Sun Apr 14 13:15:26 UTC 2024 I: starting to build mdtraj/trixie/i386 on jenkins on '2024-04-14 13:15' Sun Apr 14 13:15:26 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_4/15961/console.log Sun Apr 14 13:15:26 UTC 2024 I: Downloading source for trixie/mdtraj=1.9.9-1 --2024-04-14 13:15:27-- http://deb.debian.org/debian/pool/main/m/mdtraj/mdtraj_1.9.9-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2619 (2.6K) [text/prs.lines.tag] Saving to: ‘mdtraj_1.9.9-1.dsc’ 0K .. 100% 388M=0s 2024-04-14 13:15:27 (388 MB/s) - ‘mdtraj_1.9.9-1.dsc’ saved [2619/2619] Sun Apr 14 13:15:27 UTC 2024 I: mdtraj_1.9.9-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: mdtraj Binary: python3-mdtraj, python-mdtraj-doc Architecture: any-amd64 arm64 i386 all Version: 1.9.9-1 Maintainer: Debichem Team Uploaders: Drew Parsons Homepage: https://mdtraj.org/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/debichem-team/mdtraj Vcs-Git: https://salsa.debian.org/debichem-team/mdtraj.git Testsuite: autopkgtest Testsuite-Triggers: python3-ipykernel, python3-jupyter-client, python3-matplotlib, python3-nbformat, python3-pandas, python3-pytest, python3-six, python3-sklearn Build-Depends: debhelper-compat (= 13), dh-sequence-python3, cython3-legacy, python3-setuptools, python3-all-dev, python3-numpy, python3-scipy, python3-astunparse, 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-six, python3-sklearn Package-List: python-mdtraj-doc deb doc optional arch=all python3-mdtraj deb python optional arch=any-amd64,arm64,i386 Checksums-Sha1: c33b12e29fcc75773206d6a89895fc394bb014e1 21668968 mdtraj_1.9.9.orig.tar.gz 556d1cae25c6e3a4d2af0fcfccd7b385869567d5 299468 mdtraj_1.9.9-1.debian.tar.xz Checksums-Sha256: c920e2014c8ca0f9cfa123852d658574c3b88f2480dc3720c3ba115c3bfb3cbb 21668968 mdtraj_1.9.9.orig.tar.gz 66268521dcf0b35365478179399bdc71b35c35c6552ffa2b53e46928c41efbd8 299468 mdtraj_1.9.9-1.debian.tar.xz Files: b4bc22d356e5fc05ba0b5e3dbff158aa 21668968 mdtraj_1.9.9.orig.tar.gz b02981d5e10d6c2ffd0f9597a848ef30 299468 mdtraj_1.9.9-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmWmZCoRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFKoRAAjzJHaOQ48N9z5RBR1HTmBln5Q/R0OS5V 2KGZ9kQMW/8+YfixYwGyVHjs4y7UR8RzERum6g7OrVywbj/Cxpdnl6zIcn3ybi6R pBDpUypcswLWhNKsQtBHf9bdUI87LjbgaEnpVKj8BtgtZXCyHKI05XrciwXRzlHa ztSaYAw39CJHOdcYfNZM+sgye3hpHg/8Vll6AL5+U7ZfGFngkuHiA7aKtqRQtPde sTGoDs8cSpIM9bahQTjDWFNQb3CSdTr7r6wDVCx9ZmDeVfkBtOYcKfq2O1xqXqjf ZGkpqeW+nQfxiRB2T2GL6qkQ/Yyz8jqW1kWyf1barXEY/rXrGonj1qEYma7mK9e7 uN8U/eeQWEmpJTtqiulk3Bgfv0ZyUsaIqaqowzcNDeWieB9cV/p+qQGWmuQyg4un +ZljYXPHRSxRzJxd8BwOTPyocId3Imv+MgDEQOiILp05Ak+Oz/EdYE2DifG+dqYe Ar1O2TaGSLL10ppnB43KqlsBJ6wpk790h2eMInn6YV7MawM4sZBrnrDbuN1bwdgp +0/+VFvFAKxRYyCymam+3pOeP1pbVZ8vO5F+QbIoNQHZH6WuYuVvyuZFM8ynd6Sr +Jx5px4Dwv+HmQ0iFGnw0w8RZX7WbwH/RLjNhvqj1TJhSde5NiJkrsE0vJ5heTM5 Ujs/0x1nYqA= =BFHC -----END PGP SIGNATURE----- Sun Apr 14 13:15:27 UTC 2024 I: Checking whether the package is not for us Sun Apr 14 13:15:27 UTC 2024 I: Starting 1st build on remote node ionos16-i386.debian.net. Sun Apr 14 13:15:27 UTC 2024 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Sun Apr 14 13:34:10 UTC 2024 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat May 17 07:38:29 -12 2025 I: pbuilder-time-stamp: 1747510709 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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_1.9.9-1.dsc] I: copying [./mdtraj_1.9.9.orig.tar.gz] I: copying [./mdtraj_1.9.9-1.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Jan 16 11:10:34 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.9.9-1.dsc: no acceptable signature found dpkg-source: info: extracting mdtraj in mdtraj-1.9.9 dpkg-source: info: unpacking mdtraj_1.9.9.orig.tar.gz dpkg-source: info: unpacking mdtraj_1.9.9-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying docs_use_local_mathjax.patch dpkg-source: info: applying build_dir_pybuild.patch dpkg-source: info: applying python_hashbang.patch dpkg-source: info: applying test_gsd_skip.patch dpkg-source: info: applying 32bit_skip_image_molecule.patch dpkg-source: info: applying test_relax_tol.patch dpkg-source: info: applying rename-mdconvert-mdtraj.patch dpkg-source: info: applying drop_notebook_in_docs.patch dpkg-source: info: applying test_increase_timeout.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/40816/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=22 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='d69c6c0d1fb44f44a2ce92b467d709c0' 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='40816' 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.EYEMTr0p/pbuilderrc_0dtj --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.EYEMTr0p/b1 --logfile b1/build.log mdtraj_1.9.9-1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos16-i386 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 15 17:46 /bin -> usr/bin I: user script /srv/workspace/pbuilder/40816/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-numpy, python3-scipy, python3-astunparse, 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-six, 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 ... 19874 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-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-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-six; however: Package python3-six 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} libbrotli1{a} libbsd0{a} libcurl3-gnutls{a} libcurl4{a} libdebhelper-perl{a} libdebuginfod-common{a} libdebuginfod1{a} libdeflate0{a} libdw1{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libhdf5-103-1{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} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblzo2-2{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libnorm1{a} libopenjp2-7{a} libpgm-5.3-0{a} libpipeline1{a} libpng16-16{a} libproc2-0{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsnappy1v5{a} libsodium23{a} libsource-highlight-common{a} libsource-highlight4v5{a} libssh2-1{a} libsub-override-perl{a} libsz2{a} libtcl8.6{a} libtiff6{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-babel{a} python3-bleach{a} python3-brotli{a} python3-bs4{a} python3-bytecode{a} python3-certifi{a} python3-cffi-backend{a} python3-chardet{a} python3-charset-normalizer{a} python3-comm{a} python3-contourpy{a} python3-coverage{a} python3-cycler{a} python3-dateutil{a} python3-debugpy{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-distutils{a} python3-docutils{a} python3-editables{a} python3-entrypoints{a} python3-executing{a} python3-fastjsonschema{a} python3-fonttools{a} python3-fs{a} python3-hatch-vcs{a} python3-hatchling{a} python3-html5lib{a} python3-idna{a} python3-imagesize{a} python3-ipykernel{a} python3-ipython{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-lib2to3{a} python3-lxml{a} python3-lz4{a} python3-markupsafe{a} python3-matplotlib{a} python3-matplotlib-inline{a} python3-minimal{a} python3-mpmath{a} python3-msmb-theme{a} python3-nbclient{a} python3-nbconvert{a} python3-nbformat{a} python3-nest-asyncio{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-pydevd{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-typeshed{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-urllib3{a} python3-wcwidth{a} python3-webencodings{a} python3-zmq{a} python3-zombie-imp{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} python3.12{a} python3.12-dev{a} python3.12-minimal{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 libarchive-cpio-perl libc6-dbg libglib2.0-data libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules 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, 276 newly installed, 0 to remove and 0 not upgraded. Need to get 184 MB of archives. After unpacking 843 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 ucf all 3.0043+nmu1 [55.2 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 libdebuginfod-common all 0.190-1 [22.3 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 libpython3.11-minimal i386 3.11.8-1 [817 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.5.0-2+b2 [104 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 python3.11-minimal i386 3.11.8-1 [2087 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.11.6-1 [26.2 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 tzdata all 2024a-1 [255 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-3 [69.1 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 libreadline8 i386 8.2-3+b1 [171 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 libpython3.11-stdlib i386 3.11.8-1 [1821 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 python3.11 i386 3.11.8-1 [597 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.11.6-1 [9224 B] Get: 17 http://deb.debian.org/debian trixie/main i386 python3 i386 3.11.6-1 [26.2 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libpython3.12-minimal i386 3.12.2-1 [807 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 python3.12-minimal i386 3.12.2-1 [2244 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 sgml-base all 1.31 [15.4 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libproc2-0 i386 2:4.0.4-4 [65.4 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 procps i386 2:4.0.4-4 [876 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 openssl i386 3.1.5-1 [1246 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 ca-certificates all 20240203 [158 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3 [1195 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 libtcl8.6 i386 8.6.14+dfsg-1 [1095 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 libpng16-16 i386 1.6.43-1 [285 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 libfreetype6 i386 2.13.2+dfsg-1+b1 [449 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 fontconfig-config i386 2.15.0-1.1 [317 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libfontconfig1 i386 2.15.0-1.1 [401 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 libbsd0 i386 0.12.2-1 [134 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 libx11-6 i386 2:1.8.7-1 [822 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 libxrender1 i386 1:0.9.10-1.1 [34.1 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 libxft2 i386 2.3.6-1+b1 [55.3 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 x11-common all 1:7.7+23 [252 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 libxss1 i386 1:1.2.3-1 [18.1 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 libtk8.6 i386 8.6.14-1 [826 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 tk8.6-blt2.5 i386 2.5.3+dfsg-7 [616 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 blt i386 2.5.3+dfsg-7 [6024 B] Get: 61 http://deb.debian.org/debian trixie/main i386 python3-zombie-imp all 0.0.2-2 [11.7 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 cython3-legacy i386 0.29.37-2 [2930 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 70 http://deb.debian.org/debian trixie/main i386 libelf1 i386 0.190-1+b1 [182 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1 [118 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 python3-lib2to3 all 3.11.5-1 [77.5 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 python3-distutils all 3.11.5-1 [131 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 python3-setuptools all 68.1.2-2 [468 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 dh-python all 6.20240401 [107 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 xml-core all 0.19 [20.1 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 docutils-common all 0.20.1+dfsg-3 [128 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 fonts-lyx all 2.4.0~RC3-1 [189 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 libdw1 i386 0.190-1+b1 [274 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 libglib2.0-0 i386 2.78.4-1 [1520 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 libbabeltrace1 i386 1.5.11-3+b3 [195 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-4+b1 [20.7 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-4+b1 [60.7 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5+b3 [196 kB] Get: 94 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.59.0-1 [82.5 kB] Get: 95 http://deb.debian.org/debian trixie/main i386 libpsl5 i386 0.21.2-1+b1 [59.7 kB] Get: 96 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 97 http://deb.debian.org/debian trixie/main i386 libssh2-1 i386 1.11.0-4 [224 kB] Get: 98 http://deb.debian.org/debian trixie/main i386 libcurl3-gnutls i386 8.5.0-2 [454 kB] Get: 99 http://deb.debian.org/debian trixie/main i386 libdebuginfod1 i386 0.190-1+b1 [29.3 kB] Get: 100 http://deb.debian.org/debian trixie/main i386 libipt2 i386 2.0.6-1 [52.6 kB] Get: 101 http://deb.debian.org/debian trixie/main i386 libpython3.11 i386 3.11.8-1 [2009 kB] Get: 102 http://deb.debian.org/debian trixie/main i386 libsource-highlight-common all 3.1.9-4.2 [77.4 kB] Get: 103 http://deb.debian.org/debian trixie/main i386 libsource-highlight4v5 i386 3.1.9-4.2+b4 [349 kB] Get: 104 http://deb.debian.org/debian trixie/main i386 gdb i386 13.2-1 [4065 kB] Get: 105 http://deb.debian.org/debian trixie/main i386 libaec0 i386 1.1.3-1 [24.5 kB] Get: 106 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-3 [140 kB] Get: 107 http://deb.debian.org/debian trixie/main i386 libsnappy1v5 i386 1.1.10-1+b1 [29.5 kB] Get: 108 http://deb.debian.org/debian trixie/main i386 libblosc1 i386 1.21.5+ds-1+b1 [51.4 kB] Get: 109 http://deb.debian.org/debian trixie/main i386 libcurl4 i386 8.5.0-2 [463 kB] Get: 110 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.20-1 [46.9 kB] Get: 111 http://deb.debian.org/debian trixie/main i386 libexpat1-dev i386 2.5.0-2+b2 [159 kB] Get: 112 http://deb.debian.org/debian trixie/main i386 libfribidi0 i386 1.0.13-3+b1 [71.8 kB] Get: 113 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14-20240201-3 [733 kB] Get: 114 http://deb.debian.org/debian trixie/main i386 libgraphite2-3 i386 1.3.14-2 [77.7 kB] Get: 115 http://deb.debian.org/debian trixie/main i386 libharfbuzz0b i386 8.3.0-2 [2234 kB] Get: 116 http://deb.debian.org/debian trixie/main i386 libsz2 i386 1.1.3-1 [7824 B] Get: 117 http://deb.debian.org/debian trixie/main i386 libhdf5-103-1 i386 1.10.10+repack-3+b1 [1177 kB] Get: 118 http://deb.debian.org/debian trixie/main i386 libimagequant0 i386 2.18.0-1 [35.6 kB] Get: 119 http://deb.debian.org/debian trixie/main i386 libjbig0 i386 2.1-6.1+b1 [31.8 kB] Get: 120 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-2+b2 [169 kB] Get: 121 http://deb.debian.org/debian trixie/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 122 http://deb.debian.org/debian trixie/main i386 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 123 http://deb.debian.org/debian trixie/main i386 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 124 http://deb.debian.org/debian trixie/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 125 http://deb.debian.org/debian trixie/main i386 libjs-sphinxdoc all 7.2.6-6 [150 kB] Get: 126 http://deb.debian.org/debian trixie/main i386 libjson-perl all 4.10000-1 [87.5 kB] Get: 127 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.0-3 [2167 kB] Get: 128 http://deb.debian.org/debian trixie/main i386 liblbfgsb0 i386 3.0+dfsg.4-1+b1 [29.1 kB] Get: 129 http://deb.debian.org/debian trixie/main i386 liblcms2-2 i386 2.14-2+b1 [165 kB] Get: 130 http://deb.debian.org/debian trixie/main i386 liblerc4 i386 4.0.0+ds-4+b1 [180 kB] Get: 131 http://deb.debian.org/debian trixie/main i386 liblzo2-2 i386 2.10-2+b1 [58.0 kB] Get: 132 http://deb.debian.org/debian trixie/main i386 libnorm1 i386 1.5.9+dfsg-3 [237 kB] Get: 133 http://deb.debian.org/debian trixie/main i386 libopenjp2-7 i386 2.5.0-2+b2 [197 kB] Get: 134 http://deb.debian.org/debian trixie/main i386 libpgm-5.3-0 i386 5.3.128~dfsg-2 [168 kB] Get: 135 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg-3+b1 [915 kB] Get: 136 http://deb.debian.org/debian trixie/main i386 libpython3.11-dev i386 3.11.8-1 [4726 kB] Get: 137 http://deb.debian.org/debian trixie/main i386 libpython3-dev i386 3.11.6-1 [9496 B] Get: 138 http://deb.debian.org/debian trixie/main i386 libpython3.12-stdlib i386 3.12.2-1 [1927 kB] Get: 139 http://deb.debian.org/debian trixie/main i386 libpython3.12 i386 3.12.2-1 [2156 kB] Get: 140 http://deb.debian.org/debian trixie/main i386 libpython3.12-dev i386 3.12.2-1 [5108 kB] Get: 141 http://deb.debian.org/debian trixie/main i386 libpython3-all-dev i386 3.11.6-1 [1072 B] Get: 142 http://deb.debian.org/debian trixie/main i386 libqhull-r8.0 i386 2020.2-6+b1 [256 kB] Get: 143 http://deb.debian.org/debian trixie/main i386 libraqm0 i386 0.10.1-1+b1 [14.7 kB] Get: 144 http://deb.debian.org/debian trixie/main i386 libsharpyuv0 i386 1.3.2-0.4 [107 kB] Get: 145 http://deb.debian.org/debian trixie/main i386 libsodium23 i386 1.0.18-1 [186 kB] Get: 146 http://deb.debian.org/debian trixie/main i386 libwebp7 i386 1.3.2-0.4 [314 kB] Get: 147 http://deb.debian.org/debian trixie/main i386 libtiff6 i386 4.5.1+git230720-4 [338 kB] Get: 148 http://deb.debian.org/debian trixie/main i386 libwebpdemux2 i386 1.3.2-0.4 [108 kB] Get: 149 http://deb.debian.org/debian trixie/main i386 libwebpmux3 i386 1.3.2-0.4 [121 kB] Get: 150 http://deb.debian.org/debian trixie/main i386 libxslt1.1 i386 1.1.35-1 [253 kB] Get: 151 http://deb.debian.org/debian trixie/main i386 libzmq5 i386 4.3.5-1+b1 [306 kB] Get: 152 http://deb.debian.org/debian trixie/main i386 python-babel-localedata all 2.10.3-3 [5611 kB] Get: 153 http://deb.debian.org/debian trixie/main i386 python-matplotlib-data all 3.6.3-1 [2744 kB] Get: 154 http://deb.debian.org/debian trixie/main i386 python-tables-data all 3.7.0-10 [47.6 kB] Get: 155 http://deb.debian.org/debian trixie/main i386 python-tinycss2-common all 1.2.1-2 [31.5 kB] Get: 156 http://deb.debian.org/debian trixie/main i386 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 157 http://deb.debian.org/debian trixie/main i386 python3.12 i386 3.12.2-1 [653 kB] Get: 158 http://deb.debian.org/debian trixie/main i386 python3-all i386 3.11.6-1 [1060 B] Get: 159 http://deb.debian.org/debian trixie/main i386 python3.11-dev i386 3.11.8-1 [509 kB] Get: 160 http://deb.debian.org/debian trixie/main i386 python3-dev i386 3.11.6-1 [26.1 kB] Get: 161 http://deb.debian.org/debian trixie/main i386 python3.12-dev i386 3.12.2-1 [507 kB] Get: 162 http://deb.debian.org/debian trixie/main i386 python3-all-dev i386 3.11.6-1 [1080 B] Get: 163 http://deb.debian.org/debian trixie/main i386 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 164 http://deb.debian.org/debian trixie/main i386 python3-six all 1.16.0-6 [16.3 kB] Get: 165 http://deb.debian.org/debian trixie/main i386 python3-asttokens all 2.4.1-1 [20.6 kB] Get: 166 http://deb.debian.org/debian trixie/main i386 python3-astunparse all 1.6.3-2 [13.8 kB] Get: 167 http://deb.debian.org/debian trixie/main i386 python3-attr all 23.2.0-2 [65.5 kB] Get: 168 http://deb.debian.org/debian trixie/main i386 python3-tz all 2024.1-2 [30.9 kB] Get: 169 http://deb.debian.org/debian trixie/main i386 python3-babel all 2.10.3-3 [100.0 kB] Get: 170 http://deb.debian.org/debian trixie/main i386 python3-webencodings all 0.5.1-5 [11.1 kB] Get: 171 http://deb.debian.org/debian trixie/main i386 python3-html5lib all 1.1-6 [90.5 kB] Get: 172 http://deb.debian.org/debian trixie/main i386 python3-bleach all 6.1.0-2 [50.7 kB] Get: 173 http://deb.debian.org/debian trixie/main i386 python3-brotli i386 1.1.0-2+b3 [323 kB] Get: 174 http://deb.debian.org/debian trixie/main i386 python3-soupsieve all 2.5-1 [38.1 kB] Get: 175 http://deb.debian.org/debian trixie/main i386 python3-bs4 all 4.12.3-1 [133 kB] Get: 176 http://deb.debian.org/debian trixie/main i386 python3-typing-extensions all 4.10.0-1 [66.2 kB] Get: 177 http://deb.debian.org/debian trixie/main i386 python3-bytecode all 0.15.1-3 [41.5 kB] Get: 178 http://deb.debian.org/debian trixie/main i386 python3-certifi all 2023.11.17-1 [155 kB] Get: 179 http://deb.debian.org/debian trixie/main i386 python3-cffi-backend i386 1.16.0-2+b1 [114 kB] Get: 180 http://deb.debian.org/debian trixie/main i386 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 181 http://deb.debian.org/debian trixie/main i386 python3-charset-normalizer all 3.3.2-1 [51.6 kB] Get: 182 http://deb.debian.org/debian trixie/main i386 python3-traitlets all 5.5.0-2 [90.7 kB] Get: 183 http://deb.debian.org/debian trixie/main i386 python3-comm all 0.2.1-1 [8104 B] Get: 184 http://deb.debian.org/debian trixie/main i386 python3-numpy i386 1:1.24.2-2 [4879 kB] Get: 185 http://deb.debian.org/debian trixie/main i386 python3-contourpy i386 1.0.7-3 [295 kB] Get: 186 http://deb.debian.org/debian trixie/main i386 python3-coverage i386 7.2.7+dfsg1-1+b1 [170 kB] Get: 187 http://deb.debian.org/debian trixie/main i386 python3-cycler all 0.12.1-1 [9496 B] Get: 188 http://deb.debian.org/debian trixie/main i386 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 189 http://deb.debian.org/debian trixie/main i386 python3-pydevd i386 2.10.0+ds-10 [605 kB] Get: 190 http://deb.debian.org/debian trixie/main i386 python3-debugpy all 1.8.0+ds-4 [66.7 kB] Get: 191 http://deb.debian.org/debian trixie/main i386 python3-decorator all 5.1.1-5 [15.1 kB] Get: 192 http://deb.debian.org/debian trixie/main i386 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 193 http://deb.debian.org/debian trixie/main i386 python3-roman all 3.3-3 [9880 B] Get: 194 http://deb.debian.org/debian trixie/main i386 python3-docutils all 0.20.1+dfsg-3 [389 kB] Get: 195 http://deb.debian.org/debian trixie/main i386 python3-editables all 0.5-1 [14.8 kB] Get: 196 http://deb.debian.org/debian trixie/main i386 python3-entrypoints all 0.4-2 [7184 B] Get: 197 http://deb.debian.org/debian trixie/main i386 python3-executing all 2.0.1-0.1 [22.7 kB] Get: 198 http://deb.debian.org/debian trixie/main i386 python3-fastjsonschema all 2.19.1-1 [21.3 kB] Get: 199 http://deb.debian.org/debian trixie/main i386 python3-scipy i386 1.11.4-6 [19.0 MB] Get: 200 http://deb.debian.org/debian trixie/main i386 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get: 201 http://deb.debian.org/debian trixie/main i386 python3-mpmath all 1.3.0-1 [419 kB] Get: 202 http://deb.debian.org/debian trixie/main i386 python3-sympy all 1.12-7 [3869 kB] Get: 203 http://deb.debian.org/debian trixie/main i386 python3-fs all 2.4.16-4 [95.4 kB] Get: 204 http://deb.debian.org/debian trixie/main i386 python3-lxml i386 5.1.0-1 [2065 kB] Get: 205 http://deb.debian.org/debian trixie/main i386 python3-lz4 i386 4.0.2+dfsg-1+b3 [25.6 kB] Get: 206 http://deb.debian.org/debian trixie/main i386 unicode-data all 15.1.0-1 [8547 kB] Get: 207 http://deb.debian.org/debian trixie/main i386 python3-fonttools i386 4.46.0-1 [1613 kB] Get: 208 http://deb.debian.org/debian trixie/main i386 python3-packaging all 24.0-1 [45.5 kB] Get: 209 http://deb.debian.org/debian trixie/main i386 python3-pathspec all 0.12.1-1 [28.1 kB] Get: 210 http://deb.debian.org/debian trixie/main i386 python3-pluggy all 1.4.0-1 [26.2 kB] Get: 211 http://deb.debian.org/debian trixie/main i386 python3-trove-classifiers all 2024.1.31-1 [9968 B] Get: 212 http://deb.debian.org/debian trixie/main i386 python3-hatchling all 1.21.0-1 [48.4 kB] Get: 213 http://deb.debian.org/debian trixie/main i386 python3-setuptools-scm all 8.0.4-2 [39.5 kB] Get: 214 http://deb.debian.org/debian trixie/main i386 python3-hatch-vcs all 0.4.0-1 [8336 B] Get: 215 http://deb.debian.org/debian trixie/main i386 python3-idna all 3.6-2 [37.0 kB] Get: 216 http://deb.debian.org/debian trixie/main i386 python3-imagesize all 1.4.1-1 [6688 B] Get: 217 http://deb.debian.org/debian trixie/main i386 python3-parso all 0.8.3-1 [67.4 kB] Get: 218 http://deb.debian.org/debian trixie/main i386 python3-typeshed all 0.0~git20231111.6764465-3 [1258 kB] Get: 219 http://deb.debian.org/debian trixie/main i386 python3-jedi all 0.19.1+ds1-1 [691 kB] Get: 220 http://deb.debian.org/debian trixie/main i386 python3-matplotlib-inline all 0.1.6-2 [8652 B] Get: 221 http://deb.debian.org/debian trixie/main i386 python3-ptyprocess all 0.7.0-5 [14.7 kB] Get: 222 http://deb.debian.org/debian trixie/main i386 python3-pexpect all 4.9-2 [55.5 kB] Get: 223 http://deb.debian.org/debian trixie/main i386 python3-wcwidth all 0.2.13+dfsg1-1 [24.9 kB] Get: 224 http://deb.debian.org/debian trixie/main i386 python3-prompt-toolkit all 3.0.43-1 [276 kB] Get: 225 http://deb.debian.org/debian trixie/main i386 python3-pygments all 2.17.2+dfsg-1 [818 kB] Get: 226 http://deb.debian.org/debian trixie/main i386 python3-pure-eval all 0.2.2-1 [11.2 kB] Get: 227 http://deb.debian.org/debian trixie/main i386 python3-stack-data all 0.6.3-1 [21.6 kB] Get: 228 http://deb.debian.org/debian trixie/main i386 python3-ipython all 8.20.0-1 [556 kB] Get: 229 http://deb.debian.org/debian trixie/main i386 python3-platformdirs all 4.2.0-1 [15.9 kB] Get: 230 http://deb.debian.org/debian trixie/main i386 python3-jupyter-core all 5.3.2-1 [31.5 kB] Get: 231 http://deb.debian.org/debian trixie/main i386 python3-nest-asyncio all 1.5.4-1 [6248 B] Get: 232 http://deb.debian.org/debian trixie/main i386 python3-tornado i386 6.4.0-1 [347 kB] Get: 233 http://deb.debian.org/debian trixie/main i386 python3-py all 1.11.0-2 [88.7 kB] Get: 234 http://deb.debian.org/debian trixie/main i386 python3-zmq i386 24.0.1-5+b1 [362 kB] Get: 235 http://deb.debian.org/debian trixie/main i386 python3-jupyter-client all 7.4.9-2 [103 kB] Get: 236 http://deb.debian.org/debian trixie/main i386 python3-psutil i386 5.9.8-2 [226 kB] Get: 237 http://deb.debian.org/debian trixie/main i386 python3-ipykernel all 6.29.3-1 [102 kB] Get: 238 http://deb.debian.org/debian trixie/main i386 python3-markupsafe i386 2.1.5-1 [14.4 kB] Get: 239 http://deb.debian.org/debian trixie/main i386 python3-jinja2 all 3.1.3-1 [119 kB] Get: 240 http://deb.debian.org/debian trixie/main i386 python3-joblib all 1.3.2-2 [218 kB] Get: 241 http://deb.debian.org/debian trixie/main i386 python3-rpds-py i386 0.12.0-3 [298 kB] Get: 242 http://deb.debian.org/debian trixie/main i386 python3-referencing all 0.31.0-1 [22.2 kB] Get: 243 http://deb.debian.org/debian trixie/main i386 python3-jsonschema-specifications all 2023.12.1-1 [8976 B] Get: 244 http://deb.debian.org/debian trixie/main i386 python3-jsonschema all 4.19.2-2 [71.2 kB] Get: 245 http://deb.debian.org/debian trixie/main i386 python3-jupyterlab-pygments all 0.2.2-3 [6096 B] Get: 246 http://deb.debian.org/debian trixie/main i386 python3-kiwisolver i386 1.4.4-3 [84.0 kB] Get: 247 http://deb.debian.org/debian trixie/main i386 python3-pil i386 10.2.0-1 [526 kB] Get: 248 http://deb.debian.org/debian trixie/main i386 python3-tk i386 3.11.5-1 [108 kB] Get: 249 http://deb.debian.org/debian trixie/main i386 python3-pil.imagetk i386 10.2.0-1 [78.0 kB] Get: 250 http://deb.debian.org/debian trixie/main i386 python3-pyparsing all 3.1.1-1 [145 kB] Get: 251 http://deb.debian.org/debian trixie/main i386 python3-matplotlib i386 3.6.3-1+b2 [8100 kB] Get: 252 http://deb.debian.org/debian trixie/main i386 sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1021 kB] Get: 253 http://deb.debian.org/debian trixie/main i386 sphinx-common all 7.2.6-6 [702 kB] Get: 254 http://deb.debian.org/debian trixie/main i386 python3-urllib3 all 1.26.18-2 [116 kB] Get: 255 http://deb.debian.org/debian trixie/main i386 python3-requests all 2.31.0+dfsg-1 [68.6 kB] Get: 256 http://deb.debian.org/debian trixie/main i386 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 257 http://deb.debian.org/debian trixie/main i386 python3-sphinx all 7.2.6-6 [552 kB] Get: 258 http://deb.debian.org/debian trixie/main i386 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 259 http://deb.debian.org/debian trixie/main i386 python3-sphinx-rtd-theme all 2.0.0+dfsg-1 [28.3 kB] Get: 260 http://deb.debian.org/debian trixie/main i386 python3-msmb-theme all 1.2.0-4 [33.8 kB] Get: 261 http://deb.debian.org/debian trixie/main i386 python3-nbformat all 5.9.1-1 [45.1 kB] Get: 262 http://deb.debian.org/debian trixie/main i386 python3-nbclient all 0.8.0-1 [64.0 kB] Get: 263 http://deb.debian.org/debian trixie/main i386 python3-pandocfilters all 1.5.1-1 [23.7 kB] Get: 264 http://deb.debian.org/debian trixie/main i386 python3-tinycss2 all 1.2.1-2 [21.9 kB] Get: 265 http://deb.debian.org/debian trixie/main i386 python3-nbconvert all 6.5.3-4 [163 kB] Get: 266 http://deb.debian.org/debian trixie/main i386 python3-networkx all 2.8.8-2 [1425 kB] Get: 267 http://deb.debian.org/debian trixie/main i386 python3-numexpr i386 2.9.0-1 [103 kB] Get: 268 http://deb.debian.org/debian trixie/main i386 python3-tabulate all 0.8.10-1 [38.8 kB] Get: 269 http://deb.debian.org/debian trixie/main i386 python3-numpydoc all 1.6.0-2 [49.6 kB] Get: 270 http://deb.debian.org/debian trixie/main i386 python3-pandas-lib i386 2.1.4+dfsg-5 [7492 kB] Get: 271 http://deb.debian.org/debian trixie/main i386 python3-pandas all 2.1.4+dfsg-5 [3015 kB] Get: 272 http://deb.debian.org/debian trixie/main i386 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 273 http://deb.debian.org/debian trixie/main i386 python3-sklearn-lib i386 1.4.1.post1+dfsg-1 [6130 kB] Get: 274 http://deb.debian.org/debian trixie/main i386 python3-sklearn all 1.4.1.post1+dfsg-1 [2246 kB] Get: 275 http://deb.debian.org/debian trixie/main i386 python3-tables-lib i386 3.7.0-10+b1 [715 kB] Get: 276 http://deb.debian.org/debian trixie/main i386 python3-tables all 3.7.0-10 [338 kB] Fetched 184 MB in 3s (66.2 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 ... 19874 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_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... 