6961:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 6961 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1917:95: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1917 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8429:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8429 | __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:6961:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 6961 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8420:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8420 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6961:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 6961 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8424:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8424 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6961:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 6961 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/trr.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so building 'mdtraj.formats.dcd' extension i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-i686-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:782: /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:6621:17: mdtraj/formats/dcd/dcd.c:694:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 694 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/dcd/dcd.c:13637:20: note: in expansion of macro 'PyInt_FromLong' 13637 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:5440:7: note: '__pyx_v_i' was declared here 5440 | int __pyx_v_i; | ^~~~~~~~~ i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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-i686-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/dcd/dcd.o build/temp.linux-i686-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so building 'mdtraj.formats.dtr' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -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-i686-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:803: /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 " \ | ^~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -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-i686-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:486:64: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d 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 long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %lld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long 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 long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %lld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:494:60: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 494 | "non-constant time interval at frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d mdtraj/formats/dtr/src/dtrplugin.cxx:499:60: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)': mdtraj/formats/dtr/src/dtrplugin.cxx:1301:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", | ~~^ | | | long int | %lld 1302 | 3*natoms, pos.count); | ~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:1310:71: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", | ~~^ | | | long int | %lld 1311 | 3*natoms, vel.count); | ~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)': mdtraj/formats/dtr/src/dtrplugin.cxx:1572:45: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", | ~~^ | | | long int | %lld 1573 | velblob.count, 3*natoms); | ~~~~~~~~~~~~~ | | | uint64_t {aka long 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/i386-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/i386-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/i386-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/i386-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 ()); | ~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/dtr/dtr.o build/temp.linux-i686-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-i386-linux-gnu.so building 'mdtraj._rmsd' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-cpython-312/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/rmsd/_rmsd.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so building 'mdtraj._lprmsd' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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:814: /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 " \ | ^~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/rmsd/_lprmsd.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/Munkres.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/fancy_index.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry._geometry' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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:816: /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 " \ | ^~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/geometry/src/_geometry.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/dssp.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/geometry.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/sasa.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.drid' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-cpython-312/mdtraj/geometry/drid.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/geometry/drid.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/dridkernels.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/moments.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.neighbors' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-cpython-312/mdtraj/geometry/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/geometry/neighbors.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/neighbors.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-cpython-312/mdtraj/geometry/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/geometry/neighborlist.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/neighborlist.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so running install_lib creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12 creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/residue_names.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/topology.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/element.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/trajectory.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/selection.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/libtheobald.a -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/center.h -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/theobald_rmsd.h -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__pycache__/version.