I: pbuilder: network access will be disabled during build I: Current time: Tue Jan 23 03:37:29 +14 2024 I: pbuilder-time-stamp: 1705930649 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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_1.9.7-6.dsc] I: copying [./mdtraj_1.9.7.orig.tar.gz] I: copying [./mdtraj_1.9.7-6.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Mar 1 10:55:59 2023 gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA gpgv: issuer "dparsons@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.9.7-6.dsc: no acceptable signature found dpkg-source: info: extracting mdtraj in mdtraj-1.9.7 dpkg-source: info: unpacking mdtraj_1.9.7.orig.tar.gz dpkg-source: info: unpacking mdtraj_1.9.7-6.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 check_sse2.patch dpkg-source: info: applying 32bit_skip_image_molecule.patch dpkg-source: info: applying test_relax_tol.patch dpkg-source: info: applying rename-mdconvert-mdtraj.patch dpkg-source: info: applying drop_notebook_in_docs.patch dpkg-source: info: applying test_increase_timeout.patch dpkg-source: info: applying python3.11_PR1758.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/13800/tmp/hooks/D01_modify_environment starting debug: Running on ionos2-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 22 13:37 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/13800/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/13800/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=eee235fd867b400d82b86831e4f2b1c2 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=13800 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.7kG59fCH/pbuilderrc_Z3rH --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.7kG59fCH/b2 --logfile b2/build.log mdtraj_1.9.7-6.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-17-686-pae #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) i686 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp -rwxr-xr-x 1 root root 136916 Jan 5 2023 dash -rwxr-xr-x 1 root root 137160 Sep 20 2022 date -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd -rwxr-xr-x 1 root root 108940 Sep 20 2022 df -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir -rwxr-xr-x 1 root root 87760 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 84272 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 218680 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln -rwxr-xr-x 1 root root 55600 Mar 23 2023 login -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls -rwxr-xr-x 1 root root 214568 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 23 2023 more -rwsr-xr-x 1 root root 58912 Mar 23 2023 mount -rwxr-xr-x 1 root root 13856 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 22308 Jul 28 23:46 run-parts -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed lrwxrwxrwx 1 root root 9 Jan 22 13:37 sh -> /bin/bash -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty -rwsr-xr-x 1 root root 83492 Mar 23 2023 su -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar -rwxr-xr-x 1 root root 13860 Jul 28 23:46 tempfile -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch -rwxr-xr-x 1 root root 34664 Sep 20 2022 true -rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 23 2023 umount -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/13800/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-python, cython3 (>= 0.29~), python3-setuptools, python3-all-dev, python3-numpy (>= 1.6~), 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 ... 