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_0.190-1_all.deb ... Unpacking libdebuginfod-common (0.190-1) ... Selecting previously unselected package libpython3.11-minimal:i386. Preparing to unpack .../4-libpython3.11-minimal_3.11.8-1_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.8-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../5-libexpat1_2.5.0-2+b2_i386.deb ... Unpacking libexpat1:i386 (2.5.0-2+b2) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../6-python3.11-minimal_3.11.8-1_i386.deb ... Unpacking python3.11-minimal (3.11.8-1) ... Setting up libpython3.11-minimal:i386 (3.11.8-1) ... Setting up libexpat1:i386 (2.5.0-2+b2) ... Setting up python3.11-minimal (3.11.8-1) ... 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 ... 20303 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.6-1_i386.deb ... Unpacking python3-minimal (3.11.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-1_all.deb ... Unpacking tzdata (2024a-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-3_all.deb ... Unpacking readline-common (8.2-3) ... Selecting previously unselected package libreadline8:i386. Preparing to unpack .../5-libreadline8_8.2-3+b1_i386.deb ... Unpacking libreadline8:i386 (8.2-3+b1) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../6-libpython3.11-stdlib_3.11.8-1_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.8-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.8-1_i386.deb ... Unpacking python3.11 (3.11.8-1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../8-libpython3-stdlib_3.11.6-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.11.6-1) ... Setting up python3-minimal (3.11.6-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21291 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.6-1_i386.deb ... Unpacking python3 (3.11.6-1) ... Selecting previously unselected package libpython3.12-minimal:i386. Preparing to unpack .../001-libpython3.12-minimal_3.12.2-1_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.2-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../002-python3.12-minimal_3.12.2-1_i386.deb ... Unpacking python3.12-minimal (3.12.2-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../003-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:i386. Preparing to unpack .../004-libproc2-0_2%3a4.0.4-4_i386.deb ... Unpacking libproc2-0:i386 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../005-procps_2%3a4.0.4-4_i386.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package openssl. Preparing to unpack .../006-openssl_3.1.5-1_i386.deb ... Unpacking openssl (3.1.5-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../007-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../008-libmagic-mgc_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../009-libmagic1_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic1:i386 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../010-file_1%3a5.45-2+b1_i386.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../011-gettext-base_0.21-14+b1_i386.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../012-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 .../013-groff-base_1.23.0-3_i386.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../014-bsdextrautils_2.39.3-6_i386.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../015-libpipeline1_1.5.7-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../016-man-db_2.12.0-3_i386.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../017-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../018-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../019-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../020-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../021-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libtcl8.6:i386. Preparing to unpack .../022-libtcl8.6_8.6.14+dfsg-1_i386.deb ... Unpacking libtcl8.6:i386 (8.6.14+dfsg-1) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../023-libbrotli1_1.1.0-2+b3_i386.deb ... Unpacking libbrotli1:i386 (1.1.0-2+b3) ... Selecting previously unselected package libpng16-16:i386. Preparing to unpack .../024-libpng16-16_1.6.43-1_i386.deb ... Unpacking libpng16-16:i386 (1.6.43-1) ... Selecting previously unselected package libfreetype6:i386. Preparing to unpack .../025-libfreetype6_2.13.2+dfsg-1+b1_i386.deb ... Unpacking libfreetype6:i386 (2.13.2+dfsg-1+b1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../026-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../027-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../028-fontconfig-config_2.15.0-1.1_i386.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package libfontconfig1:i386. Preparing to unpack .../029-libfontconfig1_2.15.0-1.1_i386.deb ... Unpacking libfontconfig1:i386 (2.15.0-1.1) ... Selecting previously unselected package libxau6:i386. Preparing to unpack .../030-libxau6_1%3a1.0.9-1_i386.deb ... Unpacking libxau6:i386 (1:1.0.9-1) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../031-libbsd0_0.12.2-1_i386.deb ... Unpacking libbsd0:i386 (0.12.2-1) ... Selecting previously unselected package libxdmcp6:i386. Preparing to unpack .../032-libxdmcp6_1%3a1.1.2-3_i386.deb ... Unpacking libxdmcp6:i386 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:i386. Preparing to unpack .../033-libxcb1_1.15-1_i386.deb ... Unpacking libxcb1:i386 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../034-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:i386. Preparing to unpack .../035-libx11-6_2%3a1.8.7-1_i386.deb ... Unpacking libx11-6:i386 (2:1.8.7-1) ... Selecting previously unselected package libxrender1:i386. Preparing to unpack .../036-libxrender1_1%3a0.9.10-1.1_i386.deb ... Unpacking libxrender1:i386 (1:0.9.10-1.1) ... Selecting previously unselected package libxft2:i386. Preparing to unpack .../037-libxft2_2.3.6-1+b1_i386.deb ... Unpacking libxft2:i386 (2.3.6-1+b1) ... Selecting previously unselected package libxext6:i386. Preparing to unpack .../038-libxext6_2%3a1.3.4-1+b1_i386.deb ... Unpacking libxext6:i386 (2:1.3.4-1+b1) ... Selecting previously unselected package x11-common. Preparing to unpack .../039-x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) ... Selecting previously unselected package libxss1:i386. Preparing to unpack .../040-libxss1_1%3a1.2.3-1_i386.deb ... Unpacking libxss1:i386 (1:1.2.3-1) ... Selecting previously unselected package libtk8.6:i386. Preparing to unpack .../041-libtk8.6_8.6.14-1_i386.deb ... Unpacking libtk8.6:i386 (8.6.14-1) ... Selecting previously unselected package tk8.6-blt2.5. Preparing to unpack .../042-tk8.6-blt2.5_2.5.3+dfsg-7_i386.deb ... Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7) ... Selecting previously unselected package blt. Preparing to unpack .../043-blt_2.5.3+dfsg-7_i386.deb ... Unpacking blt (2.5.3+dfsg-7) ... Selecting previously unselected package python3-zombie-imp. Preparing to unpack .../044-python3-zombie-imp_0.0.2-2_all.deb ... Unpacking python3-zombie-imp (0.0.2-2) ... Selecting previously unselected package cython3-legacy. Preparing to unpack .../045-cython3-legacy_0.29.37-2_i386.deb ... Unpacking cython3-legacy (0.29.37-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../046-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../047-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../048-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../049-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../050-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../051-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... 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Current default time zone: 'Etc/UTC' Local time is now: Sat May 17 19:39:06 UTC 2025. Universal Time is now: Sat May 17 19:39:06 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.12.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libexpat1-dev:i386 (2.5.0-2+b2) ... Setting up libjpeg62-turbo:i386 (1:2.1.5-2+b2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libfribidi0:i386 (1.0.13-3+b1) ... Setting up libimagequant0:i386 (2.18.0-1) ... Setting up libproc2-0:i386 (2:4.0.4-4) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16:i386 (1.6.43-1) ... Setting up libtcl8.6:i386 (8.6.14+dfsg-1) ... Setting up autopoint (0.21-14) ... 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Setting up python3-tk:i386 (3.11.5-1) ... Setting up python3-networkx (2.8.8-2) ... /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' "graph [edge [ source u'u\4200' target u'u\4200' ] " /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' + "node [ id u'u\4200' label b ] ]" Setting up python3-setuptools-scm (8.0.4-2) ... Setting up python3-bs4 (4.12.3-1) ... Setting up python3-bleach (6.1.0-2) ... Setting up python3-matplotlib-inline (0.1.6-2) ... Setting up python3-comm (0.2.1-1) ... Setting up python3-fs (2.4.16-4) ... Setting up python3-pygments (2.17.2+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-pil.imagetk:i386 (10.2.0-1) ... Setting up python3-executing (2.0.1-0.1) ... Setting up libpython3-all-dev:i386 (3.11.6-1) ... Setting up python3-pexpect (4.9-2) ... Setting up python3-zmq (24.0.1-5+b1) ... 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Setting up python3-sphinx-rtd-theme (2.0.0+dfsg-1) ... Setting up python3-msmb-theme (1.2.0-4) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/mdtraj-1.9.9/ && 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_1.9.9-1_source.changes dpkg-buildpackage: info: source package mdtraj dpkg-buildpackage: info: source version 1.9.9-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 dpkg-source: info: using options from mdtraj-1.9.9/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/mdtraj-1.9.9' dh_auto_clean || /bin/true pybuild --clean -i python{version} -p "3.12 3.11" 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/13/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-13' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --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-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 13.2.0 (Debian 13.2.0-13) /build/reproducible-path/mdtraj-1.9.9/basesetup.py:451: UserWarning: Unrecognized setuptools command ('clean'), proceeding with generating Cython sources and expanding templates warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " 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 [ 1/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 2/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 3/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 4/12] Cythonizing mdtraj/formats/tng/tng.pyx [ 5/12] Cythonizing mdtraj/formats/xtc/trr.pyx [ 6/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 7/12] Cythonizing mdtraj/geometry/drid.pyx [ 8/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 9/12] Cythonizing mdtraj/geometry/neighbors.pyx [10/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [11/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running clean removing '/build/reproducible-path/mdtraj-1.9.9/.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 I: pybuild base:311: python3.11 setup.py clean Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-linux-gnu/13/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-13' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --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-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 13.2.0 (Debian 13.2.0-13) /build/reproducible-path/mdtraj-1.9.9/basesetup.py:451: UserWarning: Unrecognized setuptools command ('clean'), proceeding with generating Cython sources and expanding templates warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " 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 [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/12] Cythonizing mdtraj/geometry/drid.pyx [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running clean removing '/build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build' (and everything under it) 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; 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 __pycache__ .pybuild find . -name "lib*.a" -delete make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.9.9' 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 3.11" 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/13/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-13' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --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-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 13.2.0 (Debian 13.2.0-13) /build/reproducible-path/mdtraj-1.9.9/basesetup.py:451: UserWarning: Unrecognized setuptools command ('config'), proceeding with generating Cython sources and expanding templates warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " 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 [ 1/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 2/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 3/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 4/12] Cythonizing mdtraj/formats/tng/tng.pyx [ 5/12] Cythonizing mdtraj/formats/xtc/trr.pyx [ 6/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 7/12] Cythonizing mdtraj/geometry/drid.pyx [ 8/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 9/12] Cythonizing mdtraj/geometry/neighbors.pyx [10/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [11/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running config I: pybuild base:311: python3.11 setup.py config Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-linux-gnu/13/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-13' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --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-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 13.2.0 (Debian 13.2.0-13) /build/reproducible-path/mdtraj-1.9.9/basesetup.py:451: UserWarning: Unrecognized setuptools command ('config'), proceeding with generating Cython sources and expanding templates warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " 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 [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/12] Cythonizing mdtraj/geometry/drid.pyx [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running config debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/mdtraj-1.9.9' dh_auto_build pybuild --build -i python{version} -p "3.12 3.11" I: pybuild base:311: /usr/bin/python3.12 setup.py build Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-linux-gnu/13/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-13' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --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-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 13.2.0 (Debian 13.2.0-13) 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 [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/12] Cythonizing mdtraj/geometry/drid.pyx [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running build running build_py creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj copying mdtraj/io.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj copying mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj copying mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/six.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.9.9/.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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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:1940, 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:9850:16: 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:19348:20: note: in expansion of macro 'PyInt_FromLong' 19348 | 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:9570:7: note: '__pyx_v_status' was declared here 9570 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:7672:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7672 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7676:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 7676 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8053:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8053 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8057:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8057 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8061:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8061 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8099:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8099 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6480:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 6480 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8023:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8023 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6484:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 6484 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8041:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8041 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6488:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 6488 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8081:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8081 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8085:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8085 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8089:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8089 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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:1940, 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:11623:16: 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:21046:20: note: in expansion of macro 'PyInt_FromLong' 21046 | 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:11096:7: note: '__pyx_v_status' was declared here 11096 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:8671:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8671 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8675:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8675 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8619:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8619 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8623:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8623 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8778:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8778 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8782:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8782 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8382:56: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8382 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:95: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8397:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8397 | __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:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8388:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8388 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8392:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8392 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8439:59: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8439 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:95: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8454:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8454 | __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:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8445:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8445 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8449:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8449 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so building 'mdtraj.formats.tng' extension creating build/temp.linux-i686-cpython-312/mdtraj/formats/tng creating build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src creating build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression creating build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/lib i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/bwlzh.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/bwt.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/coder.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/dict.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/fixpoint.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/huffman.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/huffmem.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/lz77.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/merge_sort.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/mtf.o mdtraj/formats/tng/src/compression/mtf.c: In function 'Ptngc_comp_conv_to_mtf': mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 196 | while (dict[ptr]!=v) | ^~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/rle.o mdtraj/formats/tng/src/compression/rle.c: In function 'Ptngc_comp_conv_to_rle': mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 56 | if (v==vals[i]) | ^~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/tng_compress.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/vals16.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/warnmalloc.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/widemuldiv.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/xtc2.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/xtc3.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/lib/md5.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/lib/tng_io.o mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_block_header_read': mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 1064 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 1073 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 1089 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 1098 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_output_file_endianness_get': mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast 9565 | if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast 9570 | else if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast 9588 | if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast 9593 | else if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_output_file_endianness_set': mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 9651 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 9660 | tng_data->output_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 9673 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 9682 | tng_data->output_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_block_add': mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^ mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5969:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'n_particles' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5684:13: note: 'n_particles' was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5962:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'num_first_particle' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5684:26: note: 'num_first_particle' was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/tng.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/tng.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, 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/tng/tng.c:810: /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 " \ | ^~~~~~~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__': mdtraj/formats/tng/tng.c:3706:104: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3706 | __pyx_t_1 = ((tng_util_trajectory_open(__pyx_v_filename, __pyx_v_self->mode, (&__pyx_v_self->_traj)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3761:88: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3761 | __pyx_t_1 = ((tng_num_particles_get(__pyx_v_self->_traj, (&__pyx_v_self->n_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3793:90: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3793 | __pyx_t_1 = ((tng_num_frames_get(__pyx_v_self->_traj, (&__pyx_v_self->tot_n_frames)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3825:95: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3825 | __pyx_t_1 = ((tng_distance_unit_exponential_get(__pyx_v_self->_traj, (&__pyx_v_exponent)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3895:113: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3895 | __pyx_t_1 = ((tng_num_frames_per_frame_set_get(__pyx_v_self->_traj, (&__pyx_v_self->_frames_per_frame_set)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3939:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3939 | __pyx_t_1 = ((tng_last_program_name_set(__pyx_v_self->_traj, __pyx_t_8) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_8_read_topology': mdtraj/formats/tng/tng.c:4735:106: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4735 | __pyx_t_7 = ((tng_chain_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4780:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4780 | __pyx_t_7 = ((tng_residue_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4887:115: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4887 | __pyx_t_8 = ((tng_global_residue_id_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, (&__pyx_v_residue_id)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4917:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4917 | __pyx_t_8 = ((tng_atom_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:5045:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5045 | __pyx_t_8 = ((tng_atom_type_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:5646:126: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5646 | __pyx_t_7 = ((tng_molsystem_bonds_get(__pyx_v_self->_traj, (&__pyx_v_n_bonds), (&__pyx_v_from_atoms), (&__pyx_v_to_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_10_read_frame': mdtraj/formats/tng/tng.c:6056:152: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6056 | __pyx_t_1 = ((tng_util_pos_read_range(__pyx_v_self->_traj, __pyx_v_self->_pos, __pyx_v_self->_pos, (&__pyx_v_positions), (&__pyx_v_stride_length)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:6324:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6324 | __pyx_t_1 = ((tng_util_time_of_frame_get(__pyx_v_self->_traj, __pyx_v_self->_pos, (&__pyx_v_frame_time)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:6426:304: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6426 | __pyx_t_1 = ((tng_data_vector_interval_get(__pyx_v_self->_traj, __pyx_v_6mdtraj_7formats_3tng_TNG_TRAJ_BOX_SHAPE, __pyx_v_self->_pos, __pyx_v_self->_pos, __pyx_e_6mdtraj_7formats_3tng_TNG_USE_HASH, (&__pyx_v_box_shape), (&__pyx_v_stride_length), (&__pyx_v_n_values_per_frame), (&__pyx_v_data_type)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_16write': mdtraj/formats/tng/tng.c:8918:94: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8918 | __pyx_t_1 = ((tng_implicit_num_particles_set(__pyx_v_self->_traj, __pyx_v_self->n_atoms) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:8950:75: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8950 | __pyx_t_1 = ((tng_util_pos_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:8982:81: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8982 | __pyx_t_1 = ((tng_util_box_shape_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9305:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9305 | __pyx_t_9 = ((tng_time_per_frame_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9496:372: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9496 | __pyx_t_1 = ((tng_util_pos_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz_array.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_xyz_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_xyz_array.diminfo[1].strides, __pyx_t_20, __pyx_pybuffernd_xyz_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9548:378: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9548 | __pyx_t_1 = ((tng_util_box_shape_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box_array.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_box_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_box_array.diminfo[1].strides, __pyx_t_18, __pyx_pybuffernd_box_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9610:89: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9610 | __pyx_t_1 = ((tng_frame_set_first_frame_time_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib/i386-linux-gnu -lz -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/tng.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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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:1940, 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:6646:17: 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:13600:20: note: in expansion of macro 'PyInt_FromLong' 13600 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:5465:7: note: '__pyx_v_i' was declared here 5465 | int __pyx_v_i; | ^~~~~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so building 'mdtraj.formats.binpos' extension creating build/temp.linux-i686-cpython-312/mdtraj/formats/binpos creating build/temp.linux-i686-cpython-312/mdtraj/formats/binpos/src i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/binpos/binpos.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:1940, 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/binpos/binpos.