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__ creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/testing.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/docstrings.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/docscrape.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/dcdreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/hdf5reporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/basereporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/xtcreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/netcdfreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/registry.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/lammpstrj.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/psf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/lh5.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/arc.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/amberrst.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/hdf5.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/gsd.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/xyzfile.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/pdbx.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/openmmxml.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/prmtop.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/mol2.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/netcdf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/hoomdxml.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/mdcrd.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/gro.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbstructure.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbfile.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/shift_wrappers.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/scalar_couplings.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/io.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/version.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/contextmanagers.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/rotation.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/singleton.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/validation.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/delay_import.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/unitcell.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/zipped.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/baseunit.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/basedimension.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/mymatrix.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/quantity.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_operators.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_definitions.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/standard_dimensions.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/prefix.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/shape.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/dssp.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/contact.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/rdf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/thermodynamic_properties.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/dihedral.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/angle.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/rg.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/order.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/distance.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/hbond.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/sasa.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/trajectory.py to trajectory.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/topology.py to topology.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/selection.py to selection.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/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-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/element.py to element.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/testing.py to testing.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/docstrings.py to docstrings.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/docscrape.py to docscrape.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/gro.py to gro.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/hdf5.py to hdf5.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/amberrst.py to amberrst.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/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-1.10.0/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-1.10.0/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-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/arc.py to arc.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/mol2.py to mol2.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/prmtop.py to prmtop.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/psf.py to psf.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/gsd.py to gsd.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/netcdf.py to netcdf.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdbx.py to pdbx.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/lh5.py to lh5.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/registry.py to registry.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/mdconvert.py to mdconvert.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/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-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/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-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/io.py to io.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/version.py to version.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/zipped.py to zipped.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/validation.py to validation.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/singleton.py to singleton.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/rotation.py to rotation.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unitcell.py to unitcell.