18156 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-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on cython3 (>= 0.29~); however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy (>= 1.6~); 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{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-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} libboost-dev{a} libboost-regex1.74.0{a} libboost1.74-dev{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} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{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} libqhull-r8.0{a} libraqm0{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{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} libxsimd-dev{a} libxslt1.1{a} libxss1{a} libzmq5{a} m4{a} man-db{a} media-types{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-backcall{a} python3-beniget{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-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-entrypoints{a} python3-executing{a} python3-fastjsonschema{a} python3-fonttools{a} python3-fs{a} python3-gast{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-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-pexpect{a} python3-pickleshare{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-ply{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-pyrsistent{a} python3-pythran{a} python3-requests{a} python3-roman{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-sklearn{a} python3-sklearn-lib{a} python3-snowballstemmer{a} python3-soupsieve{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-stack-data{a} python3-sympy{a} python3-tables{a} python3-tables-lib{a} python3-threadpoolctl{a} python3-tinycss2{a} python3-tk{a} python3-tornado{a} python3-traitlets{a} python3-tz{a} python3-ufolib2{a} python3-urllib3{a} python3-wcwidth{a} python3-webencodings{a} python3-zmq{a} python3.11{a} python3.11-dev{a} python3.11-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-gdal python3-json-pointer python3-nose 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, 264 newly installed, 0 to remove and 0 not upgraded. Need to get 170 MB of archives. After unpacking 868 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 fonts-lato all 2.0-2.1 [2696 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 ucf all 3.0043+nmu1 [55.2 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 libdebuginfod-common all 0.188-2.1 [21.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 libpython3.11-minimal i386 3.11.2-6 [813 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 python3.11-minimal i386 3.11.2-6 [2130 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 python3-minimal i386 3.11.2-1+b1 [26.3 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 media-types all 10.0.0 [26.1 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 readline-common all 8.2-1.3 [69.0 kB] Get: 11 http://deb.debian.org/debian bookworm/main i386 libreadline8 i386 8.2-1.3 [171 kB] Get: 12 http://deb.debian.org/debian bookworm/main i386 libpython3.11-stdlib i386 3.11.2-6 [1799 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 python3.11 i386 3.11.2-6 [572 kB] Get: 14 http://deb.debian.org/debian bookworm/main i386 libpython3-stdlib i386 3.11.2-1+b1 [9308 B] Get: 15 http://deb.debian.org/debian bookworm/main i386 python3 i386 3.11.2-1+b1 [26.3 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 sgml-base all 1.31 [15.4 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 tzdata all 2023c-5+deb12u1 [296 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 libproc2-0 i386 2:4.0.2-3 [63.7 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 procps i386 2:4.0.2-3 [706 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 openssl i386 3.0.11-1~deb12u2 [1423 kB] Get: 21 http://deb.debian.org/debian bookworm/main i386 ca-certificates all 20230311 [153 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 23 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 28 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 32 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 33 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 34 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 35 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 36 http://deb.debian.org/debian bookworm/main i386 libtcl8.6 i386 8.6.13+dfsg-2 [1095 kB] Get: 37 