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_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read', inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:5526:6: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 5526 | if (__pyx_t_2) { | ^ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5006:7: note: '__pyx_v_status' was declared here 5006 | int __pyx_v_status; | ^~~~~~~~~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read' at mdtraj/formats/binpos/binpos.c:5536:17, inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:694:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 694 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/binpos/binpos.c:13100:20: note: in expansion of macro 'PyInt_FromLong' 13100 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5003:7: note: '__pyx_v_i' was declared here 5003 | int __pyx_v_i; | ^~~~~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/binpos/src/binposplugin.c: In function 'open_binpos_read': mdtraj/formats/binpos/src/binposplugin.c:59:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | fread(magicchar,sizeof(char),4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/binpos/src/binposplugin.c:69:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fread(&igarb,sizeof(int),1,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/binpos/binpos.o build/temp.linux-i686-cpython-312/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/binpos.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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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:1940, 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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 constructor '{anonymous}::DDException::DDException(const std::string&, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: '*this.{anonymous}::DDException::eno' is used uninitialized [-Wuninitialized] 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} | ~~~~~~~~^~~~~ 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:906, 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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so building 'mdtraj._lprmsd' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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:1940, 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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so building 'mdtraj.core.lib.libtheobald' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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:1940, 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 " \ | ^~~~~~~ mdtraj/geometry/src/_geometry.cpp: In function 'void __pyx_f_6mdtraj_8geometry_9_geometry_make_whole(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice)': mdtraj/geometry/src/_geometry.cpp:6131:296: warning: '__pyx_v_offset[1]' may be used uninitialized [-Wmaybe-uninitialized] 6131 | (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) ))))))); | ~~~~~~~~~~~~~~~~~^~ mdtraj/geometry/src/_geometry.cpp:6037:9: note: '__pyx_v_offset[1]' was declared here 6037 | float __pyx_v_offset[3]; | ^~~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6131:274: warning: '__pyx_v_delta[1]' may be used uninitialized [-Wmaybe-uninitialized] 6131 | (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) ))))))); | ~~~~~~~~~~~~~~~~^~ mdtraj/geometry/src/_geometry.cpp:6038:9: note: '__pyx_v_delta[1]' was declared here 6038 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6117:242: warning: '__pyx_v_delta[2]' may be used uninitialized [-Wmaybe-uninitialized] 6117 | (__pyx_v_offset[__pyx_v_k]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_8 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_7)) ))) * roundf(((__pyx_v_delta[2]) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_5 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_4)) )))))); | ~~~~~~~~~~~~~~~~^~ mdtraj/geometry/src/_geometry.cpp:6038:9: note: '__pyx_v_delta[2]' was declared here 6038 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.drid' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.neighbors' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:50:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:51:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 51 | periodicBoxSize[1] = periodicBoxVectors[1][1]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:52:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 52 | periodicBoxSize[2] = periodicBoxVectors[2][2]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:56:45: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so 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/13/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-13' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --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-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 13.2.0 (Debian 13.2.0-13) 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 [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/12] Cythonizing mdtraj/geometry/drid.pyx [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running build running build_py creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj copying mdtraj/io.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj copying mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj copying mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core copying mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core copying mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core copying mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core copying mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core copying mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core copying mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing copying mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing copying mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing copying mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing copying mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/six.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/data running build_ext building 'mdtraj.formats.xtc' extension creating build/temp.linux-i686-cpython-311 creating build/temp.linux-i686-cpython-311/mdtraj creating build/temp.linux-i686-cpython-311/mdtraj/formats creating build/temp.linux-i686-cpython-311/mdtraj/formats/xtc creating build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-i686-cpython-311/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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-i686-cpython-311/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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-i686-cpython-311/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:1940, 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:9850:16: 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:19348:20: note: in expansion of macro 'PyInt_FromLong' 19348 | 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:9570:7: note: '__pyx_v_status' was declared here 9570 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:7672:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7672 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7676:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 7676 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8053:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8053 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8057:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8057 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8061:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8061 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8099:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8099 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6480:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 6480 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8023:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8023 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6484:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 6484 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8041:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8041 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6488:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 6488 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8081:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8081 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8085:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8085 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8089:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8089 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/xtc.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/xtc.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.trr' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-i686-cpython-311/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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-i686-cpython-311/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:1940, 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:11623:16: 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:21046:20: note: in expansion of macro 'PyInt_FromLong' 21046 | 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:11096:7: note: '__pyx_v_status' was declared here 11096 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:8671:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8671 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8675:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8675 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8619:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8619 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8623:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8623 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8778:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8778 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8782:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8782 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8382:56: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8382 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:95: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8397:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8397 | __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:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8388:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8388 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8392:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8392 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8439:59: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8439 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:95: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8454:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8454 | __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:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8445:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8445 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8449:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8449 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/trr.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/trr.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.tng' extension creating build/temp.linux-i686-cpython-311/mdtraj/formats/tng creating build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src creating build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression creating build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/lib i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/bwlzh.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/bwt.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/coder.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/dict.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/fixpoint.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/huffman.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/huffmem.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/lz77.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/merge_sort.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/mtf.o mdtraj/formats/tng/src/compression/mtf.c: In function 'Ptngc_comp_conv_to_mtf': mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 196 | while (dict[ptr]!=v) | ^~ i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/rle.o mdtraj/formats/tng/src/compression/rle.c: In function 'Ptngc_comp_conv_to_rle': mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 56 | if (v==vals[i]) | ^~ i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/tng_compress.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/vals16.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/warnmalloc.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/widemuldiv.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/xtc2.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/xtc3.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/lib/md5.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/lib/tng_io.o mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_block_header_read': mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 1064 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 1073 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 1089 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 1098 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_output_file_endianness_get': mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast 9565 | if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast 9570 | else if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast 9588 | if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast 9593 | else if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_output_file_endianness_set': mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 9651 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 9660 | tng_data->output_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 9673 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 9682 | tng_data->output_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_block_add': mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^ mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5969:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'n_particles' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5684:13: note: 'n_particles' was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5962:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'num_first_particle' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5684:26: note: 'num_first_particle' was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/tng.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/tng.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, 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/tng/tng.c:810: /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 " \ | ^~~~~~~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__': mdtraj/formats/tng/tng.c:3706:104: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3706 | __pyx_t_1 = ((tng_util_trajectory_open(__pyx_v_filename, __pyx_v_self->mode, (&__pyx_v_self->_traj)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3761:88: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3761 | __pyx_t_1 = ((tng_num_particles_get(__pyx_v_self->_traj, (&__pyx_v_self->n_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3793:90: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3793 | __pyx_t_1 = ((tng_num_frames_get(__pyx_v_self->_traj, (&__pyx_v_self->tot_n_frames)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3825:95: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3825 | __pyx_t_1 = ((tng_distance_unit_exponential_get(__pyx_v_self->_traj, (&__pyx_v_exponent)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3895:113: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3895 | __pyx_t_1 = ((tng_num_frames_per_frame_set_get(__pyx_v_self->_traj, (&__pyx_v_self->_frames_per_frame_set)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3939:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3939 | __pyx_t_1 = ((tng_last_program_name_set(__pyx_v_self->_traj, __pyx_t_8) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_8_read_topology': mdtraj/formats/tng/tng.c:4735:106: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4735 | __pyx_t_7 = ((tng_chain_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4780:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4780 | __pyx_t_7 = ((tng_residue_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4887:115: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4887 | __pyx_t_8 = ((tng_global_residue_id_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, (&__pyx_v_residue_id)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4917:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4917 | __pyx_t_8 = ((tng_atom_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:5045:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5045 | __pyx_t_8 = ((tng_atom_type_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:5646:126: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5646 | __pyx_t_7 = ((tng_molsystem_bonds_get(__pyx_v_self->_traj, (&__pyx_v_n_bonds), (&__pyx_v_from_atoms), (&__pyx_v_to_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_10_read_frame': mdtraj/formats/tng/tng.c:6056:152: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6056 | __pyx_t_1 = ((tng_util_pos_read_range(__pyx_v_self->_traj, __pyx_v_self->_pos, __pyx_v_self->_pos, (&__pyx_v_positions), (&__pyx_v_stride_length)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:6324:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6324 | __pyx_t_1 = ((tng_util_time_of_frame_get(__pyx_v_self->_traj, __pyx_v_self->_pos, (&__pyx_v_frame_time)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:6426:304: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6426 | __pyx_t_1 = ((tng_data_vector_interval_get(__pyx_v_self->_traj, __pyx_v_6mdtraj_7formats_3tng_TNG_TRAJ_BOX_SHAPE, __pyx_v_self->_pos, __pyx_v_self->_pos, __pyx_e_6mdtraj_7formats_3tng_TNG_USE_HASH, (&__pyx_v_box_shape), (&__pyx_v_stride_length), (&__pyx_v_n_values_per_frame), (&__pyx_v_data_type)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_16write': mdtraj/formats/tng/tng.c:8918:94: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8918 | __pyx_t_1 = ((tng_implicit_num_particles_set(__pyx_v_self->_traj, __pyx_v_self->n_atoms) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:8950:75: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8950 | __pyx_t_1 = ((tng_util_pos_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:8982:81: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8982 | __pyx_t_1 = ((tng_util_box_shape_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9305:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9305 | __pyx_t_9 = ((tng_time_per_frame_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9496:372: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9496 | __pyx_t_1 = ((tng_util_pos_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz_array.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_xyz_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_xyz_array.diminfo[1].strides, __pyx_t_20, __pyx_pybuffernd_xyz_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9548:378: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9548 | __pyx_t_1 = ((tng_util_box_shape_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box_array.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_box_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_box_array.diminfo[1].strides, __pyx_t_18, __pyx_pybuffernd_box_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9610:89: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9610 | __pyx_t_1 = ((tng_frame_set_first_frame_time_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib/i386-linux-gnu -lz -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/tng.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.dcd' extension creating build/temp.linux-i686-cpython-311/mdtraj/formats/dcd creating build/temp.linux-i686-cpython-311/mdtraj/formats/dcd/src i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-i686-cpython-311/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:1940, 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:6646:17: 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:13600:20: note: in expansion of macro 'PyInt_FromLong' 13600 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:5465:7: note: '__pyx_v_i' was declared here 5465 | int __pyx_v_i; | ^~~~~~~~~ i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-i686-cpython-311/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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/formats/dcd/dcd.o build/temp.linux-i686-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dcd.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.binpos' extension creating build/temp.linux-i686-cpython-311/mdtraj/formats/binpos creating build/temp.linux-i686-cpython-311/mdtraj/formats/binpos/src i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/binpos/binpos.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:1940, 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/binpos/binpos.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_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read', inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:5526:6: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 5526 | if (__pyx_t_2) { | ^ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5006:7: note: '__pyx_v_status' was declared here 5006 | int __pyx_v_status; | ^~~~~~~~~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read' at mdtraj/formats/binpos/binpos.c:5536:17, inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:694:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 694 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/binpos/binpos.c:13100:20: note: in expansion of macro 'PyInt_FromLong' 13100 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5003:7: note: '__pyx_v_i' was declared here 5003 | int __pyx_v_i; | ^~~~~~~~~ i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/binpos/src/binposplugin.c: In function 'open_binpos_read': mdtraj/formats/binpos/src/binposplugin.c:59:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | fread(magicchar,sizeof(char),4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/binpos/src/binposplugin.c:69:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fread(&igarb,sizeof(int),1,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/formats/binpos/binpos.o build/temp.linux-i686-cpython-311/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/binpos.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.dtr' extension creating build/temp.linux-i686-cpython-311/mdtraj/formats/dtr creating build/temp.linux-i686-cpython-311/mdtraj/formats/dtr/src i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-i686-cpython-311/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:1940, 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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-i686-cpython-311/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 constructor '{anonymous}::DDException::DDException(const std::string&, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: '*this.{anonymous}::DDException::eno' is used uninitialized [-Wuninitialized] 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} | ~~~~~~~~^~~~~ 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:906, 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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/formats/dtr/dtr.o build/temp.linux-i686-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dtr.cpython-311-i386-linux-gnu.so building 'mdtraj._rmsd' extension creating build/temp.linux-i686-cpython-311/mdtraj/rmsd creating build/temp.linux-i686-cpython-311/mdtraj/rmsd/src i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-i686-cpython-311/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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/rmsd/_rmsd.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_rmsd.cpython-311-i386-linux-gnu.so building 'mdtraj._lprmsd' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-i686-cpython-311/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:1940, 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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-i686-cpython-311/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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/rmsd/_lprmsd.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/Munkres.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/fancy_index.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_lprmsd.cpython-311-i386-linux-gnu.so building 'mdtraj.core.lib.libtheobald' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -msse2 -mssse3 -O3 -funroll-loops --std=c++11 i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/center.o -msse2 -mssse3 -O3 -funroll-loops --std=c++11 i686-linux-gnu-gcc-ar rcs /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/lib/libtheobald.a build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/center.o building 'mdtraj.geometry._geometry' extension creating build/temp.linux-i686-cpython-311/mdtraj/geometry creating build/temp.linux-i686-cpython-311/mdtraj/geometry/src i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-i686-cpython-311/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:1940, 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 " \ | ^~~~~~~ mdtraj/geometry/src/_geometry.cpp: In function 'void __pyx_f_6mdtraj_8geometry_9_geometry_make_whole(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice)': mdtraj/geometry/src/_geometry.cpp:6131:296: warning: '__pyx_v_offset[1]' may be used uninitialized [-Wmaybe-uninitialized] 6131 | (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) ))))))); | ~~~~~~~~~~~~~~~~~^~ mdtraj/geometry/src/_geometry.cpp:6037:9: note: '__pyx_v_offset[1]' was declared here 6037 | float __pyx_v_offset[3]; | ^~~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6131:274: warning: '__pyx_v_delta[1]' may be used uninitialized [-Wmaybe-uninitialized] 6131 | (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) ))))))); | ~~~~~~~~~~~~~~~~^~ mdtraj/geometry/src/_geometry.cpp:6038:9: note: '__pyx_v_delta[1]' was declared here 6038 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6117:242: warning: '__pyx_v_delta[2]' may be used uninitialized [-Wmaybe-uninitialized] 6117 | (__pyx_v_offset[__pyx_v_k]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_8 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_7)) ))) * roundf(((__pyx_v_delta[2]) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_5 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_4)) )))))); | ~~~~~~~~~~~~~~~~^~ mdtraj/geometry/src/_geometry.cpp:6038:9: note: '__pyx_v_delta[2]' was declared here 6038 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-i686-cpython-311/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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/geometry/src/_geometry.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/dssp.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/geometry.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/sasa.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/_geometry.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry.drid' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/drid.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-i686-cpython-311/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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/geometry/drid.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/dridkernels.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/moments.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/drid.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry.neighbors' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-i686-cpython-311/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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/geometry/neighbors.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/neighbors.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighbors.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:50:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:51:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 51 | periodicBoxSize[1] = periodicBoxVectors[1][1]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:52:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 52 | periodicBoxSize[2] = periodicBoxVectors[2][2]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:56:45: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/geometry/neighborlist.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/neighborlist.