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/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-1.10.0/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-1.10.0/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-1.10.0/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-1.10.0/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-1.10.0/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-1.10.0/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-1.10.0/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-1.10.0/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-1.10.0/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-1.10.0/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-1.10.0/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-1.10.0/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-1.10.0/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-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/dssp.py to dssp.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/contact.py to contact.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/rg.py to rg.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/internal.py to internal.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/sasa.py to sasa.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/shape.py to shape.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/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-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/alignment.py to alignment.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/order.py to order.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/distance.py to distance.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/hbond.py to hbond.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/rdf.py to rdf.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/angle.py to angle.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-1.10.0/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj-1.9.10.dev0.egg-info Skipping SOURCES.txt running install_scripts Installing mdconvert-mdtraj script to /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/bin Installing mdinspect script to /build/reproducible-path/mdtraj-1.10.0/debian/python3-mdtraj/usr/bin debian/rules execute_after_dh_auto_install-indep make[1]: Entering directory '/build/reproducible-path/mdtraj-1.10.0' cp -a /build/reproducible-path/mdtraj-1.10.0/examples /build/reproducible-path/mdtraj-1.10.0/examples.orig mkdir -p /build/reproducible-path/mdtraj-1.10.0/build/html/examples/iterload ln -s /build/reproducible-path/mdtraj-1.10.0/examples/data /build/reproducible-path/mdtraj-1.10.0/build/html/examples/iterload/data sed "s|http://www.rcsb.org/pdb/files|/build/reproducible-path/mdtraj-1.10.0/debian/external|g" -i /build/reproducible-path/mdtraj-1.10.0/examples/*.ipynb PYTHONPATH=/build/reproducible-path/mdtraj-1.10.0/.pybuild/cpython3_3.12_mdtraj/build \ MPLCONFIGDIR=/build/reproducible-path/mdtraj-1.10.0/build/matplotlib \ make -C docs BUILDDIR=/build/reproducible-path/mdtraj-1.10.0/build html make[2]: Entering directory '/build/reproducible-path/mdtraj-1.10.0/docs' sphinx-build -b html -d /build/reproducible-path/mdtraj-1.10.0/build/doctrees . /build/reproducible-path/mdtraj-1.10.0/build/html Running Sphinx v7.4.7 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, ..., examples/solvent-accessible-surface-area.rst, examples/two-pass-clustering.rst, faq.rst, hdf5_format.rst, index.rst, installation.rst, load_functions.rst, mdconvert.rst, new_to_python.rst, whatsnew.rst [autosummary] generating autosummary for: /build/reproducible-path/mdtraj-1.10.0/docs/api/generated/mdtraj.Topology.rst, /build/reproducible-path/mdtraj-1.10.0/docs/api/generated/mdtraj.Trajectory.rst, /build/reproducible-path/mdtraj-1.10.0/docs/api/generated/mdtraj.Trajectory.superpose.rst, /build/reproducible-path/mdtraj-1.10.0/docs/api/generated/mdtraj.acylindricity.rst, /build/reproducible-path/mdtraj-1.10.0/docs/api/generated/mdtraj.asphericity.rst, /build/reproducible-path/mdtraj-1.10.0/docs/api/generated/mdtraj.baker_hubbard.rst, /build/reproducible-path/mdtraj-1.10.0/docs/api/generated/mdtraj.chemical_shifts_ppm.rst, /build/reproducible-path/mdtraj-1.10.0/docs/api/generated/mdtraj.chemical_shifts_shiftx2.rst, /build/reproducible-path/mdtraj-1.10.0/docs/api/generated/mdtraj.chemical_shifts_spartaplus.rst, /build/reproducible-path/mdtraj-1.10.0/docs/api/generated/mdtraj.compute_J3_HN_C.rst, ..., /build/reproducible-path/mdtraj-1.10.0/docs/api/generated/mdtraj.utils.check_random_state.rst, /build/reproducible-path/mdtraj-1.10.0/docs/api/generated/mdtraj.utils.ensure_type.rst, /build/reproducible-path/mdtraj-1.10.0/docs/api/generated/mdtraj.utils.ilen.rst, /build/reproducible-path/mdtraj-1.10.0/docs/api/generated/mdtraj.utils.import_.rst, /build/reproducible-path/mdtraj-1.10.0/docs/api/generated/mdtraj.utils.in_units_of.rst, /build/reproducible-path/mdtraj-1.10.0/docs/api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors.rst, /build/reproducible-path/mdtraj-1.10.0/docs/api/generated/mdtraj.utils.rotation_matrix_from_quaternion.rst, /build/reproducible-path/mdtraj-1.10.0/docs/api/generated/mdtraj.utils.timing.rst, /build/reproducible-path/mdtraj-1.10.0/docs/api/generated/mdtraj.utils.uniform_quaternion.rst, /build/reproducible-path/mdtraj-1.10.0/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 29 source files that are out of date updating environment: [new config] 125 added, 0 changed, 0 removed reading sources... [ 1%] analysis reading sources... [ 2%] 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-1.10.0/.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... [ 5%] api/generated/mdtraj.asphericity reading sources... [ 6%] api/generated/mdtraj.baker_hubbard reading sources... [ 6%] api/generated/mdtraj.chemical_shifts_ppm reading sources... [ 7%] api/generated/mdtraj.chemical_shifts_shiftx2 reading sources... [ 8%] api/generated/mdtraj.chemical_shifts_spartaplus reading sources... [ 9%] api/generated/mdtraj.compute_J3_HN_C reading sources... [ 10%] api/generated/mdtraj.compute_J3_HN_CB reading sources... [ 10%] api/generated/mdtraj.compute_J3_HN_HA reading sources... [ 11%] api/generated/mdtraj.compute_angles reading sources... [ 12%] api/generated/mdtraj.compute_center_of_mass reading sources... [ 13%] api/generated/mdtraj.compute_chi1 reading sources... [ 14%] api/generated/mdtraj.compute_chi2 reading sources... [ 14%] api/generated/mdtraj.compute_chi3 reading sources... [ 15%] api/generated/mdtraj.compute_chi4 reading sources... [ 16%] api/generated/mdtraj.compute_contacts reading sources... [ 17%] api/generated/mdtraj.compute_dihedrals reading sources... [ 18%] api/generated/mdtraj.compute_directors reading sources... [ 18%] api/generated/mdtraj.compute_displacements reading sources... [ 19%] api/generated/mdtraj.compute_distances reading sources... [ 20%] api/generated/mdtraj.compute_drid reading sources... [ 21%] api/generated/mdtraj.compute_dssp reading sources... [ 