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB] Get: 38 http://deb.debian.org/debian bookworm/main i386 libpng16-16 i386 1.6.39-2 [283 kB] Get: 39 http://deb.debian.org/debian bookworm/main i386 libfreetype6 i386 2.12.1+dfsg-5 [410 kB] Get: 40 http://deb.debian.org/debian bookworm/main i386 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 41 http://deb.debian.org/debian bookworm/main i386 fontconfig-config i386 2.14.1-4 [315 kB] Get: 42 http://deb.debian.org/debian bookworm/main i386 libfontconfig1 i386 2.14.1-4 [398 kB] Get: 43 http://deb.debian.org/debian bookworm/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 44 http://deb.debian.org/debian bookworm/main i386 libbsd0 i386 0.11.7-2 [121 kB] Get: 45 http://deb.debian.org/debian bookworm/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 46 http://deb.debian.org/debian bookworm/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 47 http://deb.debian.org/debian bookworm/main i386 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get: 48 http://deb.debian.org/debian bookworm/main i386 libx11-6 i386 2:1.8.4-2+deb12u2 [782 kB] Get: 49 http://deb.debian.org/debian bookworm/main i386 libxrender1 i386 1:0.9.10-1.1 [34.1 kB] Get: 50 http://deb.debian.org/debian bookworm/main i386 libxft2 i386 2.3.6-1 [62.8 kB] Get: 51 http://deb.debian.org/debian bookworm/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 52 http://deb.debian.org/debian bookworm/main i386 x11-common all 1:7.7+23 [252 kB] Get: 53 http://deb.debian.org/debian bookworm/main i386 libxss1 i386 1:1.2.3-1 [18.1 kB] Get: 54 http://deb.debian.org/debian bookworm/main i386 libtk8.6 i386 8.6.13-2 [824 kB] Get: 55 http://deb.debian.org/debian bookworm/main i386 tk8.6-blt2.5 i386 2.5.3+dfsg-4.1 [622 kB] Get: 56 http://deb.debian.org/debian bookworm/main i386 blt i386 2.5.3+dfsg-4.1 [14.9 kB] Get: 57 http://deb.debian.org/debian bookworm/main i386 cython3 i386 0.29.32-2+b1 [1297 kB] Get: 58 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 59 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 60 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 61 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 62 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 63 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 64 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 65 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 66 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 67 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 68 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.3~deb12u1 [720 kB] Get: 69 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 70 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 71 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 72 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 73 http://deb.debian.org/debian bookworm/main i386 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 74 http://deb.debian.org/debian bookworm/main i386 python3-distutils all 3.11.2-3 [131 kB] Get: 75 http://deb.debian.org/debian bookworm/main i386 dh-python all 5.20230130+deb12u1 [104 kB] Get: 76 http://deb.debian.org/debian bookworm/main i386 xml-core all 0.18+nmu1 [23.8 kB] Get: 77 http://deb.debian.org/debian bookworm/main i386 docutils-common all 0.19+dfsg-6 [127 kB] Get: 78 http://deb.debian.org/debian bookworm/main i386 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 79 http://deb.debian.org/debian bookworm/main i386 fonts-lyx all 2.3.7-1 [186 kB] Get: 80 http://deb.debian.org/debian bookworm/main i386 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 81 http://deb.debian.org/debian bookworm/main i386 libdw1 i386 0.188-2.1 [265 kB] Get: 82 http://deb.debian.org/debian bookworm/main i386 libglib2.0-0 i386 2.74.6-2 [1467 kB] Get: 83 http://deb.debian.org/debian bookworm/main i386 libbabeltrace1 i386 1.5.11-1+b2 [192 kB] Get: 84 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB] Get: 85 