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighborlist.cpython-311-i386-linux-gnu.so cp -a /build/reproducible-path/mdtraj-1.9.9/examples /build/reproducible-path/mdtraj-1.9.9/examples.orig mkdir -p /build/reproducible-path/mdtraj-1.9.9/build/html/examples/iterload ln -s /build/reproducible-path/mdtraj-1.9.9/examples/data /build/reproducible-path/mdtraj-1.9.9/build/html/examples/iterload/data sed "s|http://www.rcsb.org/pdb/files|/build/reproducible-path/mdtraj-1.9.9/debian/external|g" -i /build/reproducible-path/mdtraj-1.9.9/examples/*.ipynb PYTHONPATH=/build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build \ MPLCONFIGDIR=/build/reproducible-path/mdtraj-1.9.9/build/matplotlib \ make -C docs BUILDDIR=/build/reproducible-path/mdtraj-1.9.9/build html make[2]: Entering directory '/build/reproducible-path/mdtraj-1.9.9/docs' sphinx-build -b html -d /build/reproducible-path/mdtraj-1.9.9/build/doctrees . /build/reproducible-path/mdtraj-1.9.9/build/html Running Sphinx v7.2.6 [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-1.9.9/docs/api/generated/mdtraj.Topology.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.Trajectory.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.Trajectory.superpose.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.acylindricity.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.asphericity.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.baker_hubbard.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.chemical_shifts_ppm.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.chemical_shifts_shiftx2.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.chemical_shifts_spartaplus.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.compute_J3_HN_C.rst, ..., /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.utils.check_random_state.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.utils.ensure_type.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.utils.ilen.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.utils.import_.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.utils.in_units_of.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.utils.rotation_matrix_from_quaternion.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.utils.timing.rst, /build/reproducible-path/mdtraj-1.9.9/docs/api/generated/mdtraj.utils.uniform_quaternion.rst, /build/reproducible-path/mdtraj-1.9.9/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] 127 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-1.9.9/.pybuild/cpython3_3.11_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... 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[ 55%] api/generated/mdtraj.load_pdb reading sources... [ 56%] api/generated/mdtraj.load_prmtop reading sources... [ 57%] api/generated/mdtraj.load_trr reading sources... [ 57%] api/generated/mdtraj.load_xml reading sources... [ 58%] api/generated/mdtraj.load_xtc reading sources... [ 59%] api/generated/mdtraj.load_xyz reading sources... [ 60%] api/generated/mdtraj.lprmsd reading sources... [ 61%] api/generated/mdtraj.open reading sources... [ 61%] api/generated/mdtraj.principal_moments reading sources... [ 62%] api/generated/mdtraj.reindex_dataframe_by_atoms reading sources... [ 63%] api/generated/mdtraj.relative_shape_antisotropy reading sources... [ 64%] api/generated/mdtraj.reporters.DCDReporter reading sources... [ 65%] api/generated/mdtraj.reporters.HDF5Reporter reading sources... [ 65%] api/generated/mdtraj.reporters.NetCDFReporter reading sources... [ 66%] api/generated/mdtraj.rmsd reading sources... [ 67%] api/generated/mdtraj.rmsf reading sources... 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[ 79%] api/reporters reading sources... [ 80%] api/trajectory_files reading sources... [ 80%] api/utils reading sources... [ 81%] atom_selection reading sources... [ 82%] building_docs reading sources... [ 83%] 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... [ 87%] 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... [ 91%] 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-1.9.9/.pybuild/cpython3_3.11_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-1.9.9/.pybuild/cpython3_3.11_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-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:36: ERROR: Unexpected indentation. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_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-1.9.9/.pybuild/cpython3_3.11_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. docstring of mdtraj._rmsd.rmsf:46: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_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-1.9.9/docs/examples/atom-selection.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/atom-selection.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/centroids.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/centroids.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/clustering.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/clustering.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/hbonds.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/hbonds.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/iterload.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/iterload.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/native-contact.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/native-contact.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/nmr.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/nmr.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/openmm.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/simulation-with-openmm.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/pca.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/principal-components.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/ramachandran-plot.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/ramachandran-plot.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/examples/rmsd-benchmark.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/rmsd-benchmark.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/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-1.9.9/docs/examples/two-pass-clustering.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/two-pass-clustering.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.9/docs/installation.rst:1: WARNING: malformed hyperlink target. /build/reproducible-path/mdtraj-1.9.9/docs/mdconvert.rst:2: WARNING: Title underline too short. ``mdconvert`` (``mdconvert-mdtraj``) ============= /build/reproducible-path/mdtraj-1.9.9/docs/whatsnew.rst:7: WARNING: Title underline too short. v1.9.9 (July 22, 2023) --------------------- /build/reproducible-path/mdtraj-1.9.9/docs/whatsnew.rst:62: WARNING: Title underline too short. v1.9.7 (November 12, 2021) ----------------------- /build/reproducible-path/mdtraj-1.9.9/docs/whatsnew.rst:62: 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-1.9.9/docs/building_docs.rst: WARNING: document isn't included in any toctree /build/reproducible-path/mdtraj-1.9.9/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 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... [ 9%] 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... [ 13%] 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... [ 17%] 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... [ 20%] api/generated/mdtraj.compute_dssp writing output... [ 21%] 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... [ 24%] api/generated/mdtraj.compute_omega writing output... [ 25%] 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... [ 28%] api/generated/mdtraj.density writing output... [ 29%] api/generated/mdtraj.dipole_moments writing output... [ 30%] api/generated/mdtraj.formats.AmberNetCDFRestartFile writing output... [ 31%] api/generated/mdtraj.formats.AmberRestartFile writing output... [ 31%] api/generated/mdtraj.formats.ArcTrajectoryFile writing output... [ 32%] api/generated/mdtraj.formats.BINPOSTrajectoryFile writing output... [ 33%] api/generated/mdtraj.formats.DCDTrajectoryFile writing output... [ 34%] api/generated/mdtraj.formats.DTRTrajectoryFile writing output... [ 35%] 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... [ 39%] 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... [ 43%] 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_binpos writing output... [ 49%] api/generated/mdtraj.load_dcd writing output... [ 50%] api/generated/mdtraj.load_dtr writing output... [ 50%] api/generated/mdtraj.load_frame writing output... [ 51%] api/generated/mdtraj.load_hdf5 writing output... [ 52%] api/generated/mdtraj.load_hoomdxml writing output... [ 53%] api/generated/mdtraj.load_lammpstrj writing output... [ 54%] api/generated/mdtraj.load_lh5 writing output... [ 54%] api/generated/mdtraj.load_netcdf writing output... [ 55%] api/generated/mdtraj.load_pdb writing output... [ 56%] api/generated/mdtraj.load_prmtop writing output... [ 57%] api/generated/mdtraj.load_trr writing output... [ 57%] api/generated/mdtraj.load_xml writing output... [ 58%] api/generated/mdtraj.load_xtc writing output... [ 59%] api/generated/mdtraj.load_xyz writing output... [ 60%] api/generated/mdtraj.lprmsd writing output... [ 61%] api/generated/mdtraj.open writing output... [ 61%] api/generated/mdtraj.principal_moments writing output... [ 62%] api/generated/mdtraj.reindex_dataframe_by_atoms writing output... [ 63%] api/generated/mdtraj.relative_shape_antisotropy writing output... [ 64%] api/generated/mdtraj.reporters.DCDReporter writing output... [ 65%] api/generated/mdtraj.reporters.HDF5Reporter writing output... [ 65%] api/generated/mdtraj.reporters.NetCDFReporter writing output... [ 66%] api/generated/mdtraj.rmsd writing output... [ 67%] api/generated/mdtraj.rmsf writing output... [ 68%] api/generated/mdtraj.shrake_rupley writing output... [ 69%] 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... [ 71%] api/generated/mdtraj.utils.check_random_state writing output... [ 72%] 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... [ 75%] api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors writing output... [ 76%] 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... [ 79%] api/reporters writing output... [ 80%] api/trajectory_files writing output... [ 80%] api/utils writing output... [ 81%] atom_selection writing output... [ 82%] building_docs writing output... [ 83%] 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... [ 87%] 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... [ 91%] 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, 28 warnings. The HTML pages are in ../build/html. Build finished. The HTML pages are in /build/reproducible-path/mdtraj-1.9.9/build/html. make[2]: Leaving directory '/build/reproducible-path/mdtraj-1.9.9/docs' for img in `find /build/reproducible-path/mdtraj-1.9.9/build/html/examples -name *.png`; do \ mv $img /build/reproducible-path/mdtraj-1.9.9/build/html/examples; \ done sed "s|/build/reproducible-path/mdtraj-1.9.9/build/html/examples/|./|g; s|.ipynb|.ipynb.gz|g" -i /build/reproducible-path/mdtraj-1.9.9/build/html/examples/*.html sed "s|/build/reproducible-path/mdtraj-1.9.9/debian/external|http://www.rcsb.org/pdb/files|g" -i /build/reproducible-path/mdtraj-1.9.9/build/html/examples/*.html rm /build/reproducible-path/mdtraj-1.9.9/build/html/examples/iterload/data rm -rf /build/reproducible-path/mdtraj-1.9.9/examples mv /build/reproducible-path/mdtraj-1.9.9/examples.orig /build/reproducible-path/mdtraj-1.9.9/examples make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.9.9' dh_auto_build -O--buildsystem=pybuild -Npython-mdtraj-doc pybuild --build -i python{version} -p "3.12 3.11" I: pybuild base:311: /usr/bin/python3.12 setup.py build Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-linux-gnu/13/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-13' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --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-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 13.2.0 (Debian 13.2.0-13) 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 [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/12] Cythonizing mdtraj/geometry/drid.pyx [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running build running build_py copying mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.9/.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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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:1940, 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:9850:16: 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:19348:20: note: in expansion of macro 'PyInt_FromLong' 19348 | 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:9570:7: note: '__pyx_v_status' was declared here 9570 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:7672:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7672 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7676:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 7676 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8053:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8053 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8057:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8057 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8061:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8061 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8099:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8099 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6480:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 6480 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8023:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8023 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6484:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 6484 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8041:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8041 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6488:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 6488 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8081:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8081 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8085:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8085 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8089:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8089 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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:1940, 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:11623:16: 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:21046:20: note: in expansion of macro 'PyInt_FromLong' 21046 | 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:11096:7: note: '__pyx_v_status' was declared here 11096 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:8671:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8671 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8675:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8675 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8619:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8619 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8623:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8623 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8778:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8778 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8782:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8782 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8382:56: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8382 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:95: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8397:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8397 | __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:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8388:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8388 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8392:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8392 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8439:59: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8439 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:95: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8454:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8454 | __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:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8445:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8445 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8449:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8449 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so building 'mdtraj.formats.tng' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/bwlzh.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/bwt.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/coder.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/dict.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/fixpoint.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/huffman.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/huffmem.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/lz77.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/merge_sort.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/mtf.o mdtraj/formats/tng/src/compression/mtf.c: In function 'Ptngc_comp_conv_to_mtf': mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 196 | while (dict[ptr]!=v) | ^~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/rle.o mdtraj/formats/tng/src/compression/rle.c: In function 'Ptngc_comp_conv_to_rle': mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 56 | if (v==vals[i]) | ^~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/tng_compress.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/vals16.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/warnmalloc.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/widemuldiv.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/xtc2.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/xtc3.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/lib/md5.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/lib/tng_io.o mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_block_header_read': mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 1064 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 1073 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 1089 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 1098 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_output_file_endianness_get': mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast 9565 | if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast 9570 | else if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast 9588 | if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast 9593 | else if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_output_file_endianness_set': mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 9651 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 9660 | tng_data->output_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 9673 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 9682 | tng_data->output_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_block_add': mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^ mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5969:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'n_particles' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5684:13: note: 'n_particles' was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5962:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'num_first_particle' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5684:26: note: 'num_first_particle' was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/tng.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/tng.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, 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/tng/tng.c:810: /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 " \ | ^~~~~~~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__': mdtraj/formats/tng/tng.c:3706:104: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3706 | __pyx_t_1 = ((tng_util_trajectory_open(__pyx_v_filename, __pyx_v_self->mode, (&__pyx_v_self->_traj)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3761:88: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3761 | __pyx_t_1 = ((tng_num_particles_get(__pyx_v_self->_traj, (&__pyx_v_self->n_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3793:90: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3793 | __pyx_t_1 = ((tng_num_frames_get(__pyx_v_self->_traj, (&__pyx_v_self->tot_n_frames)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3825:95: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3825 | __pyx_t_1 = ((tng_distance_unit_exponential_get(__pyx_v_self->_traj, (&__pyx_v_exponent)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3895:113: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3895 | __pyx_t_1 = ((tng_num_frames_per_frame_set_get(__pyx_v_self->_traj, (&__pyx_v_self->_frames_per_frame_set)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3939:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3939 | __pyx_t_1 = ((tng_last_program_name_set(__pyx_v_self->_traj, __pyx_t_8) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_8_read_topology': mdtraj/formats/tng/tng.c:4735:106: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4735 | __pyx_t_7 = ((tng_chain_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4780:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4780 | __pyx_t_7 = ((tng_residue_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4887:115: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4887 | __pyx_t_8 = ((tng_global_residue_id_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, (&__pyx_v_residue_id)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4917:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4917 | __pyx_t_8 = ((tng_atom_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:5045:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5045 | __pyx_t_8 = ((tng_atom_type_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:5646:126: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5646 | __pyx_t_7 = ((tng_molsystem_bonds_get(__pyx_v_self->_traj, (&__pyx_v_n_bonds), (&__pyx_v_from_atoms), (&__pyx_v_to_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_10_read_frame': mdtraj/formats/tng/tng.c:6056:152: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6056 | __pyx_t_1 = ((tng_util_pos_read_range(__pyx_v_self->_traj, __pyx_v_self->_pos, __pyx_v_self->_pos, (&__pyx_v_positions), (&__pyx_v_stride_length)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:6324:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6324 | __pyx_t_1 = ((tng_util_time_of_frame_get(__pyx_v_self->_traj, __pyx_v_self->_pos, (&__pyx_v_frame_time)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:6426:304: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6426 | __pyx_t_1 = ((tng_data_vector_interval_get(__pyx_v_self->_traj, __pyx_v_6mdtraj_7formats_3tng_TNG_TRAJ_BOX_SHAPE, __pyx_v_self->_pos, __pyx_v_self->_pos, __pyx_e_6mdtraj_7formats_3tng_TNG_USE_HASH, (&__pyx_v_box_shape), (&__pyx_v_stride_length), (&__pyx_v_n_values_per_frame), (&__pyx_v_data_type)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_16write': mdtraj/formats/tng/tng.c:8918:94: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8918 | __pyx_t_1 = ((tng_implicit_num_particles_set(__pyx_v_self->_traj, __pyx_v_self->n_atoms) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:8950:75: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8950 | __pyx_t_1 = ((tng_util_pos_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:8982:81: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8982 | __pyx_t_1 = ((tng_util_box_shape_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9305:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9305 | __pyx_t_9 = ((tng_time_per_frame_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9496:372: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9496 | __pyx_t_1 = ((tng_util_pos_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz_array.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_xyz_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_xyz_array.diminfo[1].strides, __pyx_t_20, __pyx_pybuffernd_xyz_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9548:378: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9548 | __pyx_t_1 = ((tng_util_box_shape_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box_array.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_box_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_box_array.diminfo[1].strides, __pyx_t_18, __pyx_pybuffernd_box_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9610:89: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9610 | __pyx_t_1 = ((tng_frame_set_first_frame_time_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib/i386-linux-gnu -lz -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/tng.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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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:1940, 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:6646:17: 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:13600:20: note: in expansion of macro 'PyInt_FromLong' 13600 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:5465:7: note: '__pyx_v_i' was declared here 5465 | int __pyx_v_i; | ^~~~~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so building 'mdtraj.formats.binpos' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/binpos/binpos.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:1940, 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/binpos/binpos.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_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read', inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:5526:6: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 5526 | if (__pyx_t_2) { | ^ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5006:7: note: '__pyx_v_status' was declared here 5006 | int __pyx_v_status; | ^~~~~~~~~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read' at mdtraj/formats/binpos/binpos.c:5536:17, inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:694:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 694 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/binpos/binpos.c:13100:20: note: in expansion of macro 'PyInt_FromLong' 13100 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5003:7: note: '__pyx_v_i' was declared here 5003 | int __pyx_v_i; | ^~~~~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/binpos/src/binposplugin.c: In function 'open_binpos_read': mdtraj/formats/binpos/src/binposplugin.c:59:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | fread(magicchar,sizeof(char),4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/binpos/src/binposplugin.c:69:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fread(&igarb,sizeof(int),1,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/binpos/binpos.o build/temp.linux-i686-cpython-312/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/binpos.cpython-312-i386-linux-gnu.so building 'mdtraj.formats.dtr' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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:1940, 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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 constructor '{anonymous}::DDException::DDException(const std::string&, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: '*this.