22%] api/generated/mdtraj.compute_gyration_tensor reading sources... [ 22%] api/generated/mdtraj.compute_inertia_tensor reading sources... [ 23%] api/generated/mdtraj.compute_neighbors reading sources... [ 24%] api/generated/mdtraj.compute_nematic_order reading sources... [ 25%] api/generated/mdtraj.compute_omega reading sources... [ 26%] api/generated/mdtraj.compute_phi reading sources... [ 26%] api/generated/mdtraj.compute_psi reading sources... [ 27%] api/generated/mdtraj.compute_rdf reading sources... [ 28%] api/generated/mdtraj.compute_rg reading sources... [ 29%] api/generated/mdtraj.density reading sources... [ 30%] api/generated/mdtraj.dipole_moments reading sources... [ 30%] api/generated/mdtraj.formats.AmberNetCDFRestartFile reading sources... [ 31%] api/generated/mdtraj.formats.AmberRestartFile reading sources... [ 32%] api/generated/mdtraj.formats.ArcTrajectoryFile reading sources... [ 33%] api/generated/mdtraj.formats.DCDTrajectoryFile reading sources... [ 34%] api/generated/mdtraj.formats.DTRTrajectoryFile reading sources... [ 34%] api/generated/mdtraj.formats.GroTrajectoryFile reading sources... [ 35%] api/generated/mdtraj.formats.HDF5TrajectoryFile reading sources... [ 36%] api/generated/mdtraj.formats.LAMMPSTrajectoryFile reading sources... [ 37%] api/generated/mdtraj.formats.LH5TrajectoryFile reading sources... [ 38%] api/generated/mdtraj.formats.MDCRDTrajectoryFile reading sources... [ 38%] api/generated/mdtraj.formats.NetCDFTrajectoryFile reading sources... [ 39%] api/generated/mdtraj.formats.PDBTrajectoryFile reading sources... [ 40%] api/generated/mdtraj.formats.TRRTrajectoryFile reading sources... [ 41%] api/generated/mdtraj.formats.XTCTrajectoryFile reading sources... [ 42%] api/generated/mdtraj.formats.XYZTrajectoryFile reading sources... [ 42%] api/generated/mdtraj.geometry.squareform reading sources... [ 43%] api/generated/mdtraj.isothermal_compressability_kappa_T reading sources... [ 44%] api/generated/mdtraj.iterload reading sources... [ 45%] api/generated/mdtraj.join reading sources... [ 46%] api/generated/mdtraj.kabsch_sander reading sources... [ 46%] api/generated/mdtraj.load reading sources... [ 47%] api/generated/mdtraj.load_arc reading sources... [ 48%] api/generated/mdtraj.load_dcd reading sources... [ 49%] api/generated/mdtraj.load_dtr reading sources... [ 50%] api/generated/mdtraj.load_frame reading sources... [ 50%] api/generated/mdtraj.load_hdf5 reading sources... [ 51%] api/generated/mdtraj.load_hoomdxml reading sources... [ 52%] api/generated/mdtraj.load_lammpstrj reading sources... [ 53%] api/generated/mdtraj.load_lh5 reading sources... [ 54%] api/generated/mdtraj.load_netcdf reading sources... [ 54%] api/generated/mdtraj.load_pdb reading sources... [ 55%] api/generated/mdtraj.load_prmtop reading sources... [ 56%] api/generated/mdtraj.load_trr reading sources... [ 57%] api/generated/mdtraj.load_xml reading sources... [ 58%] api/generated/mdtraj.load_xtc reading sources... [ 58%] api/generated/mdtraj.load_xyz reading sources... [ 59%] api/generated/mdtraj.lprmsd reading sources... [ 60%] api/generated/mdtraj.open reading sources... [ 61%] api/generated/mdtraj.principal_moments reading sources... [ 62%] api/generated/mdtraj.reindex_dataframe_by_atoms reading sources... [ 62%] api/generated/mdtraj.relative_shape_antisotropy reading sources... [ 63%] api/generated/mdtraj.reporters.DCDReporter reading sources... [ 64%] api/generated/mdtraj.reporters.HDF5Reporter reading sources... [ 65%] api/generated/mdtraj.reporters.NetCDFReporter reading sources... [ 66%] api/generated/mdtraj.rmsd reading sources... [ 66%] api/generated/mdtraj.rmsf reading sources... [ 67%] api/generated/mdtraj.shrake_rupley reading sources... [ 68%] api/generated/mdtraj.static_dielectric reading sources... [ 69%] api/generated/mdtraj.thermal_expansion_alpha_P reading sources... [ 70%] api/generated/mdtraj.utils.box_vectors_to_lengths_and_angles reading sources... [ 70%] api/generated/mdtraj.utils.check_random_state reading sources... [ 71%] api/generated/mdtraj.utils.ensure_type reading sources... [ 72%] api/generated/mdtraj.utils.ilen reading sources... [ 73%] api/generated/mdtraj.utils.import_ reading sources... [ 74%] api/generated/mdtraj.utils.in_units_of reading sources... [ 74%] api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors reading sources... [ 75%] api/generated/mdtraj.utils.rotation_matrix_from_quaternion reading sources... [ 76%] api/generated/mdtraj.utils.timing reading sources... [ 77%] api/generated/mdtraj.utils.uniform_quaternion reading sources... [ 78%] api/generated/mdtraj.wernet_nilsson reading sources... [ 78%] api/reporters reading sources... [ 79%] api/trajectory_files reading sources... [ 80%] api/utils reading sources... [ 81%] atom_selection reading sources... [ 82%] building_docs reading sources... [ 82%] examples/atom-selection reading sources... [ 83%] examples/centroids reading sources... [ 84%] examples/clustering reading sources... [ 85%] examples/hbonds reading sources... [ 86%] examples/index reading sources... [ 86%] examples/introduction reading sources... [ 87%] examples/iterload reading sources... [ 88%] examples/native-contact reading sources... [ 89%] examples/nmr reading sources... [ 90%] examples/openmm reading sources... [ 90%] examples/pca reading sources... [ 91%] examples/ramachandran-plot reading sources... [ 92%] examples/rmsd-benchmark reading sources... [ 93%] examples/solvent-accessible-surface-area reading sources... [ 94%] examples/two-pass-clustering reading sources... [ 94%] faq reading sources... [ 95%] hdf5_format reading sources... [ 96%] index reading sources... [ 97%] installation reading sources... [ 98%] load_functions reading sources... [ 98%] mdconvert reading sources... [ 99%] new_to_python reading sources... [100%] whatsnew /build/reproducible-path/mdtraj-1.10.0/.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-1.10.0/.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-1.10.0/.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-1.10.0/.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-1.10.0/.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-1.10.0/.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-1.10.0/.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-1.10.0/.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-1.10.0/.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. docstring of mdtraj._rmsd.rmsf:46: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/mdtraj-1.10.0/.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-1.10.0/docs/examples/atom-selection.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/atom-selection.