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB] Get: 86 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB] Get: 87 http://deb.debian.org/debian bookworm/main i386 libnghttp2-14 i386 1.52.0-1+deb12u1 [80.7 kB] Get: 88 http://deb.debian.org/debian bookworm/main i386 libpsl5 i386 0.21.2-1 [59.3 kB] Get: 89 http://deb.debian.org/debian bookworm/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 90 http://deb.debian.org/debian bookworm/main i386 libssh2-1 i386 1.10.0-3+b1 [187 kB] Get: 91 http://deb.debian.org/debian bookworm/main i386 libcurl3-gnutls i386 7.88.1-10+deb12u4 [417 kB] Get: 92 http://deb.debian.org/debian bookworm/main i386 libdebuginfod1 i386 0.188-2.1 [28.5 kB] Get: 93 http://deb.debian.org/debian bookworm/main i386 libipt2 i386 2.0.5-1 [53.1 kB] Get: 94 http://deb.debian.org/debian bookworm/main i386 libpython3.11 i386 3.11.2-6 [2013 kB] Get: 95 http://deb.debian.org/debian bookworm/main i386 libsource-highlight-common all 3.1.9-4.2 [77.4 kB] Get: 96 http://deb.debian.org/debian bookworm/main i386 libboost-regex1.74.0 i386 1.74.0+ds1-21 [509 kB] Get: 97 http://deb.debian.org/debian bookworm/main i386 libsource-highlight4v5 i386 3.1.9-4.2+b3 [281 kB] Get: 98 http://deb.debian.org/debian bookworm/main i386 gdb i386 13.1-3 [4065 kB] Get: 99 http://deb.debian.org/debian bookworm/main i386 libaec0 i386 1.0.6-1+b1 [22.4 kB] Get: 100 http://deb.debian.org/debian bookworm/main i386 libblas3 i386 3.11.0-2 [139 kB] Get: 101 http://deb.debian.org/debian bookworm/main i386 libsnappy1v5 i386 1.1.9-3 [27.7 kB] Get: 102 http://deb.debian.org/debian bookworm/main i386 libblosc1 i386 1.21.3+ds-1 [51.1 kB] Get: 103 http://deb.debian.org/debian bookworm/main i386 libboost1.74-dev i386 1.74.0+ds1-21 [9508 kB] Get: 104 http://deb.debian.org/debian bookworm/main i386 libboost-dev i386 1.74.0.3 [4548 B] Get: 105 http://deb.debian.org/debian bookworm/main i386 libcurl4 i386 7.88.1-10+deb12u4 [424 kB] Get: 106 http://deb.debian.org/debian bookworm/main i386 libdeflate0 i386 1.14-1 [57.5 kB] Get: 107 http://deb.debian.org/debian bookworm/main i386 libexpat1-dev i386 2.5.0-1 [158 kB] Get: 108 http://deb.debian.org/debian bookworm/main i386 libfribidi0 i386 1.0.8-2.1 [65.6 kB] Get: 109 http://deb.debian.org/debian bookworm/main i386 libgfortran5 i386 12.2.0-14 [698 kB] Get: 110 http://deb.debian.org/debian bookworm/main i386 libgraphite2-3 i386 1.3.14-1 [84.0 kB] Get: 111 http://deb.debian.org/debian bookworm/main i386 libharfbuzz0b i386 6.0.0+dfsg-3 [1966 kB] Get: 112 http://deb.debian.org/debian bookworm/main i386 libsz2 i386 1.0.6-1+b1 [7884 B] Get: 113 http://deb.debian.org/debian bookworm/main i386 libhdf5-103-1 i386 1.10.8+repack1-1 [1175 kB] Get: 114 http://deb.debian.org/debian bookworm/main i386 libimagequant0 i386 2.17.0-1 [32.9 kB] Get: 115 http://deb.debian.org/debian bookworm/main i386 libjbig0 i386 2.1-6.1 [31.6 kB] Get: 116 http://deb.debian.org/debian bookworm/main i386 libjpeg62-turbo i386 1:2.1.5-2 [169 kB] Get: 117 http://deb.debian.org/debian bookworm/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 118 http://deb.debian.org/debian bookworm/main i386 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 119 http://deb.debian.org/debian bookworm/main i386 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 120 http://deb.debian.org/debian bookworm/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 121 http://deb.debian.org/debian bookworm/main i386 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 122 http://deb.debian.org/debian bookworm/main i386 libjson-perl all 4.10000-1 [87.5 kB] Get: 123 http://deb.debian.org/debian bookworm/main i386 libopenblas0-pthread i386 0.3.21+ds-4 [5148 kB] Get: 124 http://deb.debian.org/debian bookworm/main i386 liblapack3 i386 3.11.0-2 [2092 kB] Get: 125 http://deb.debian.org/debian bookworm/main i386 liblbfgsb0 i386 3.0+dfsg.4-1 [28.5 kB] Get: 126 http://deb.debian.org/debian bookworm/main i386 liblcms2-2 i386 2.14-2 [165 kB] Get: 