{anonymous}::DDException::eno' is used uninitialized [-Wuninitialized] 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} | ~~~~~~~~^~~~~ 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:906, 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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-i386-linux-gnu.so building 'mdtraj._rmsd' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so building 'mdtraj._lprmsd' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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:1940, 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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry._geometry' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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:1940, 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 " \ | ^~~~~~~ mdtraj/geometry/src/_geometry.cpp: In function 'void __pyx_f_6mdtraj_8geometry_9_geometry_make_whole(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice)': mdtraj/geometry/src/_geometry.cpp:6131:296: warning: '__pyx_v_offset[1]' may be used uninitialized [-Wmaybe-uninitialized] 6131 | (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) ))))))); | ~~~~~~~~~~~~~~~~~^~ mdtraj/geometry/src/_geometry.cpp:6037:9: note: '__pyx_v_offset[1]' was declared here 6037 | float __pyx_v_offset[3]; | ^~~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6131:274: warning: '__pyx_v_delta[1]' may be used uninitialized [-Wmaybe-uninitialized] 6131 | (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) ))))))); | ~~~~~~~~~~~~~~~~^~ mdtraj/geometry/src/_geometry.cpp:6038:9: note: '__pyx_v_delta[1]' was declared here 6038 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6117:242: warning: '__pyx_v_delta[2]' may be used uninitialized [-Wmaybe-uninitialized] 6117 | (__pyx_v_offset[__pyx_v_k]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_8 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_7)) ))) * roundf(((__pyx_v_delta[2]) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_5 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_4)) )))))); | ~~~~~~~~~~~~~~~~^~ mdtraj/geometry/src/_geometry.cpp:6038:9: note: '__pyx_v_delta[2]' was declared here 6038 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.drid' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.neighbors' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:50:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:51:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 51 | periodicBoxSize[1] = periodicBoxVectors[1][1]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:52:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 52 | periodicBoxSize[2] = periodicBoxVectors[2][2]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:56:45: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so 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/13/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-13' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --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-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 13.2.0 (Debian 13.2.0-13) 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 [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/12] Cythonizing mdtraj/geometry/drid.pyx [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx running build running build_py copying mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj running build_ext building 'mdtraj.formats.xtc' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-i686-cpython-311/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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-i686-cpython-311/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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-i686-cpython-311/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:1940, 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:9850:16: 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:19348:20: note: in expansion of macro 'PyInt_FromLong' 19348 | 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:9570:7: note: '__pyx_v_status' was declared here 9570 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:7672:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7672 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7676:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 7676 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8053:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8053 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8057:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8057 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8061:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8061 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8099:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8099 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6480:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 6480 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8023:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8023 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6484:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 6484 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8041:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8041 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6488:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 6488 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8081:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8081 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8085:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8085 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8089:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8089 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/xtc.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/xtc.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.trr' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-i686-cpython-311/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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-i686-cpython-311/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:1940, 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:11623:16: 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:21046:20: note: in expansion of macro 'PyInt_FromLong' 21046 | 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:11096:7: note: '__pyx_v_status' was declared here 11096 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:8671:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8671 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8675:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8675 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8619:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8619 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8623:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8623 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8778:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8778 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8782:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8782 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8382:56: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8382 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:95: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8397:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8397 | __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:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8388:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8388 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8392:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8392 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8439:59: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8439 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:95: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8454:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8454 | __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:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8445:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8445 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8449:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8449 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/trr.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/trr.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.tng' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/bwlzh.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/bwt.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/coder.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/dict.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/fixpoint.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/huffman.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/huffmem.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/lz77.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/merge_sort.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/mtf.o mdtraj/formats/tng/src/compression/mtf.c: In function 'Ptngc_comp_conv_to_mtf': mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 196 | while (dict[ptr]!=v) | ^~ i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/rle.o mdtraj/formats/tng/src/compression/rle.c: In function 'Ptngc_comp_conv_to_rle': mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 56 | if (v==vals[i]) | ^~ i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/tng_compress.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/vals16.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/warnmalloc.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/widemuldiv.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/xtc2.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/xtc3.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/lib/md5.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/lib/tng_io.o mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_block_header_read': mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 1064 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 1073 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 1089 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 1098 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_output_file_endianness_get': mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast 9565 | if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast 9570 | else if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast 9588 | if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast 9593 | else if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_output_file_endianness_set': mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 9651 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 9660 | tng_data->output_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 9673 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 9682 | tng_data->output_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_block_add': mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^ mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5969:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'n_particles' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5684:13: note: 'n_particles' was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5962:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'num_first_particle' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5684:26: note: 'num_first_particle' was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/tng.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/tng.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, 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/tng/tng.c:810: /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 " \ | ^~~~~~~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__': mdtraj/formats/tng/tng.c:3706:104: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3706 | __pyx_t_1 = ((tng_util_trajectory_open(__pyx_v_filename, __pyx_v_self->mode, (&__pyx_v_self->_traj)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3761:88: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3761 | __pyx_t_1 = ((tng_num_particles_get(__pyx_v_self->_traj, (&__pyx_v_self->n_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3793:90: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3793 | __pyx_t_1 = ((tng_num_frames_get(__pyx_v_self->_traj, (&__pyx_v_self->tot_n_frames)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3825:95: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3825 | __pyx_t_1 = ((tng_distance_unit_exponential_get(__pyx_v_self->_traj, (&__pyx_v_exponent)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3895:113: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3895 | __pyx_t_1 = ((tng_num_frames_per_frame_set_get(__pyx_v_self->_traj, (&__pyx_v_self->_frames_per_frame_set)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3939:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3939 | __pyx_t_1 = ((tng_last_program_name_set(__pyx_v_self->_traj, __pyx_t_8) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_8_read_topology': mdtraj/formats/tng/tng.c:4735:106: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4735 | __pyx_t_7 = ((tng_chain_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4780:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4780 | __pyx_t_7 = ((tng_residue_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4887:115: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4887 | __pyx_t_8 = ((tng_global_residue_id_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, (&__pyx_v_residue_id)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4917:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4917 | __pyx_t_8 = ((tng_atom_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:5045:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5045 | __pyx_t_8 = ((tng_atom_type_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:5646:126: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5646 | __pyx_t_7 = ((tng_molsystem_bonds_get(__pyx_v_self->_traj, (&__pyx_v_n_bonds), (&__pyx_v_from_atoms), (&__pyx_v_to_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_10_read_frame': mdtraj/formats/tng/tng.c:6056:152: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6056 | __pyx_t_1 = ((tng_util_pos_read_range(__pyx_v_self->_traj, __pyx_v_self->_pos, __pyx_v_self->_pos, (&__pyx_v_positions), (&__pyx_v_stride_length)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:6324:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6324 | __pyx_t_1 = ((tng_util_time_of_frame_get(__pyx_v_self->_traj, __pyx_v_self->_pos, (&__pyx_v_frame_time)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:6426:304: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6426 | __pyx_t_1 = ((tng_data_vector_interval_get(__pyx_v_self->_traj, __pyx_v_6mdtraj_7formats_3tng_TNG_TRAJ_BOX_SHAPE, __pyx_v_self->_pos, __pyx_v_self->_pos, __pyx_e_6mdtraj_7formats_3tng_TNG_USE_HASH, (&__pyx_v_box_shape), (&__pyx_v_stride_length), (&__pyx_v_n_values_per_frame), (&__pyx_v_data_type)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_16write': mdtraj/formats/tng/tng.c:8918:94: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8918 | __pyx_t_1 = ((tng_implicit_num_particles_set(__pyx_v_self->_traj, __pyx_v_self->n_atoms) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:8950:75: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8950 | __pyx_t_1 = ((tng_util_pos_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:8982:81: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8982 | __pyx_t_1 = ((tng_util_box_shape_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9305:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9305 | __pyx_t_9 = ((tng_time_per_frame_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9496:372: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9496 | __pyx_t_1 = ((tng_util_pos_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz_array.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_xyz_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_xyz_array.diminfo[1].strides, __pyx_t_20, __pyx_pybuffernd_xyz_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9548:378: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9548 | __pyx_t_1 = ((tng_util_box_shape_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box_array.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_box_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_box_array.diminfo[1].strides, __pyx_t_18, __pyx_pybuffernd_box_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9610:89: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9610 | __pyx_t_1 = ((tng_frame_set_first_frame_time_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib/i386-linux-gnu -lz -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/tng.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.dcd' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-i686-cpython-311/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:1940, 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:6646:17: 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:13600:20: note: in expansion of macro 'PyInt_FromLong' 13600 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:5465:7: note: '__pyx_v_i' was declared here 5465 | int __pyx_v_i; | ^~~~~~~~~ i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-i686-cpython-311/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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/formats/dcd/dcd.o build/temp.linux-i686-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dcd.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.binpos' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/binpos/binpos.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:1940, 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/binpos/binpos.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_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read', inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:5526:6: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 5526 | if (__pyx_t_2) { | ^ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5006:7: note: '__pyx_v_status' was declared here 5006 | int __pyx_v_status; | ^~~~~~~~~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read' at mdtraj/formats/binpos/binpos.c:5536:17, inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:694:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 694 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/binpos/binpos.c:13100:20: note: in expansion of macro 'PyInt_FromLong' 13100 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5003:7: note: '__pyx_v_i' was declared here 5003 | int __pyx_v_i; | ^~~~~~~~~ i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/binpos/src/binposplugin.c: In function 'open_binpos_read': mdtraj/formats/binpos/src/binposplugin.c:59:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | fread(magicchar,sizeof(char),4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/binpos/src/binposplugin.c:69:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fread(&igarb,sizeof(int),1,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/formats/binpos/binpos.o build/temp.linux-i686-cpython-311/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/binpos.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.dtr' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-i686-cpython-311/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:1940, 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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-i686-cpython-311/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 constructor '{anonymous}::DDException::DDException(const std::string&, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: '*this.{anonymous}::DDException::eno' is used uninitialized [-Wuninitialized] 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} | ~~~~~~~~^~~~~ 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:906, 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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/formats/dtr/dtr.o build/temp.linux-i686-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dtr.cpython-311-i386-linux-gnu.so building 'mdtraj._rmsd' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-i686-cpython-311/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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/rmsd/_rmsd.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_rmsd.cpython-311-i386-linux-gnu.so building 'mdtraj._lprmsd' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-i686-cpython-311/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:1940, 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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-i686-cpython-311/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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/rmsd/_lprmsd.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/Munkres.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/fancy_index.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_lprmsd.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry._geometry' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-i686-cpython-311/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:1940, 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 " \ | ^~~~~~~ mdtraj/geometry/src/_geometry.cpp: In function 'void __pyx_f_6mdtraj_8geometry_9_geometry_make_whole(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice)': mdtraj/geometry/src/_geometry.cpp:6131:296: warning: '__pyx_v_offset[1]' may be used uninitialized [-Wmaybe-uninitialized] 6131 | (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) ))))))); | ~~~~~~~~~~~~~~~~~^~ mdtraj/geometry/src/_geometry.cpp:6037:9: note: '__pyx_v_offset[1]' was declared here 6037 | float __pyx_v_offset[3]; | ^~~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6131:274: warning: '__pyx_v_delta[1]' may be used uninitialized [-Wmaybe-uninitialized] 6131 | (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) ))))))); | ~~~~~~~~~~~~~~~~^~ mdtraj/geometry/src/_geometry.cpp:6038:9: note: '__pyx_v_delta[1]' was declared here 6038 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6117:242: warning: '__pyx_v_delta[2]' may be used uninitialized [-Wmaybe-uninitialized] 6117 | (__pyx_v_offset[__pyx_v_k]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_8 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_7)) ))) * roundf(((__pyx_v_delta[2]) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_5 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_4)) )))))); | ~~~~~~~~~~~~~~~~^~ mdtraj/geometry/src/_geometry.cpp:6038:9: note: '__pyx_v_delta[2]' was declared here 6038 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-i686-cpython-311/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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/geometry/src/_geometry.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/dssp.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/geometry.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/sasa.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/_geometry.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry.drid' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/drid.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-i686-cpython-311/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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/geometry/drid.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/dridkernels.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/moments.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/drid.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry.neighbors' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-i686-cpython-311/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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/geometry/neighbors.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/neighbors.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighbors.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:50:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:51:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 51 | periodicBoxSize[1] = periodicBoxVectors[1][1]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:52:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 52 | periodicBoxSize[2] = periodicBoxVectors[2][2]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:56:45: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/geometry/neighborlist.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/neighborlist.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighborlist.cpython-311-i386-linux-gnu.so dh_auto_test -O--buildsystem=pybuild pybuild --test -i python{version} -p "3.12 3.11" I: pybuild base:311: cd /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build; python3.12 -m unittest discover -v /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/netcdf.py:217: SyntaxWarning: invalid escape sequence '\g' """Read data from a molecular dynamics trajectory in the AMBER NetCDF /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/netcdf.py:323: SyntaxWarning: invalid escape sequence '\g' """Write one or more frames of a molecular dynamics trajectory to disk /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/amberrst.py:271: SyntaxWarning: invalid escape sequence '\g' """Read data from an AMBER ASCII restart file /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/amberrst.py:534: SyntaxWarning: invalid escape sequence '\g' """Read data from an AMBER NetCDF restart file /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lammpstrj.py:237: SyntaxWarning: invalid escape sequence '\g' """Read data from a lammpstrj file. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lammpstrj.py:429: SyntaxWarning: invalid escape sequence '\g' """Write the box lines in the header of a frame. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lammpstrj.py:476: SyntaxWarning: invalid escape sequence '\g' """Write one or more frames of data to a lammpstrj file. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gro.py:394: SyntaxWarning: invalid escape sequence '\d' time = float(findall('t= *(\d+\.\d+)',comment)[-1]) /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gro.py:500: SyntaxWarning: invalid escape sequence '\.' return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/prmtop.py:63: SyntaxWarning: invalid escape sequence '\.' FORMAT_RE_PATTERN = re.compile("([0-9]+)([a-zA-Z]+)([0-9]+)\.?([0-9]*)") /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/mol2.py:215: SyntaxWarning: invalid escape sequence '\s' index_col=0, header=None, sep="\s+", engine='python') /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/mol2.py:222: SyntaxWarning: invalid escape sequence '\s' atoms_frame = pd.read_csv(csv, sep="\s+", engine='python', header=None) /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/hbond.py:251: SyntaxWarning: invalid escape sequence '\c' """Compute the Kabsch-Sander hydrogen bond energy between each pair /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/contact.py:44: SyntaxWarning: invalid escape sequence '\s' """Compute the distance between pairs of residues in a trajectory. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:80: SyntaxWarning: invalid escape sequence '\l' """Compute the asphericity of a trajectory. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:105: SyntaxWarning: invalid escape sequence '\l' """Compute the acylindricity of a trajectory. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:130: SyntaxWarning: invalid escape sequence '\k' """Compute the relative shape anisotropy of a trajectory. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gsd.py:228: SyntaxWarning: invalid escape sequence '\g' """Write one or more frames of data to a gsd file. /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/shift_wrappers.py:214: SyntaxWarning: invalid escape sequence '\s' d = pd.read_table("./bb_details.dat", index_col=False, header=None, sep="\s+").drop([3], axis=1) /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/shift_wrappers.py:292: SyntaxWarning: invalid escape sequence '\s' d = pd.read_table("./trj%d_pred.tab" % i, names=names, header=None, sep="\s+", skiprows=lines_to_skip) /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docstrings.py:126: SyntaxWarning: invalid escape sequence '\d' m = re.search('takes at most (\d+) positional arguments', str(e)) /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docscrape.py:305: SyntaxWarning: invalid escape sequence '\w' if re.compile('^([\w., ]+=)?\s*[\w\.]+\(.*\)$').match(summary_str): /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docscrape.py:345: SyntaxWarning: invalid escape sequence '\*' return [self['Signature'].replace('*','\*')] + [''] /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docscrape.py:464: SyntaxWarning: invalid escape sequence '\*' argspec = argspec.replace('*','\*') /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docscrape.py:482: SyntaxWarning: invalid escape sequence '\*' signature = self['Signature'].replace('*', '\*') ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN I: pybuild base:311: cd /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build; python3.11 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s OK rm -fr -- /tmp/dh-xdg-rundir-sZ3GG0vo 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-1.9.9/debian/tmp pybuild --install -i python{version} -p "3.12 3.11" --dest-dir /build/reproducible-path/mdtraj-1.9.9/debian/tmp I: pybuild base:311: /usr/bin/python3.12 setup.py install --root /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-linux-gnu/13/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-13' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --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-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 13.2.0 (Debian 13.2.0-13) 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 [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/12] Cythonizing mdtraj/geometry/drid.pyx [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [12/12] 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-1.9.9/.