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.0/docs/examples/centroids.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/centroids.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.0/docs/examples/clustering.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/clustering.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.0/docs/examples/hbonds.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/hbonds.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.0/docs/examples/iterload.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/iterload.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.0/docs/examples/native-contact.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/native-contact.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.0/docs/examples/nmr.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/nmr.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.0/docs/examples/openmm.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/simulation-with-openmm.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.0/docs/examples/pca.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/principal-components.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.0/docs/examples/ramachandran-plot.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/ramachandran-plot.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.0/docs/examples/rmsd-benchmark.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/rmsd-benchmark.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.0/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-1.10.0/docs/examples/two-pass-clustering.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/two-pass-clustering.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.10.0/docs/installation.rst:1: WARNING: malformed hyperlink target. /build/reproducible-path/mdtraj-1.10.0/docs/mdconvert.rst:2: WARNING: Title underline too short. ``mdconvert`` (``mdconvert-mdtraj``) ============= /build/reproducible-path/mdtraj-1.10.0/docs/whatsnew.rst:23: WARNING: Title underline too short. v1.9.9 (July 22, 2023) --------------------- /build/reproducible-path/mdtraj-1.10.0/docs/whatsnew.rst:23: WARNING: Title underline too short. v1.9.9 (July 22, 2023) --------------------- /build/reproducible-path/mdtraj-1.10.0/docs/whatsnew.rst:78: WARNING: Title underline too short. v1.9.7 (November 12, 2021) ----------------------- /build/reproducible-path/mdtraj-1.10.0/docs/whatsnew.rst:78: WARNING: Title underline too short. v1.9.7 (November 12, 2021) ----------------------- looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/mdtraj-1.10.0/docs/building_docs.rst: WARNING: document isn't included in any toctree /build/reproducible-path/mdtraj-1.10.0/docs/faq.rst: WARNING: document isn't included in any toctree done preparing documents... done copying assets... copying static files... done copying extra files... done copying assets: done writing output... [ 1%] analysis writing output... [ 2%] api/generated/mdtraj.Topology writing output... [ 2%] api/generated/mdtraj.Trajectory writing output... [ 3%] api/generated/mdtraj.Trajectory.superpose writing output... [ 4%] api/generated/mdtraj.acylindricity writing output... [ 5%] api/generated/mdtraj.asphericity writing output... [ 6%] api/generated/mdtraj.baker_hubbard writing output... [ 6%] api/generated/mdtraj.chemical_shifts_ppm writing output... [ 7%] api/generated/mdtraj.chemical_shifts_shiftx2 writing output... [ 8%] api/generated/mdtraj.chemical_shifts_spartaplus writing output... [ 9%] api/generated/mdtraj.compute_J3_HN_C writing output... [ 10%] api/generated/mdtraj.compute_J3_HN_CB writing output... [ 10%] api/generated/mdtraj.compute_J3_HN_HA writing output... [ 11%] api/generated/mdtraj.compute_angles writing output... [ 12%] api/generated/mdtraj.compute_center_of_mass writing output... [ 13%] api/generated/mdtraj.compute_chi1 writing output... [ 14%] api/generated/mdtraj.compute_chi2 writing output... [ 14%] api/generated/mdtraj.compute_chi3 writing output... [ 15%] api/generated/mdtraj.compute_chi4 writing output... [ 16%] api/generated/mdtraj.compute_contacts writing output... [ 17%] api/generated/mdtraj.compute_dihedrals writing output... [ 18%] api/generated/mdtraj.compute_directors writing output... [ 18%] api/generated/mdtraj.compute_displacements writing output... [ 19%] api/generated/mdtraj.compute_distances writing output... [ 20%] api/generated/mdtraj.compute_drid writing output... [ 21%] api/generated/mdtraj.compute_dssp writing output... [ 22%] api/generated/mdtraj.compute_gyration_tensor writing output... [ 22%] api/generated/mdtraj.compute_inertia_tensor writing output... [ 23%] api/generated/mdtraj.compute_neighbors writing output... [ 24%] api/generated/mdtraj.compute_nematic_order writing output... [ 25%] api/generated/mdtraj.compute_omega writing output... [ 26%] api/generated/mdtraj.compute_phi writing output... [ 26%] api/generated/mdtraj.compute_psi writing output... [ 27%] api/generated/mdtraj.compute_rdf writing output... [ 28%] api/generated/mdtraj.compute_rg writing output... [ 29%] api/generated/mdtraj.density writing output... [ 30%] api/generated/mdtraj.dipole_moments writing output... [ 30%] api/generated/mdtraj.formats.AmberNetCDFRestartFile writing output... [ 31%] api/generated/mdtraj.formats.AmberRestartFile writing output... [ 32%] api/generated/mdtraj.formats.ArcTrajectoryFile writing output... [ 33%] api/generated/mdtraj.formats.DCDTrajectoryFile writing output... [ 34%] api/generated/mdtraj.formats.DTRTrajectoryFile writing output... [ 34%] api/generated/mdtraj.formats.GroTrajectoryFile writing output... [ 35%] api/generated/mdtraj.formats.HDF5TrajectoryFile writing output... [ 36%] api/generated/mdtraj.formats.LAMMPSTrajectoryFile writing output... [ 37%] api/generated/mdtraj.formats.LH5TrajectoryFile writing output... [ 38%] api/generated/mdtraj.formats.MDCRDTrajectoryFile writing output... [ 38%] api/generated/mdtraj.formats.NetCDFTrajectoryFile writing output... [ 39%] api/generated/mdtraj.formats.PDBTrajectoryFile writing output... [ 40%] api/generated/mdtraj.formats.TRRTrajectoryFile writing output... [ 41%] api/generated/mdtraj.formats.XTCTrajectoryFile writing output... [ 42%] api/generated/mdtraj.formats.XYZTrajectoryFile writing output... [ 42%] api/generated/mdtraj.geometry.squareform writing output... [ 43%] api/generated/mdtraj.isothermal_compressability_kappa_T writing output... [ 44%] api/generated/mdtraj.iterload writing output... [ 45%] api/generated/mdtraj.join writing output... [ 46%] api/generated/mdtraj.kabsch_sander writing output... [ 