127 http://deb.debian.org/debian bookworm/main i386 liblerc4 i386 4.0.0+ds-2 [181 kB] Get: 128 http://deb.debian.org/debian bookworm/main i386 liblzo2-2 i386 2.10-2 [59.7 kB] Get: 129 http://deb.debian.org/debian bookworm/main i386 libnorm1 i386 1.5.9+dfsg-2 [238 kB] Get: 130 http://deb.debian.org/debian bookworm/main i386 libopenblas0 i386 0.3.21+ds-4 [32.6 kB] Get: 131 http://deb.debian.org/debian bookworm/main i386 libopenblas-pthread-dev i386 0.3.21+ds-4 [3447 kB] Get: 132 http://deb.debian.org/debian bookworm/main i386 libopenblas-dev i386 0.3.21+ds-4 [44.9 kB] Get: 133 http://deb.debian.org/debian bookworm/main i386 libopenjp2-7 i386 2.5.0-2 [196 kB] Get: 134 http://deb.debian.org/debian bookworm/main i386 libpgm-5.3-0 i386 5.3.128~dfsg-2 [168 kB] Get: 135 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB] Get: 136 http://deb.debian.org/debian bookworm/main i386 libpython3.11-dev i386 3.11.2-6 [4906 kB] Get: 137 http://deb.debian.org/debian bookworm/main i386 libpython3-dev i386 3.11.2-1+b1 [9580 B] Get: 138 http://deb.debian.org/debian bookworm/main i386 libpython3-all-dev i386 3.11.2-1+b1 [1068 B] Get: 139 http://deb.debian.org/debian bookworm/main i386 libqhull-r8.0 i386 2020.2-5 [260 kB] Get: 140 http://deb.debian.org/debian bookworm/main i386 libraqm0 i386 0.7.0-4.1 [11.1 kB] Get: 141 http://deb.debian.org/debian bookworm/main i386 libsodium23 i386 1.0.18-1 [186 kB] Get: 142 http://deb.debian.org/debian bookworm/main i386 libwebp7 i386 1.2.4-0.2+deb12u1 [294 kB] Get: 143 http://deb.debian.org/debian bookworm/main i386 libtiff6 i386 4.5.0-6+deb12u1 [332 kB] Get: 144 http://deb.debian.org/debian bookworm/main i386 libwebpdemux2 i386 1.2.4-0.2+deb12u1 [99.8 kB] Get: 145 http://deb.debian.org/debian bookworm/main i386 libwebpmux3 i386 1.2.4-0.2+deb12u1 [111 kB] Get: 146 http://deb.debian.org/debian bookworm/main i386 libxsimd-dev i386 8.1.0-7 [88.8 kB] Get: 147 http://deb.debian.org/debian bookworm/main i386 libxslt1.1 i386 1.1.35-1 [253 kB] Get: 148 http://deb.debian.org/debian bookworm/main i386 libzmq5 i386 4.3.4-6 [298 kB] Get: 149 http://deb.debian.org/debian bookworm/main i386 python-babel-localedata all 2.10.3-1 [5615 kB] Get: 150 http://deb.debian.org/debian bookworm/main i386 python-matplotlib-data all 3.6.3-1 [2744 kB] Get: 151 http://deb.debian.org/debian bookworm/main i386 python-tables-data all 3.7.0-5 [47.2 kB] Get: 152 http://deb.debian.org/debian bookworm/main i386 python-tinycss2-common all 1.2.1-2 [31.5 kB] Get: 153 http://deb.debian.org/debian bookworm/main i386 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 154 http://deb.debian.org/debian bookworm/main i386 python3-all i386 3.11.2-1+b1 [1056 B] Get: 155 http://deb.debian.org/debian bookworm/main i386 python3.11-dev i386 3.11.2-6 [615 kB] Get: 156 http://deb.debian.org/debian bookworm/main i386 python3-dev i386 3.11.2-1+b1 [26.2 kB] Get: 157 http://deb.debian.org/debian bookworm/main i386 python3-all-dev i386 3.11.2-1+b1 [1072 B] Get: 158 http://deb.debian.org/debian bookworm/main i386 python3-appdirs all 1.4.4-3 [13.0 kB] Get: 159 http://deb.debian.org/debian bookworm/main i386 python3-six all 1.16.0-4 [17.5 kB] Get: 160 http://deb.debian.org/debian bookworm/main i386 python3-asttokens all 2.2.1-1 [19.8 kB] Get: 161 http://deb.debian.org/debian bookworm/main i386 python3-astunparse all 1.6.3-2 [13.8 kB] Get: 162 http://deb.debian.org/debian bookworm/main i386 python3-attr all 22.2.0-1 [65.4 kB] Get: 163 http://deb.debian.org/debian bookworm/main i386 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 164 http://deb.debian.org/debian bookworm/main i386 python3-tz all 2022.7.1-4 [30.1 kB] Get: 165 http://deb.debian.org/debian bookworm/main i386 python3-babel all 2.10.3-1 [103 kB] Get: 166 http://deb.debian.org/debian bookworm/main i386 python3-backcall all 0.2.0-4 [12.1 kB] Get: 167 http://deb.debian.org/debian bookworm/main i386 python3-gast all 0.5.2-2 [9364 B] Get: 168 http://deb.debian.org/debian