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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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:1940, 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:9850:16: 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:19348:20: note: in expansion of macro 'PyInt_FromLong' 19348 | 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:9570:7: note: '__pyx_v_status' was declared here 9570 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:7672:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7672 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7676:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 7676 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8053:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8053 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8057:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8057 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8061:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8061 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8099:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8099 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6480:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 6480 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8023:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8023 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6484:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 6484 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8041:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8041 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6488:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 6488 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8081:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8081 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8085:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8085 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8089:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8089 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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:1940, 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:11623:16: 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:21046:20: note: in expansion of macro 'PyInt_FromLong' 21046 | 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:11096:7: note: '__pyx_v_status' was declared here 11096 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:8671:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8671 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8675:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8675 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8619:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8619 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8623:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8623 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8778:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8778 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8782:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8782 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8382:56: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8382 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:95: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8397:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8397 | __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:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8388:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8388 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8392:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8392 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8439:59: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8439 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:95: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8454:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8454 | __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:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8445:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8445 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8449:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8449 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so building 'mdtraj.formats.tng' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/bwlzh.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/bwt.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/coder.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/dict.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/fixpoint.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/huffman.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/huffmem.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/lz77.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/merge_sort.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/mtf.o mdtraj/formats/tng/src/compression/mtf.c: In function 'Ptngc_comp_conv_to_mtf': mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 196 | while (dict[ptr]!=v) | ^~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/rle.o mdtraj/formats/tng/src/compression/rle.c: In function 'Ptngc_comp_conv_to_rle': mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 56 | if (v==vals[i]) | ^~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/tng_compress.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/vals16.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/warnmalloc.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/widemuldiv.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/xtc2.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/xtc3.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/lib/md5.o i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/lib/tng_io.o mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_block_header_read': mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 1064 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 1073 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 1089 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 1098 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_output_file_endianness_get': mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast 9565 | if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast 9570 | else if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast 9588 | if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast 9593 | else if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_output_file_endianness_set': mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 9651 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 9660 | tng_data->output_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 9673 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 9682 | tng_data->output_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_block_add': mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^ mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5969:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'n_particles' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5684:13: note: 'n_particles' was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5962:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'num_first_particle' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5684:26: note: 'num_first_particle' was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/tng/tng.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/tng.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, 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/tng/tng.c:810: /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 " \ | ^~~~~~~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__': mdtraj/formats/tng/tng.c:3706:104: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3706 | __pyx_t_1 = ((tng_util_trajectory_open(__pyx_v_filename, __pyx_v_self->mode, (&__pyx_v_self->_traj)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3761:88: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3761 | __pyx_t_1 = ((tng_num_particles_get(__pyx_v_self->_traj, (&__pyx_v_self->n_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3793:90: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3793 | __pyx_t_1 = ((tng_num_frames_get(__pyx_v_self->_traj, (&__pyx_v_self->tot_n_frames)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3825:95: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3825 | __pyx_t_1 = ((tng_distance_unit_exponential_get(__pyx_v_self->_traj, (&__pyx_v_exponent)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3895:113: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3895 | __pyx_t_1 = ((tng_num_frames_per_frame_set_get(__pyx_v_self->_traj, (&__pyx_v_self->_frames_per_frame_set)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3939:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3939 | __pyx_t_1 = ((tng_last_program_name_set(__pyx_v_self->_traj, __pyx_t_8) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_8_read_topology': mdtraj/formats/tng/tng.c:4735:106: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4735 | __pyx_t_7 = ((tng_chain_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4780:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4780 | __pyx_t_7 = ((tng_residue_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4887:115: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4887 | __pyx_t_8 = ((tng_global_residue_id_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, (&__pyx_v_residue_id)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4917:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4917 | __pyx_t_8 = ((tng_atom_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:5045:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5045 | __pyx_t_8 = ((tng_atom_type_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:5646:126: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5646 | __pyx_t_7 = ((tng_molsystem_bonds_get(__pyx_v_self->_traj, (&__pyx_v_n_bonds), (&__pyx_v_from_atoms), (&__pyx_v_to_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_10_read_frame': mdtraj/formats/tng/tng.c:6056:152: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6056 | __pyx_t_1 = ((tng_util_pos_read_range(__pyx_v_self->_traj, __pyx_v_self->_pos, __pyx_v_self->_pos, (&__pyx_v_positions), (&__pyx_v_stride_length)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:6324:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6324 | __pyx_t_1 = ((tng_util_time_of_frame_get(__pyx_v_self->_traj, __pyx_v_self->_pos, (&__pyx_v_frame_time)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:6426:304: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6426 | __pyx_t_1 = ((tng_data_vector_interval_get(__pyx_v_self->_traj, __pyx_v_6mdtraj_7formats_3tng_TNG_TRAJ_BOX_SHAPE, __pyx_v_self->_pos, __pyx_v_self->_pos, __pyx_e_6mdtraj_7formats_3tng_TNG_USE_HASH, (&__pyx_v_box_shape), (&__pyx_v_stride_length), (&__pyx_v_n_values_per_frame), (&__pyx_v_data_type)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_16write': mdtraj/formats/tng/tng.c:8918:94: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8918 | __pyx_t_1 = ((tng_implicit_num_particles_set(__pyx_v_self->_traj, __pyx_v_self->n_atoms) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:8950:75: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8950 | __pyx_t_1 = ((tng_util_pos_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:8982:81: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8982 | __pyx_t_1 = ((tng_util_box_shape_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9305:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9305 | __pyx_t_9 = ((tng_time_per_frame_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9496:372: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9496 | __pyx_t_1 = ((tng_util_pos_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz_array.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_xyz_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_xyz_array.diminfo[1].strides, __pyx_t_20, __pyx_pybuffernd_xyz_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9548:378: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9548 | __pyx_t_1 = ((tng_util_box_shape_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box_array.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_box_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_box_array.diminfo[1].strides, __pyx_t_18, __pyx_pybuffernd_box_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9610:89: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9610 | __pyx_t_1 = ((tng_frame_set_first_frame_time_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-i686-cpython-312/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib/i386-linux-gnu -lz -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/tng.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 -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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:1940, 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:6646:17: 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:13600:20: note: in expansion of macro 'PyInt_FromLong' 13600 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:5465:7: note: '__pyx_v_i' was declared here 5465 | int __pyx_v_i; | ^~~~~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so building 'mdtraj.formats.binpos' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/binpos/binpos.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:1940, 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/binpos/binpos.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_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read', inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:5526:6: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 5526 | if (__pyx_t_2) { | ^ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5006:7: note: '__pyx_v_status' was declared here 5006 | int __pyx_v_status; | ^~~~~~~~~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read' at mdtraj/formats/binpos/binpos.c:5536:17, inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:694:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 694 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/binpos/binpos.c:13100:20: note: in expansion of macro 'PyInt_FromLong' 13100 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5003:7: note: '__pyx_v_i' was declared here 5003 | int __pyx_v_i; | ^~~~~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/binpos/src/binposplugin.c: In function 'open_binpos_read': mdtraj/formats/binpos/src/binposplugin.c:59:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | fread(magicchar,sizeof(char),4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/binpos/src/binposplugin.c:69:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fread(&igarb,sizeof(int),1,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/binpos/binpos.o build/temp.linux-i686-cpython-312/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/binpos.cpython-312-i386-linux-gnu.so building 'mdtraj.formats.dtr' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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:1940, 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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 constructor '{anonymous}::DDException::DDException(const std::string&, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: '*this.{anonymous}::DDException::eno' is used uninitialized [-Wuninitialized] 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} | ~~~~~~~~^~~~~ 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:906, 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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-i386-linux-gnu.so building 'mdtraj._rmsd' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so building 'mdtraj._lprmsd' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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:1940, 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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry._geometry' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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:1940, 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 " \ | ^~~~~~~ mdtraj/geometry/src/_geometry.cpp: In function 'void __pyx_f_6mdtraj_8geometry_9_geometry_make_whole(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice)': mdtraj/geometry/src/_geometry.cpp:6131:296: warning: '__pyx_v_offset[1]' may be used uninitialized [-Wmaybe-uninitialized] 6131 | (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) ))))))); | ~~~~~~~~~~~~~~~~~^~ mdtraj/geometry/src/_geometry.cpp:6037:9: note: '__pyx_v_offset[1]' was declared here 6037 | float __pyx_v_offset[3]; | ^~~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6131:274: warning: '__pyx_v_delta[1]' may be used uninitialized [-Wmaybe-uninitialized] 6131 | (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) ))))))); | ~~~~~~~~~~~~~~~~^~ mdtraj/geometry/src/_geometry.cpp:6038:9: note: '__pyx_v_delta[1]' was declared here 6038 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6117:242: warning: '__pyx_v_delta[2]' may be used uninitialized [-Wmaybe-uninitialized] 6117 | (__pyx_v_offset[__pyx_v_k]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_8 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_7)) ))) * roundf(((__pyx_v_delta[2]) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_5 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_4)) )))))); | ~~~~~~~~~~~~~~~~^~ mdtraj/geometry/src/_geometry.cpp:6038:9: note: '__pyx_v_delta[2]' was declared here 6038 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.drid' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.neighbors' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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 In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:50:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:51:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 51 | periodicBoxSize[1] = periodicBoxVectors[1][1]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:52:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 52 | periodicBoxSize[2] = periodicBoxVectors[2][2]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:56:45: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so running install_lib creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12 creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/dcdreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/netcdfreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/basereporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/hdf5reporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/xtcreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/io.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/libtheobald.a -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/theobald_rmsd.h -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/center.h -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/topology.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/trajectory.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/residue_names.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/selection.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/element.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/docstrings.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/testing.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/docscrape.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/scalar_couplings.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/shift_wrappers.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/six.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_definitions.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/standard_dimensions.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/baseunit.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/mymatrix.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_operators.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/basedimension.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/prefix.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/quantity.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/rotation.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/unitcell.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/zipped.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/six.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/contextmanagers.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/validation.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/singleton.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/delay_import.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/tng.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/hoomdxml.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/xyzfile.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/lh5.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/arc.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/gro.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/prmtop.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/openmmxml.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/hdf5.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/lammpstrj.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/mdcrd.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/mol2.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/psf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/registry.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/netcdf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/amberrst.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/gsd.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/pdbx.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbfile.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbstructure.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/binpos.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/dihedral.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/order.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/dssp.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/contact.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/shape.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/rg.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/sasa.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/rdf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/angle.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/thermodynamic_properties.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/distance.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/hbond.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__pycache__/version.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__ creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/io.py to io.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/version.py to version.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/trajectory.py to trajectory.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/element.py to element.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/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-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/selection.py to selection.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/topology.py to topology.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/docstrings.py to docstrings.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/testing/docstrings.py:126: SyntaxWarning: invalid escape sequence '\d' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/docscrape.py to docscrape.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/testing/docscrape.py:305: SyntaxWarning: invalid escape sequence '\w' /usr/lib/python3.12/dist-packages/mdtraj/testing/docscrape.py:345: SyntaxWarning: invalid escape sequence '\*' /usr/lib/python3.12/dist-packages/mdtraj/testing/docscrape.py:464: SyntaxWarning: invalid escape sequence '\*' /usr/lib/python3.12/dist-packages/mdtraj/testing/docscrape.py:482: SyntaxWarning: invalid escape sequence '\*' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/testing.py to testing.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/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-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/shift_wrappers.py to shift_wrappers.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/nmr/shift_wrappers.py:214: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/mdtraj/nmr/shift_wrappers.py:292: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/zipped.py to zipped.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/rotation.py to rotation.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/singleton.py to singleton.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/validation.py to validation.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unitcell.py to unitcell.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/six.py to six.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/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-1.9.9/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-1.9.9/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-1.9.9/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-1.9.9/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-1.9.9/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-1.9.9/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-1.9.9/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-1.9.9/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-1.9.9/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-1.9.9/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-1.9.9/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-1.9.9/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-1.9.9/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-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/lh5.py to lh5.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/psf.py to psf.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/amberrst.py to amberrst.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/formats/amberrst.py:271: SyntaxWarning: invalid escape sequence '\g' /usr/lib/python3.12/dist-packages/mdtraj/formats/amberrst.py:534: SyntaxWarning: invalid escape sequence '\g' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/formats/lammpstrj.py:237: SyntaxWarning: invalid escape sequence '\g' /usr/lib/python3.12/dist-packages/mdtraj/formats/lammpstrj.py:429: SyntaxWarning: invalid escape sequence '\g' /usr/lib/python3.12/dist-packages/mdtraj/formats/lammpstrj.py:476: SyntaxWarning: invalid escape sequence '\g' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/registry.py to registry.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/prmtop.py to prmtop.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/formats/prmtop.py:63: SyntaxWarning: invalid escape sequence '\.' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/mol2.py to mol2.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/formats/mol2.py:215: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/mdtraj/formats/mol2.py:222: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/gro.py to gro.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/formats/gro.py:394: SyntaxWarning: invalid escape sequence '\d' /usr/lib/python3.12/dist-packages/mdtraj/formats/gro.py:500: SyntaxWarning: invalid escape sequence '\.' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/arc.py to arc.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/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-1.9.9/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-1.9.9/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-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/netcdf.py to netcdf.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/formats/netcdf.py:217: SyntaxWarning: invalid escape sequence '\g' /usr/lib/python3.12/dist-packages/mdtraj/formats/netcdf.py:323: SyntaxWarning: invalid escape sequence '\g' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/gsd.py to gsd.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/formats/gsd.py:228: SyntaxWarning: invalid escape sequence '\g' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdbx.py to pdbx.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/hdf5.py to hdf5.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/shape.py to shape.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/geometry/shape.py:80: SyntaxWarning: invalid escape sequence '\l' /usr/lib/python3.12/dist-packages/mdtraj/geometry/shape.py:105: SyntaxWarning: invalid escape sequence '\l' /usr/lib/python3.12/dist-packages/mdtraj/geometry/shape.py:130: SyntaxWarning: invalid escape sequence '\k' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/rg.py to rg.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/contact.py to contact.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/geometry/contact.py:44: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/alignment.py to alignment.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/dssp.py to dssp.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/angle.py to angle.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/hbond.py to hbond.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/geometry/hbond.py:251: SyntaxWarning: invalid escape sequence '\c' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/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-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/order.py to order.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/internal.py to internal.cpython-312.pyc /usr/lib/python3.12/dist-packages/mdtraj/geometry/internal.py:370: SyntaxWarning: invalid escape sequence '\p' byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/distance.py to distance.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/rdf.py to rdf.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/sasa.py to sasa.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/mdconvert.py to mdconvert.