46%] api/generated/mdtraj.load writing output... [ 47%] api/generated/mdtraj.load_arc writing output... [ 48%] api/generated/mdtraj.load_dcd writing output... [ 49%] api/generated/mdtraj.load_dtr writing output... [ 50%] api/generated/mdtraj.load_frame writing output... [ 50%] api/generated/mdtraj.load_hdf5 writing output... [ 51%] api/generated/mdtraj.load_hoomdxml writing output... [ 52%] api/generated/mdtraj.load_lammpstrj writing output... [ 53%] api/generated/mdtraj.load_lh5 writing output... [ 54%] api/generated/mdtraj.load_netcdf writing output... [ 54%] api/generated/mdtraj.load_pdb writing output... [ 55%] api/generated/mdtraj.load_prmtop writing output... [ 56%] api/generated/mdtraj.load_trr writing output... [ 57%] api/generated/mdtraj.load_xml writing output... [ 58%] api/generated/mdtraj.load_xtc writing output... [ 58%] api/generated/mdtraj.load_xyz writing output... [ 59%] api/generated/mdtraj.lprmsd writing output... [ 60%] api/generated/mdtraj.open writing output... [ 61%] api/generated/mdtraj.principal_moments writing output... [ 62%] api/generated/mdtraj.reindex_dataframe_by_atoms writing output... [ 62%] api/generated/mdtraj.relative_shape_antisotropy writing output... [ 63%] api/generated/mdtraj.reporters.DCDReporter writing output... [ 64%] api/generated/mdtraj.reporters.HDF5Reporter writing output... [ 65%] api/generated/mdtraj.reporters.NetCDFReporter writing output... [ 66%] api/generated/mdtraj.rmsd writing output... [ 66%] api/generated/mdtraj.rmsf writing output... [ 67%] api/generated/mdtraj.shrake_rupley writing output... [ 68%] api/generated/mdtraj.static_dielectric writing output... [ 69%] api/generated/mdtraj.thermal_expansion_alpha_P writing output... [ 70%] api/generated/mdtraj.utils.box_vectors_to_lengths_and_angles writing output... [ 70%] api/generated/mdtraj.utils.check_random_state writing output... [ 71%] api/generated/mdtraj.utils.ensure_type writing output... [ 72%] api/generated/mdtraj.utils.ilen writing output... [ 73%] api/generated/mdtraj.utils.import_ writing output... [ 74%] api/generated/mdtraj.utils.in_units_of writing output... [ 74%] api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors writing output... [ 75%] api/generated/mdtraj.utils.rotation_matrix_from_quaternion writing output... [ 76%] api/generated/mdtraj.utils.timing writing output... [ 77%] api/generated/mdtraj.utils.uniform_quaternion writing output... [ 78%] api/generated/mdtraj.wernet_nilsson writing output... [ 78%] api/reporters writing output... [ 79%] api/trajectory_files writing output... [ 80%] api/utils writing output... [ 81%] atom_selection writing output... [ 82%] building_docs writing output... [ 82%] examples/atom-selection writing output... [ 83%] examples/centroids writing output... [ 84%] examples/clustering writing output... [ 85%] examples/hbonds writing output... [ 86%] examples/index writing output... [ 86%] examples/introduction writing output... [ 87%] examples/iterload writing output... [ 88%] examples/native-contact writing output... [ 89%] examples/nmr writing output... [ 90%] examples/openmm writing output... [ 90%] examples/pca writing output... [ 91%] examples/ramachandran-plot writing output... [ 92%] examples/rmsd-benchmark writing output... [ 93%] examples/solvent-accessible-surface-area writing output... [ 94%] examples/two-pass-clustering writing output... [ 94%] faq writing output... [ 95%] hdf5_format writing output... [ 96%] index writing output... [ 97%] installation writing output... [ 98%] load_functions writing output... [ 98%] mdconvert writing output... [ 99%] new_to_python writing output... [100%] whatsnew generating indices... genindex done writing additional pages... search done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 33 warnings. The HTML pages are in ../build/html. Build finished. The HTML pages are in /build/reproducible-path/mdtraj-1.10.0/build/html. make[2]: Leaving directory '/build/reproducible-path/mdtraj-1.10.0/docs' for img in `find /build/reproducible-path/mdtraj-1.10.0/build/html/examples -name *.png`; do \ mv $img /build/reproducible-path/mdtraj-1.10.0/build/html/examples; \ done sed "s|/build/reproducible-path/mdtraj-1.10.0/build/html/examples/|./|g; s|.ipynb|.ipynb.gz|g" -i /build/reproducible-path/mdtraj-1.10.0/build/html/examples/*.html sed "s|/build/reproducible-path/mdtraj-1.10.0/debian/external|http://www.rcsb.org/pdb/files|g" -i /build/reproducible-path/mdtraj-1.10.0/build/html/examples/*.html rm /build/reproducible-path/mdtraj-1.10.0/build/html/examples/iterload/data rm -rf /build/reproducible-path/mdtraj-1.10.0/examples mv /build/reproducible-path/mdtraj-1.10.0/examples.orig /build/reproducible-path/mdtraj-1.10.0/examples make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.10.0' dh_install -O--buildsystem=pybuild install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples/data cp --reflink=auto -a ./debian/external/2EQQ.pdb ./debian/external/2MI7.pdb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples/data/ install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doi-10.1016_j.bpj.2015.08.015-blue.svg cp --reflink=auto -a ./debian/external/doi-10.1016_j.bpj.2015.08.015-blue.svg debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doi-10.1016_j.bpj.2015.08.015-blue.svg/ dh_installdocs -O--buildsystem=pybuild dh_installdocs: warning: Cannot auto-detect main package for python-mdtraj-doc. If the default is wrong, please use --doc-main-package install -m0755 -d debian/python3-mdtraj/usr/share/doc/python3-mdtraj install -p -m0644 debian/copyright debian/python3-mdtraj/usr/share/doc/python3-mdtraj/copyright install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc cd './build/html/..' && find 'html' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/mdtraj-1.10.0/debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc cp --reflink=auto -a ./README.md debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc chmod -R u\+rw,go=rX debian/python-mdtraj-doc/usr/share/doc install -p -m0644 debian/copyright debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/copyright install -m0755 -d debian/python-mdtraj-doc/usr/share/doc-base/ install -p -m0644 debian/python-mdtraj-doc.doc-base debian/python-mdtraj-doc/usr/share/doc-base/python-mdtraj-doc.mdtraj debian/rules override_dh_sphinxdoc-indep make[1]: Entering directory '/build/reproducible-path/mdtraj-1.10.0' dh_sphinxdoc -i 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-Italic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.ttf ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf ln -sf ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Bold.