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 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-1.9.9/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj-1.9.9.egg-info Skipping SOURCES.txt running install_scripts Installing mdconvert-mdtraj script to /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/bin Installing mdinspect script to /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/bin I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-linux-gnu/13/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-13' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --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-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 13.2.0 (Debian 13.2.0-13) 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 [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/12] Cythonizing mdtraj/geometry/drid.pyx [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx [12/12] 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-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj running build_ext building 'mdtraj.formats.xtc' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-i686-cpython-311/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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-i686-cpython-311/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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-i686-cpython-311/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:1940, 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:9850:16: 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:19348:20: note: in expansion of macro 'PyInt_FromLong' 19348 | 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:9570:7: note: '__pyx_v_status' was declared here 9570 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:7672:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7672 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7676:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 7676 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6476:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8053:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8053 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8057:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8057 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8061:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8061 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6474:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8099:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8099 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6480:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 6480 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8023:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8023 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6484:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 6484 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8041:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8041 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6488:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 6488 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8081:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8081 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8085:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8085 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8089:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8089 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6492:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/xtc.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/xtc.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.trr' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-i686-cpython-311/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 -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-i686-cpython-311/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:1940, 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:11623:16: 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:21046:20: note: in expansion of macro 'PyInt_FromLong' 21046 | 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:11096:7: note: '__pyx_v_status' was declared here 11096 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:8671:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8671 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8675:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8675 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6988:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8619:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8619 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8623:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8623 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7004:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8778:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8778 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8782:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8782 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7008:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8382:56: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8382 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:95: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8397:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8397 | __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:7002:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8388:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8388 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8392:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8392 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:7002:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8439:59: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8439 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1935:95: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:8454:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 8454 | __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:6986:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8445:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8445 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8449:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8449 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6986:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-i686-cpython-311/mdtraj/formats/xtc/trr.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/trr.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.tng' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/bwlzh.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/bwt.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/coder.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/dict.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/fixpoint.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/huffman.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/huffmem.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/lz77.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/merge_sort.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/mtf.o mdtraj/formats/tng/src/compression/mtf.c: In function 'Ptngc_comp_conv_to_mtf': mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 196 | while (dict[ptr]!=v) | ^~ i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/rle.o mdtraj/formats/tng/src/compression/rle.c: In function 'Ptngc_comp_conv_to_rle': mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 56 | if (v==vals[i]) | ^~ i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/tng_compress.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/vals16.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/warnmalloc.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/widemuldiv.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/xtc2.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/xtc3.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/lib/md5.o i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/lib/tng_io.o mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_block_header_read': mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 1064 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 1073 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 1089 | tng_data->input_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 1098 | tng_data->input_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_output_file_endianness_get': mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast 9565 | if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast 9570 | else if(tng_data->output_endianness_swap_func_32 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast 9588 | if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast 9593 | else if(tng_data->output_endianness_swap_func_64 == | ^~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_output_file_endianness_set': mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 9651 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 9660 | tng_data->output_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint32_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, unsigned int *)'} [-Wincompatible-pointer-types] 9673 | tng_data->output_endianness_swap_func_32 = | ^ mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to 'tng_function_status (*)(struct tng_trajectory * const, int64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long int *)'} from incompatible pointer type 'tng_function_status (*)(struct tng_trajectory * const, uint64_t *)' {aka 'tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)'} [-Wincompatible-pointer-types] 9682 | tng_data->output_endianness_swap_func_64 = | ^ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_gen_data_block_add': mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^ mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5969:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'n_particles' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5684:13: note: 'n_particles' was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~ In function 'tng_file_output_numerical', inlined from 'tng_data_block_write.isra' at mdtraj/formats/tng/src/lib/tng_io.c:5962:12: mdtraj/formats/tng/src/lib/tng_io.c:759:22: warning: 'num_first_particle' may be used uninitialized [-Wmaybe-uninitialized] 759 | temp_i64 = *((int64_t *)src); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5684:26: note: 'num_first_particle' was declared here 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; | ^~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/tng.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/tng.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940, 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/tng/tng.c:810: /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 " \ | ^~~~~~~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__': mdtraj/formats/tng/tng.c:3706:104: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3706 | __pyx_t_1 = ((tng_util_trajectory_open(__pyx_v_filename, __pyx_v_self->mode, (&__pyx_v_self->_traj)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3761:88: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3761 | __pyx_t_1 = ((tng_num_particles_get(__pyx_v_self->_traj, (&__pyx_v_self->n_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3793:90: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3793 | __pyx_t_1 = ((tng_num_frames_get(__pyx_v_self->_traj, (&__pyx_v_self->tot_n_frames)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3825:95: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3825 | __pyx_t_1 = ((tng_distance_unit_exponential_get(__pyx_v_self->_traj, (&__pyx_v_exponent)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3895:113: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3895 | __pyx_t_1 = ((tng_num_frames_per_frame_set_get(__pyx_v_self->_traj, (&__pyx_v_self->_frames_per_frame_set)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:3939:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3939 | __pyx_t_1 = ((tng_last_program_name_set(__pyx_v_self->_traj, __pyx_t_8) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_8_read_topology': mdtraj/formats/tng/tng.c:4735:106: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4735 | __pyx_t_7 = ((tng_chain_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4780:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4780 | __pyx_t_7 = ((tng_residue_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4887:115: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4887 | __pyx_t_8 = ((tng_global_residue_id_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, (&__pyx_v_residue_id)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:4917:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4917 | __pyx_t_8 = ((tng_atom_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:5045:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5045 | __pyx_t_8 = ((tng_atom_type_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:5646:126: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5646 | __pyx_t_7 = ((tng_molsystem_bonds_get(__pyx_v_self->_traj, (&__pyx_v_n_bonds), (&__pyx_v_from_atoms), (&__pyx_v_to_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_10_read_frame': mdtraj/formats/tng/tng.c:6056:152: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6056 | __pyx_t_1 = ((tng_util_pos_read_range(__pyx_v_self->_traj, __pyx_v_self->_pos, __pyx_v_self->_pos, (&__pyx_v_positions), (&__pyx_v_stride_length)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:6324:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6324 | __pyx_t_1 = ((tng_util_time_of_frame_get(__pyx_v_self->_traj, __pyx_v_self->_pos, (&__pyx_v_frame_time)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:6426:304: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6426 | __pyx_t_1 = ((tng_data_vector_interval_get(__pyx_v_self->_traj, __pyx_v_6mdtraj_7formats_3tng_TNG_TRAJ_BOX_SHAPE, __pyx_v_self->_pos, __pyx_v_self->_pos, __pyx_e_6mdtraj_7formats_3tng_TNG_USE_HASH, (&__pyx_v_box_shape), (&__pyx_v_stride_length), (&__pyx_v_n_values_per_frame), (&__pyx_v_data_type)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_16write': mdtraj/formats/tng/tng.c:8918:94: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8918 | __pyx_t_1 = ((tng_implicit_num_particles_set(__pyx_v_self->_traj, __pyx_v_self->n_atoms) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:8950:75: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8950 | __pyx_t_1 = ((tng_util_pos_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:8982:81: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8982 | __pyx_t_1 = ((tng_util_box_shape_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9305:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9305 | __pyx_t_9 = ((tng_time_per_frame_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9496:372: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9496 | __pyx_t_1 = ((tng_util_pos_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz_array.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_xyz_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_xyz_array.diminfo[1].strides, __pyx_t_20, __pyx_pybuffernd_xyz_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9548:378: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9548 | __pyx_t_1 = ((tng_util_box_shape_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box_array.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_box_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_box_array.diminfo[1].strides, __pyx_t_18, __pyx_pybuffernd_box_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ mdtraj/formats/tng/tng.c:9610:89: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9610 | __pyx_t_1 = ((tng_frame_set_first_frame_time_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); | ^~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-i686-cpython-311/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib/i386-linux-gnu -lz -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/tng.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.dcd' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-i686-cpython-311/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:1940, 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:6646:17: 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:13600:20: note: in expansion of macro 'PyInt_FromLong' 13600 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:5465:7: note: '__pyx_v_i' was declared here 5465 | int __pyx_v_i; | ^~~~~~~~~ i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-i686-cpython-311/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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/formats/dcd/dcd.o build/temp.linux-i686-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dcd.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.binpos' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/binpos/binpos.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:1940, 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/binpos/binpos.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_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read', inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:5526:6: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 5526 | if (__pyx_t_2) { | ^ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5006:7: note: '__pyx_v_status' was declared here 5006 | int __pyx_v_status; | ^~~~~~~~~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read' at mdtraj/formats/binpos/binpos.c:5536:17, inlined from '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read' at mdtraj/formats/binpos/binpos.c:4994:13: mdtraj/formats/binpos/binpos.c:694:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 694 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/binpos/binpos.c:13100:20: note: in expansion of macro 'PyInt_FromLong' 13100 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:5003:7: note: '__pyx_v_i' was declared here 5003 | int __pyx_v_i; | ^~~~~~~~~ i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-i686-cpython-311/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/binpos/src/binposplugin.c: In function 'open_binpos_read': mdtraj/formats/binpos/src/binposplugin.c:59:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | fread(magicchar,sizeof(char),4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/binpos/src/binposplugin.c:69:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fread(&igarb,sizeof(int),1,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/formats/binpos/binpos.o build/temp.linux-i686-cpython-311/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/binpos.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.dtr' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-i686-cpython-311/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:1940, 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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-i686-cpython-311/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 constructor '{anonymous}::DDException::DDException(const std::string&, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: '*this.{anonymous}::DDException::eno' is used uninitialized [-Wuninitialized] 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} | ~~~~~~~~^~~~~ 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:906, 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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/formats/dtr/dtr.o build/temp.linux-i686-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dtr.cpython-311-i386-linux-gnu.so building 'mdtraj._rmsd' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-i686-cpython-311/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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/rmsd/_rmsd.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_rmsd.cpython-311-i386-linux-gnu.so building 'mdtraj._lprmsd' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-i686-cpython-311/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:1940, 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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-i686-cpython-311/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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/rmsd/_lprmsd.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/Munkres.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/fancy_index.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-i686-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_lprmsd.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry._geometry' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-i686-cpython-311/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:1940, 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 " \ | ^~~~~~~ mdtraj/geometry/src/_geometry.cpp: In function 'void __pyx_f_6mdtraj_8geometry_9_geometry_make_whole(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice)': mdtraj/geometry/src/_geometry.cpp:6131:296: warning: '__pyx_v_offset[1]' may be used uninitialized [-Wmaybe-uninitialized] 6131 | (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) ))))))); | ~~~~~~~~~~~~~~~~~^~ mdtraj/geometry/src/_geometry.cpp:6037:9: note: '__pyx_v_offset[1]' was declared here 6037 | float __pyx_v_offset[3]; | ^~~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6131:274: warning: '__pyx_v_delta[1]' may be used uninitialized [-Wmaybe-uninitialized] 6131 | (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) ))))))); | ~~~~~~~~~~~~~~~~^~ mdtraj/geometry/src/_geometry.cpp:6038:9: note: '__pyx_v_delta[1]' was declared here 6038 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6117:242: warning: '__pyx_v_delta[2]' may be used uninitialized [-Wmaybe-uninitialized] 6117 | (__pyx_v_offset[__pyx_v_k]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_8 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_7)) ))) * roundf(((__pyx_v_delta[2]) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_5 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_4)) )))))); | ~~~~~~~~~~~~~~~~^~ mdtraj/geometry/src/_geometry.cpp:6038:9: note: '__pyx_v_delta[2]' was declared here 6038 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-i686-cpython-311/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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/geometry/src/_geometry.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/dssp.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/geometry.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/sasa.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/_geometry.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry.drid' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/drid.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-i686-cpython-311/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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/geometry/drid.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/dridkernels.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/moments.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/drid.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry.neighbors' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-i686-cpython-311/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++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/geometry/neighbors.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/neighbors.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighbors.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-i686-cpython-311/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-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -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/python3.11 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:50:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:51:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 51 | periodicBoxSize[1] = periodicBoxVectors[1][1]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:52:53: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 52 | periodicBoxSize[2] = periodicBoxVectors[2][2]; | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ In constructor 'Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)', inlined from 'std::vector > _compute_neighborlist(const float*, int, float, const float*)' at mdtraj/geometry/src/neighborlist.cpp:377:116: mdtraj/geometry/src/neighborlist.cpp:56:45: warning: 'periodicBoxVectors' may be used uninitialized [-Wmaybe-uninitialized] 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || | ~~~~~~~~~~~~~~~~~~~~~~~^ mdtraj/geometry/src/neighborlist.cpp: In function 'std::vector > _compute_neighborlist(const float*, int, float, const float*)': mdtraj/geometry/src/neighborlist.cpp:341:11: note: 'periodicBoxVectors' declared here 341 | float periodicBoxVectors[3][3]; | ^~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-311/mdtraj/geometry/neighborlist.o build/temp.linux-i686-cpython-311/mdtraj/geometry/src/neighborlist.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighborlist.cpython-311-i386-linux-gnu.so running install_lib creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11 creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/hdf5reporter.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/xtcreporter.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/basereporter.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/dcdreporter.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/netcdfreporter.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/io.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_lprmsd.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/lib/libtheobald.a -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/lib/theobald_rmsd.h -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/lib/center.h -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/topology.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/trajectory.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/element.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/selection.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/residue_names.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/__pycache__/docscrape.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/__pycache__/testing.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/__pycache__/docstrings.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/__pycache__/shift_wrappers.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/__pycache__/scalar_couplings.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/six.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_definitions.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/standard_dimensions.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/basedimension.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/unit.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/baseunit.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/quantity.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/mymatrix.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/prefix.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_operators.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/unitcell.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/six.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/singleton.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/validation.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/contextmanagers.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/rotation.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/delay_import.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/zipped.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dtr.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/tng.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/trr.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/xtc.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dcd.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/mol2.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/pdbx.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/lh5.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/openmmxml.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/arc.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/netcdf.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/mdcrd.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/gsd.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/amberrst.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/gro.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/registry.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/hdf5.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/prmtop.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/hoomdxml.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/psf.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/lammpstrj.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/xyzfile.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/binpos.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/data creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbstructure.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbfile.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighbors.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/_geometry.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighborlist.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/order.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/dihedral.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/rg.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/contact.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/dssp.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/shape.