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.woff2 ln -sf 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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 ../../../../javascript/sphinxdoc/1.0/doctools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/versions.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 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-1.10.0' dh_sphinxdoc -O--buildsystem=pybuild -Npython-mdtraj-doc dh_sphinxdoc: warning: Sphinx documentation not found dh_installchangelogs -O--buildsystem=pybuild install -m0755 -d debian/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: 6.20240824 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:335: package python3-mdtraj details = {'requires.txt': {'debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.9.10.dev0.egg-info/requires.txt'}, 'egg-info': {'debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.9.10.dev0.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:173: trying to find dependency for astunparse (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for numpy<2.0.0a0,>=1.23 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for packaging (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for pyparsing (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for scipy (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 depends:253: D={'python3 (<< 3.13)', 'python3-packaging', 'python3:any', 'python3-numpy', 'python3-astunparse', 'python3-pyparsing', 'python3-scipy', 'python3 (>= 3.12~)'}; 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-1.10.0' 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-1.10.0' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css ln -s ../../../../../sphinx_rtd_theme/static/css/theme.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css ln -s ../../../../../sphinx_rtd_theme/static/css/badge_only.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/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/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-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/fontawesome-webfont.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.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-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/Lato-BoldItalic.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.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/RobotoSlab-Bold.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Bold.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-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/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/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 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 dh_strip_nondeterminism -O--buildsystem=pybuild Using 1720953453 as canonical time 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/_static/file.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 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 gzip -9nf 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/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 cd '/build/reproducible-path/mdtraj-1.10.0' cd '/build/reproducible-path/mdtraj-1.10.0' dh_fixperms -O--buildsystem=pybuild find debian/python3-mdtraj ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python-mdtraj-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python3-mdtraj/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-mdtraj/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/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/i386-linux-gnu dwz -mdebian/python3-mdtraj/usr/lib/debug/.dwz/i386-linux-gnu/python3-mdtraj.debug -M/usr/lib/debug/.dwz/i386-linux-gnu/python3-mdtraj.debug -- debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so objcopy --compress-debug-sections debian/python3-mdtraj/usr/lib/debug/.dwz/i386-linux-gnu/python3-mdtraj.debug chmod 0644 -- debian/python3-mdtraj/usr/lib/debug/.dwz/i386-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/74 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/74/b9331354b83eb1662f9267ffeaef0af25980a6.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/74/b9331354b83eb1662f9267ffeaef0af25980a6.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/74/b9331354b83eb1662f9267ffeaef0af25980a6.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/3c objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/3c/8487a8f0c9b14eda7e9fb3837e9b7c66797137.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/3c/8487a8f0c9b14eda7e9fb3837e9b7c66797137.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/3c/8487a8f0c9b14eda7e9fb3837e9b7c66797137.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/95 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/95/b297a16f16f57a28eb6fc7afc9a6f9de8e556d.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/95/b297a16f16f57a28eb6fc7afc9a6f9de8e556d.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/95/b297a16f16f57a28eb6fc7afc9a6f9de8e556d.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/5c objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/5c/2a0445448476b11c7ceff1bcc279d3807e92e8.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/5c/2a0445448476b11c7ceff1bcc279d3807e92e8.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/5c/2a0445448476b11c7ceff1bcc279d3807e92e8.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/9a objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/9a/e5454617ce5d3dd7fd308571ac7643b8c9bf86.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/9a/e5454617ce5d3dd7fd308571ac7643b8c9bf86.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/9a/e5454617ce5d3dd7fd308571ac7643b8c9bf86.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/48 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/48/48857aa0530d38012b6e84486fe5769c2713e0.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/48/48857aa0530d38012b6e84486fe5769c2713e0.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/48/48857aa0530d38012b6e84486fe5769c2713e0.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/fc objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/fc/07c99d6581934aee1a049ff946c2e52720779a.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/fc/07c99d6581934aee1a049ff946c2e52720779a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/fc/07c99d6581934aee1a049ff946c2e52720779a.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/ab objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/ab/d6e787f38806fe72221ae0b5016d0033b8ae84.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/ab/d6e787f38806fe72221ae0b5016d0033b8ae84.