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/rdf.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/hbond.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/angle.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/distance.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/thermodynamic_properties.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/sasa.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/drid.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/__pycache__/version.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/__pycache__ creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.9.9/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_rmsd.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/io.py to io.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/version.py to version.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/trajectory.py to trajectory.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/element.py to element.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/residue_names.py to residue_names.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/selection.py to selection.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/topology.py to topology.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/docstrings.py to docstrings.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/docscrape.py to docscrape.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/testing.py to testing.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/scalar_couplings.py to scalar_couplings.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/shift_wrappers.py to shift_wrappers.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/zipped.py to zipped.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/rotation.py to rotation.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/singleton.py to singleton.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/validation.py to validation.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unitcell.py to unitcell.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/six.py to six.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/constants.py to constants.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/standard_dimensions.py to standard_dimensions.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/unit_operators.py to unit_operators.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/unit.py to unit.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/unit_definitions.py to unit_definitions.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/prefix.py to prefix.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/baseunit.py to baseunit.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/unit_math.py to unit_math.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/quantity.py to quantity.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/doctests.py to doctests.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/basedimension.py to basedimension.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/mymatrix.py to mymatrix.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/delay_import.py to delay_import.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/lh5.py to lh5.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/psf.py to psf.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/amberrst.py to amberrst.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/registry.py to registry.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/prmtop.py to prmtop.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/mol2.py to mol2.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/gro.py to gro.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/arc.py to arc.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/pdbfile.py to pdbfile.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/pdbstructure.py to pdbstructure.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/netcdf.py to netcdf.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/gsd.py to gsd.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdbx.py to pdbx.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/hdf5.py to hdf5.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/shape.py to shape.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/rg.py to rg.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/contact.py to contact.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/alignment.py to alignment.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/dssp.py to dssp.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/angle.py to angle.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/hbond.py to hbond.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/thermodynamic_properties.py to thermodynamic_properties.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/order.py to order.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/internal.py to internal.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/distance.py to distance.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/rdf.py to rdf.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/sasa.py to sasa.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts/mdconvert.py to mdconvert.cpython-311.pyc running install_egg_info running 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 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 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-1.9.9/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj-1.9.9.egg-info Skipping SOURCES.txt running install_scripts Installing mdconvert-mdtraj script to /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/bin Installing mdinspect script to /build/reproducible-path/mdtraj-1.9.9/debian/python3-mdtraj/usr/bin 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-1.9.9/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 rm -f debian/python-mdtraj-doc.debhelper.log debian/rules override_dh_sphinxdoc-indep make[1]: Entering directory '/build/reproducible-path/mdtraj-1.9.9' dh_sphinxdoc -i ln -sf ../../../../../sphinx_rtd_theme/static/js/theme.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/theme.js ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/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.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.ttf ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.ttf ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.ttf ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.eot debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.eot ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.ttf ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Regular.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.svg debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.svg ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff ln -sf ../../../../../sphinx_rtd_theme/static/css/badge_only.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css ln -sf ../../../../../sphinx_rtd_theme/static/css/theme.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css ln -sf ../../../../javascript/sphinxdoc/1.0/doctools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.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 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/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 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-1.9.9' 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/mdinspect.1.dh-new debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 chmod 0644 -- 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 rm -f debian/python-mdtraj-doc.debhelper.log debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/mdtraj-1.9.9' dh_python3 D: dh_python3 dh_python3:179: version: 6.20240401 D: dh_python3 dh_python3:180: argv: ['/usr/bin/dh_python3'] D: dh_python3 dh_python3:181: 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=None) D: dh_python3 dh_python3:182: supported Python versions: 3.11,3.12 (default=3.11) 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_python3:204: processing package python3-mdtraj... D: dh_python3 fs:50: moving files from debian/python3-mdtraj/usr/lib/python3.11/dist-packages to debian/python3-mdtraj/usr/lib/python3/dist-packages/ 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/ W: dh_python3 fs:122: Paths differ: debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib/libtheobald.a and debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/core/lib/libtheobald.a D: dh_python3 fs:335: package python3-mdtraj details = {'requires.txt': {'debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.9.9.egg-info/requires.txt'}, 'egg-info': {'debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.9.9.egg-info/PKG-INFO'}, 'dist-info': set(), 'nsp.txt': set(), 'shebangs': {/usr/bin/python3, /usr/bin/python3}, 'public_vers': {Version('3'), Version('3.12')}, 'private_dirs': {}, 'compile': True, 'ext_vers': {Version('3.11'), 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>=1.6 (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-numpy', 'python3 (>= 3.11~)', 'python3:any', 'python3 (<< 3.13)', 'python3-pyparsing', 'python3-scipy', 'python3-astunparse'}; R=[]; S=[]; E=[], B=[]; RT=[] dh_numpy3 mv debian/python3-mdtraj.substvars.new debian/python3-mdtraj.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars # FIXME: No idea why a copy of this static lib (is it needed at all???) remains here. There is another one in usr/lib/python3/dist-packages rm -f debian/python3-mdtraj/usr/lib/python3.1*/dist-packages/mdtraj/core/lib/libtheobald.a make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.9.9' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css ln -s ../../../../../sphinx_rtd_theme/static/css/theme.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css ln -s ../../../../../sphinx_rtd_theme/static/css/badge_only.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.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/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-Regular.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.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.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.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.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-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/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-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/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/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 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 dh_strip_nondeterminism -O--buildsystem=pybuild Using 1705400061 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/file.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/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-1.9.9' cd '/build/reproducible-path/mdtraj-1.9.9' 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-311-i386-linux-gnu.so 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-311-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/binpos.cpython-311-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/binpos.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-311-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-311-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/tng.cpython-311-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/tng.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-311-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-311-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-311-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-311-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-311-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-311-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/21 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-311-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/21/3d275c509bad1af0ee64d552ff3abd550c9592.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/21/3d275c509bad1af0ee64d552ff3abd550c9592.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-311-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/21/3d275c509bad1af0ee64d552ff3abd550c9592.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-311-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e6 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/e6/9fb2b7f6b378e52749fc74c8052a77e94ca0fa.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e6/9fb2b7f6b378e52749fc74c8052a77e94ca0fa.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/e6/9fb2b7f6b378e52749fc74c8052a77e94ca0fa.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/da objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so 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debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4d/28e51e1ec28270f47d7786538ecf128075600e.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4d/28e51e1ec28270f47d7786538ecf128075600e.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-311-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4d/28e51e1ec28270f47d7786538ecf128075600e.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-311-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/3f objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/tng.cpython-311-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/3f/b04e25519fc12e20cffd63d0aa5214301bac93.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/3f/b04e25519fc12e20cffd63d0aa5214301bac93.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/tng.cpython-311-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/3f/b04e25519fc12e20cffd63d0aa5214301bac93.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/tng.cpython-311-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/62 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so 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debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d3/b4578e5dcc26ee2e9be78055a567d6ddde0069.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d3/b4578e5dcc26ee2e9be78055a567d6ddde0069.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-311-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d3/b4578e5dcc26ee2e9be78055a567d6ddde0069.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-311-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/70 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/70/94c037ae20515514b8d4ad458566978cfefae3.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/70/94c037ae20515514b8d4ad458566978cfefae3.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/70/94c037ae20515514b8d4ad458566978cfefae3.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/fd objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-311-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/fd/2e2dd9300d94b108f9bb2f5ffc58f0d0ce96b0.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/fd/2e2dd9300d94b108f9bb2f5ffc58f0d0ce96b0.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-311-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/fd/2e2dd9300d94b108f9bb2f5ffc58f0d0ce96b0.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-311-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d5 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/tng.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d5/31a79716467a36f626dae2b27f65fe175206cd.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d5/31a79716467a36f626dae2b27f65fe175206cd.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/tng.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d5/31a79716467a36f626dae2b27f65fe175206cd.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/tng.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/21 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-311-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/21/6ee59bdea5bc8c0798fa708e28a6105cde932d.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/21/6ee59bdea5bc8c0798fa708e28a6105cde932d.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-311-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/21/6ee59bdea5bc8c0798fa708e28a6105cde932d.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-311-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/36 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/36/f8eefdc6ce0e868739c01d159f40015fe985ac.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/36/f8eefdc6ce0e868739c01d159f40015fe985ac.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/36/f8eefdc6ce0e868739c01d159f40015fe985ac.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/88 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/binpos.cpython-311-i386-linux-gnu.so 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debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/74/dd188ef9851a90466b449b7a0a11b6c206b07a.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/74/dd188ef9851a90466b449b7a0a11b6c206b07a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-311-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/74/dd188ef9851a90466b449b7a0a11b6c206b07a.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-311-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/16 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-311-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/16/849612ffa024c5d590052a01d4afc6452f2472.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/16/849612ffa024c5d590052a01d4afc6452f2472.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-311-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/16/849612ffa024c5d590052a01d4afc6452f2472.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-311-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d2 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-311-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d2/a4d2073658950f2bf63f747a1bc501cadcfad6.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d2/a4d2073658950f2bf63f747a1bc501cadcfad6.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-311-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/d2/a4d2073658950f2bf63f747a1bc501cadcfad6.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-311-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a3 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/a3/0ba43bc433c23c47c79288ad77cc45b87efd27.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a3/0ba43bc433c23c47c79288ad77cc45b87efd27.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/a3/0ba43bc433c23c47c79288ad77cc45b87efd27.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/89 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-311-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/89/1a118da89c36d523ab67dfa5cf0d2169d11c99.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/89/1a118da89c36d523ab67dfa5cf0d2169d11c99.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-311-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/89/1a118da89c36d523ab67dfa5cf0d2169d11c99.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-311-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/03 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/03/43047d3830138d53ed196e8f1003883dbf2460.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/03/43047d3830138d53ed196e8f1003883dbf2460.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/03/43047d3830138d53ed196e8f1003883dbf2460.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/19 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/19/aacb16745295aa90b3b30ee085f92fbd0cbe5b.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/19/aacb16745295aa90b3b30ee085f92fbd0cbe5b.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/19/aacb16745295aa90b3b30ee085f92fbd0cbe5b.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.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-311-i386-linux-gnu.so 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/_rmsd.cpython-311-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-311-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/tng.cpython-311-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-311-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/xtc.cpython-311-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/tng.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-311-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/formats/binpos.cpython-311-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/binpos.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/neighbors.cpython-311-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-311-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-311-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-311-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/drid.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=0343047d3830138d53ed196e8f1003883dbf2460 16849612ffa024c5d590052a01d4afc6452f2472 19aacb16745295aa90b3b30ee085f92fbd0cbe5b 213d275c509bad1af0ee64d552ff3abd550c9592 216ee59bdea5bc8c0798fa708e28a6105cde932d 36f8eefdc6ce0e868739c01d159f40015fe985ac 3fb04e25519fc12e20cffd63d0aa5214301bac93 4d28e51e1ec28270f47d7786538ecf128075600e 55469383566ad742e69e5b8f90515c9e7d0ac211 5bee50871c024363a9cc712c21b97950d5e058d9 620c63e1801dbc23f18f4cceee17b005cc2392b4 7094c037ae20515514b8d4ad458566978cfefae3 74dd188ef9851a90466b449b7a0a11b6c206b07a 79445c6551bb4de45e28ed55a464e5717a46ff96 888f46b143b8001b62d150bc6366334cf9b6abaf 891a118da89c36d523ab67dfa5cf0d2169d11c99 a30ba43bc433c23c47c79288ad77cc45b87efd27 b2d2313368a0666f01de3ed132202970bb7db24a d2a4d2073658950f2bf63f747a1bc501cadcfad6 d3b4578e5dcc26ee2e9be78055a567d6ddde0069 d531a79716467a36f626dae2b27f65fe175206cd dac0bf4604a995f4215eb03c2dfbf0a3b4845147 e69fb2b7f6b378e52749fc74c8052a77e94ca0fa fd2e2dd9300d94b108f9bb2f5ffc58f0d0ce96b0" -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/python-mdtraj-doc/DEBIAN install -m0755 -d debian/python3-mdtraj/DEBIAN cd debian/python-mdtraj-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/python3-mdtraj >/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 chmod 0644 -- debian/python-mdtraj-doc/DEBIAN/md5sums cd debian/.debhelper/python3-mdtraj/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > 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 'python-mdtraj-doc' in '../python-mdtraj-doc_1.9.9-1_all.deb'. dpkg-deb: building package 'python3-mdtraj-dbgsym' in '../python3-mdtraj-dbgsym_1.9.9-1_i386.deb'. dpkg-deb: building package 'python3-mdtraj' in '../python3-mdtraj_1.9.9-1_i386.deb'. dpkg-genbuildinfo --build=binary -O../mdtraj_1.9.9-1_i386.buildinfo dpkg-genchanges --build=binary -O../mdtraj_1.9.9-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from mdtraj-1.9.9/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/40816 and its subdirectories I: Current time: Sat May 17 07:57:09 -12 2025 I: pbuilder-time-stamp: 1747511829 Sun Apr 14 13:34:11 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos2-i386.debian.net. Sun Apr 14 13:34:11 UTC 2024 I: Preparing to do remote build '2' on ionos2-i386.debian.net. Sun Apr 14 14:14:21 UTC 2024 I: Deleting $TMPDIR on ionos2-i386.debian.net. Sun Apr 14 14:14:21 UTC 2024 I: mdtraj_1.9.9-1_i386.changes: Format: 1.8 Date: Tue, 16 Jan 2024 11:14:21 +0100 Source: mdtraj Binary: python-mdtraj-doc python3-mdtraj python3-mdtraj-dbgsym Architecture: all i386 Version: 1.9.9-1 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Andreas Tille Description: python-mdtraj-doc - Read, write and analyze MD trajectories in Python (documentation) python3-mdtraj - Read, write and analyze MD trajectories in Python Closes: 1045994 1056815 Changes: mdtraj (1.9.9-1) unstable; urgency=medium . * Team upload. * Switch to cython3-legacy. Closes: #1056815 * Fix clean target Closes: #1045994 * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Use secure URI in Homepage field. * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository-Browse. * Fix field name typo in debian/copyright (Comments ⇒ Comment). * Explicitly call dh_python3 in d/rules * d/rules: verbose * Fix capitalisation in description * Set hardening options * Manually remove copy of libtheobald.a in /usr/lib/python3.1*/dist-packages * Update python_hashbang.patch to replace all instances of /bin/env Checksums-Sha1: 2496ea26d1a55590c5ccbf30fc269c4c0697c5d6 13738 mdtraj_1.9.9-1_i386.buildinfo 9c47175c12b6a701aa1f52473094f32c3513bfa3 696792 python-mdtraj-doc_1.9.9-1_all.deb fd601053e4d7ae485ba160e46cb33a8308067d86 10727452 python3-mdtraj-dbgsym_1.9.9-1_i386.deb 1628949674b1e1450fa6bbceaea0fae47a31121f 1638424 python3-mdtraj_1.9.9-1_i386.deb Checksums-Sha256: da732eac3b6a9fee3c6b92aae4203f42b206b7b850b1a0590a30170bd143bb91 13738 mdtraj_1.9.9-1_i386.buildinfo 6028206f9b45ecdc23fc3cd4e66bcef4b9c0f27a32f242f380ebc47d4e94acea 696792 python-mdtraj-doc_1.9.9-1_all.deb 49ea208807b41535f5089f207354cc0dbb64ee36c96beedb779676f81cec3be1 10727452 python3-mdtraj-dbgsym_1.9.9-1_i386.deb c6c709211615a304109a7605573cc23f431af44cf6e731aaf8c731a6ba96a14f 1638424 python3-mdtraj_1.9.9-1_i386.deb Files: ce7528cba80d89979568a6b707b17687 13738 python optional mdtraj_1.9.9-1_i386.buildinfo eb921edcd08ab5075b43af298f677cf6 696792 doc optional python-mdtraj-doc_1.9.9-1_all.deb e9a1333294da83283e84aad6c9a2803e 10727452 debug optional python3-mdtraj-dbgsym_1.9.9-1_i386.deb 8eef6078196d24ef3d27d238942408a8 1638424 python optional python3-mdtraj_1.9.9-1_i386.deb Sun Apr 14 14:14:23 UTC 2024 I: diffoscope 264 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_4-15961.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.EYEMTr0p/mdtraj_1.9.9-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.EYEMTr0p/mdtraj_1.9.9-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.EYEMTr0p/mdtraj_1.9.9-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.EYEMTr0p/b1/mdtraj_1.9.9-1_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.EYEMTr0p/b2/mdtraj_1.9.9-1_i386.changes ## close_archive (total time: 0.000s) 0.000s 20 calls diffoscope.comparators.xz.XzContainer 0.000s 10 calls diffoscope.comparators.deb.DebContainer 0.000s 14 calls diffoscope.comparators.tar.TarContainer 0.000s 6 calls diffoscope.comparators.deb.DebTarContainer ## command (total time: 43.293s) 16.692s 1003 calls readelf 15.976s 122 calls diff 7.827s 220 calls objdump 1.647s 20 calls xz 1.019s 2 calls objcopy 0.097s 22 calls strings 0.017s 3 calls cmp 0.017s 3 calls cmp (external) 0.001s 20 calls cmp (internal) ## compare_files (cumulative) (total time: 128.903s) 24.333s 1 call abc.DotChangesFile 24.275s 2 calls abc.DebFile 24.142s 4 calls abc.XzFile 23.005s 2 calls abc.DebDataTarFile 22.588s 2 calls abc.ElfFile 9.820s 10 calls diffoscope.comparators.elf.ElfCodeSection 0.593s 33 calls diffoscope.comparators.elf.ElfSection 0.085s 2 calls abc.TarFile 0.019s 2 calls diffoscope.comparators.elf.ElfStringSection 0.016s 1 call abc.TextFile 0.015s 2 calls abc.Md5sumsFile 0.010s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection ## container_extract (total time: 1.980s) 1.648s 20 calls diffoscope.comparators.xz.XzContainer 0.203s 300 calls diffoscope.comparators.deb.DebTarContainer 0.118s 24 calls diffoscope.comparators.deb.DebContainer 0.011s 22 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 0.509s) 0.509s 32 calls linediff ## has_same_content_as (total time: 0.020s) 0.015s 2 calls abc.DebDataTarFile 0.003s 3 calls abc.DebFile 0.001s 6 calls abc.TextFile 0.000s 4 calls abc.Md5sumsFile 0.000s 4 calls abc.XzFile 0.000s 33 calls diffoscope.comparators.elf.ElfSection 0.000s 2 calls abc.TarFile 0.000s 2 calls abc.ElfFile 0.000s 1 call abc.DotChangesFile 0.000s 1 call diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 10 calls diffoscope.comparators.elf.ElfCodeSection 0.000s 2 calls diffoscope.comparators.elf.ElfStringSection 0.000s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection ## main (total time: 25.567s) 25.566s 2 calls outputs 0.001s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 20 calls diffoscope.comparators.xz.XzContainer 0.000s 14 calls diffoscope.comparators.tar.TarContainer 0.000s 10 calls diffoscope.comparators.deb.DebContainer 0.000s 6 calls diffoscope.comparators.deb.DebTarContainer ## output (total time: 0.776s) 0.759s 1 call html 0.010s 1 call text 0.007s 1 call json ## recognizes (total time: 1.247s) 0.706s 900 calls diffoscope.comparators.utils.archive.ArchiveMember 0.310s 1904 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.151s 12 calls diffoscope.comparators.binary.FilesystemFile 0.080s 324 calls diffoscope.comparators.debian.DebControlMember ## specialize (total time: 0.176s) 0.176s 71 calls specialize Finished with result: success Main processes terminated with: code=exited/status=1 Service runtime: 25.872s CPU time consumed: 32.964s Sun Apr 14 14:14:49 UTC 2024 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Sun Apr 14 14:14:49 UTC 2024 E: mdtraj failed to build reproducibly in trixie on i386. Sun Apr 14 14:14:50 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Apr 14 14:14:50 UTC 2024 I: Submitting 16K b1/mdtraj_1.9.9-1_i386.buildinfo.asc Sun Apr 14 14:14:52 UTC 2024 I: Submitting 16K b2/mdtraj_1.9.9-1_i386.buildinfo.asc Sun Apr 14 14:14:53 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Apr 14 14:14:53 UTC 2024 I: Done submitting .buildinfo files. Sun Apr 14 14:14:53 UTC 2024 I: Removing signed mdtraj_1.9.9-1_i386.buildinfo.asc files: removed './b1/mdtraj_1.9.9-1_i386.buildinfo.asc' removed './b2/mdtraj_1.9.9-1_i386.buildinfo.asc'