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/ab/d6e787f38806fe72221ae0b5016d0033b8ae84.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/1c objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/1c/ca994e6c4b8f92e3bba98c6be419ded90ddede.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/1c/ca994e6c4b8f92e3bba98c6be419ded90ddede.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/1c/ca994e6c4b8f92e3bba98c6be419ded90ddede.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/65 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/65/855f19b0859d18d26cb285b1ac976192515b66.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/65/855f19b0859d18d26cb285b1ac976192515b66.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/65/855f19b0859d18d26cb285b1ac976192515b66.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-i386-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/i386-linux-gnu debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/python3-mdtraj/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/python3-mdtraj/usr/lib/debug install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/share/doc ln -s python3-mdtraj debian/.debhelper/python3-mdtraj/dbgsym-root/usr/share/doc/python3-mdtraj-dbgsym install -m0755 -d debian/.debhelper/python3-mdtraj dh_makeshlibs -a -O--buildsystem=pybuild rm -f debian/python3-mdtraj/DEBIAN/shlibs dh_shlibdeps -a -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/DEBIAN dpkg-shlibdeps -Tdebian/python3-mdtraj.substvars debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-i386-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=1cca994e6c4b8f92e3bba98c6be419ded90ddede 3c8487a8f0c9b14eda7e9fb3837e9b7c66797137 4848857aa0530d38012b6e84486fe5769c2713e0 5c2a0445448476b11c7ceff1bcc279d3807e92e8 65855f19b0859d18d26cb285b1ac976192515b66 74b9331354b83eb1662f9267ffeaef0af25980a6 95b297a16f16f57a28eb6fc7afc9a6f9de8e556d 9ae5454617ce5d3dd7fd308571ac7643b8c9bf86 abd6e787f38806fe72221ae0b5016d0033b8ae84 fc07c99d6581934aee1a049ff946c2e52720779a" -DSection=debug -UMulti-Arch -UReplaces -UBreaks 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/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN/control dpkg-gencontrol -ppython3-mdtraj -ldebian/changelog -Tdebian/python3-mdtraj.substvars -cdebian/control -Pdebian/python3-mdtraj 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' in '../python3-mdtraj_1.10.0-3_i386.deb'. dpkg-deb: building package 'python3-mdtraj-dbgsym' in '../python3-mdtraj-dbgsym_1.10.0-3_i386.deb'. dpkg-deb: building package 'python-mdtraj-doc' in '../python-mdtraj-doc_1.10.0-3_all.deb'. dpkg-genbuildinfo --build=binary -O../mdtraj_1.10.0-3_i386.buildinfo dpkg-genchanges --build=binary -O../mdtraj_1.10.0-3_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from mdtraj-1.10.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/30204 and its subdirectories I: Current time: Mon Oct 13 23:55:30 -12 2025 I: pbuilder-time-stamp: 1760442930 Wed Sep 11 05:32:33 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom07-i386.debian.net. Wed Sep 11 05:32:33 UTC 2024 I: Preparing to do remote build '2' on infom07-i386.debian.net. Wed Sep 11 05:38:48 UTC 2024 I: Deleting $TMPDIR on infom07-i386.debian.net. Wed Sep 11 05:38:49 UTC 2024 I: mdtraj_1.10.0-3_i386.changes: Format: 1.8 Date: Sun, 14 Jul 2024 12:37:33 +0200 Source: mdtraj Binary: python-mdtraj-doc python3-mdtraj python3-mdtraj-dbgsym Architecture: all i386 Version: 1.10.0-3 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Drew Parsons Description: python-mdtraj-doc - Read, write and analyze MD trajectories in Python (documentation) python3-mdtraj - Read, write and analyze MD trajectories in Python Closes: 1076166 Changes: mdtraj (1.10.0-3) unstable; urgency=medium . * only remove python3-specific mdtraj/core/lib (from libtheobald.a) if the excess dir exists (it's only left over if there is more than one supported python version). Closes: #1076166. Checksums-Sha1: 5f497c6443d1e063c5d87d008b6616479a7c729e 13802 mdtraj_1.10.0-3_i386.buildinfo a8a0026a50a83564e925aba4ac2abdab8ce6e761 699036 python-mdtraj-doc_1.10.0-3_all.deb 8c210346283412367790af0719e0ac67483d91e7 5104452 python3-mdtraj-dbgsym_1.10.0-3_i386.deb 1a643e4e59ea8b01e6b639ea88f130184f43504d 926696 python3-mdtraj_1.10.0-3_i386.deb Checksums-Sha256: da2730d8e1a489befb034e8b001d8bee684993b29855c95654b9c2374b7799da 13802 mdtraj_1.10.0-3_i386.buildinfo e7dcc5c1c4485e0b0c02dfa1532571684e586390a8e7442895feb9c2090b5924 699036 python-mdtraj-doc_1.10.0-3_all.deb 4aaa9544e5ba522664464ca57d491ea70bd133550e1a26d4dfdf43c8c870c4a5 5104452 python3-mdtraj-dbgsym_1.10.0-3_i386.deb 3529f4271ead9168bf18852f813285429c66c7b346468d4f7e2e9d022bcf2c66 926696 python3-mdtraj_1.10.0-3_i386.deb Files: 4b818a2c4909ec2f17adf1e3e476dc18 13802 python optional mdtraj_1.10.0-3_i386.buildinfo 10ecac9d8f8a5876ba737c039775b924 699036 doc optional python-mdtraj-doc_1.10.0-3_all.deb f0509e92392d7fc02102bae5d5bb7143 5104452 debug optional python3-mdtraj-dbgsym_1.10.0-3_i386.deb 078827f7d98fc26a96c4f55c882afee2 926696 python optional python3-mdtraj_1.10.0-3_i386.deb Wed Sep 11 05:38:50 UTC 2024 I: diffoscope 277 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_16-38928.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.mvAe80M4/mdtraj_1.10.0-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.mvAe80M4/mdtraj_1.10.0-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.mvAe80M4/mdtraj_1.10.0-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.mvAe80M4/b1/mdtraj_1.10.0-3_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.mvAe80M4/b2/mdtraj_1.10.0-3_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.569s) 0.569s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.113s) 0.113s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 982ms CPU time consumed: 981ms Wed Sep 11 05:38:52 UTC 2024 I: diffoscope 277 found no differences in the changes files, and a .buildinfo file also exists. Wed Sep 11 05:38:52 UTC 2024 I: mdtraj from unstable built successfully and reproducibly on i386. Wed Sep 11 05:38:53 UTC 2024 I: Submitting .buildinfo files to external archives: Wed Sep 11 05:38:53 UTC 2024 I: Submitting 16K b1/mdtraj_1.10.0-3_i386.buildinfo.asc Wed Sep 11 05:38:54 UTC 2024 I: Submitting 16K b2/mdtraj_1.10.0-3_i386.buildinfo.asc Wed Sep 11 05:38:55 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Sep 11 05:38:55 UTC 2024 I: Done submitting .buildinfo files. Wed Sep 11 05:38:55 UTC 2024 I: Removing signed mdtraj_1.10.0-3_i386.buildinfo.asc files: removed './b1/mdtraj_1.10.0-3_i386.buildinfo.asc' removed './b2/mdtraj_1.10.0-3_i386.buildinfo.asc'