bookworm/main i386 python3-beniget all 0.4.1-3 [9920 B] Get: 169 http://deb.debian.org/debian bookworm/main i386 python3-webencodings all 0.5.1-5 [11.1 kB] Get: 170 http://deb.debian.org/debian bookworm/main i386 python3-html5lib all 1.1-3 [93.0 kB] Get: 171 http://deb.debian.org/debian bookworm/main i386 python3-bleach all 5.0.1-2 [48.5 kB] Get: 172 http://deb.debian.org/debian bookworm/main i386 python3-brotli i386 1.0.9-2+b6 [295 kB] Get: 173 http://deb.debian.org/debian bookworm/main i386 python3-soupsieve all 2.3.2-1 [38.8 kB] Get: 174 http://deb.debian.org/debian bookworm/main i386 python3-bs4 all 4.11.2-2 [121 kB] Get: 175 http://deb.debian.org/debian bookworm/main i386 python3-bytecode all 0.14.0-2 [39.9 kB] Get: 176 http://deb.debian.org/debian bookworm/main i386 python3-certifi all 2022.9.24-1 [153 kB] Get: 177 http://deb.debian.org/debian bookworm/main i386 python3-cffi-backend i386 1.15.1-5+b1 [88.0 kB] Get: 178 http://deb.debian.org/debian bookworm/main i386 python3-chardet all 5.1.0+dfsg-2 [110 kB] Get: 179 http://deb.debian.org/debian bookworm/main i386 python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get: 180 http://deb.debian.org/debian bookworm/main i386 python3-numpy i386 1:1.24.2-1 [6115 kB] Get: 181 http://deb.debian.org/debian bookworm/main i386 python3-contourpy i386 1.0.7-1+b1 [184 kB] Get: 182 http://deb.debian.org/debian bookworm/main i386 python3-coverage i386 6.5.0+dfsg1-2+b1 [153 kB] Get: 183 http://deb.debian.org/debian bookworm/main i386 python3-cycler all 0.11.0-1 [8020 B] Get: 184 http://deb.debian.org/debian bookworm/main i386 python3-dateutil all 2.8.2-2 [78.3 kB] Get: 185 http://deb.debian.org/debian bookworm/main i386 python3-pydevd i386 2.9.5+ds-4 [472 kB] Get: 186 http://deb.debian.org/debian bookworm/main i386 python3-debugpy all 1.6.6+ds-1 [67.7 kB] Get: 187 http://deb.debian.org/debian bookworm/main i386 python3-decorator all 5.1.1-3 [14.9 kB] Get: 188 http://deb.debian.org/debian bookworm/main i386 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 189 http://deb.debian.org/debian bookworm/main i386 python3-roman all 3.3-3 [9880 B] Get: 190 http://deb.debian.org/debian bookworm/main i386 python3-docutils all 0.19+dfsg-6 [382 kB] Get: 191 http://deb.debian.org/debian bookworm/main i386 python3-entrypoints all 0.4-2 [7184 B] Get: 192 http://deb.debian.org/debian bookworm/main i386 python3-executing all 1.2.0-2 [22.6 kB] Get: 193 http://deb.debian.org/debian bookworm/main i386 python3-fastjsonschema all 2.16.3-2 [21.6 kB] Get: 194 http://deb.debian.org/debian bookworm/main i386 python3-ply all 3.11-5 [65.8 kB] Get: 195 http://deb.debian.org/debian bookworm/main i386 python3-pythran i386 0.11.0+ds-7 [427 kB] Get: 196 http://deb.debian.org/debian bookworm/main i386 python3-scipy i386 1.10.1-2 [15.2 MB] Get: 197 http://deb.debian.org/debian bookworm/main i386 python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB] Get: 198 http://deb.debian.org/debian bookworm/main i386 python3-mpmath all 1.2.1-2 [418 kB] Get: 199 http://deb.debian.org/debian bookworm/main i386 python3-sympy all 1.11.1-1 [4358 kB] Get: 200 http://deb.debian.org/debian bookworm/main i386 python3-fs all 2.4.16-2 [95.2 kB] Get: 201 http://deb.debian.org/debian bookworm/main i386 python3-lxml i386 4.9.2-1+b1 [1182 kB] Get: 202 http://deb.debian.org/debian bookworm/main i386 python3-lz4 i386 4.0.2+dfsg-1+b2 [25.1 kB] Get: 203 http://deb.debian.org/debian bookworm/main i386 unicode-data all 15.0.0-1 [7984 kB] Get: 204 http://deb.debian.org/debian bookworm/main i386 python3-fonttools i386 4.38.0-1+b1 [1010 kB] Get: 205 http://deb.debian.org/debian bookworm/main i386 python3-idna all 3.3-1 [39.4 kB] Get: 206 http://deb.debian.org/debian bookworm/main i386 python3-imagesize all 1.4.1-1 [6688 B] Get: 207 http://deb.debian.org/debian bookworm/main i386 python3-parso all 0.8.3-1 [67.4 kB] Get: 208 http://deb.debian.org/debian bookworm/main i386 python3-jedi all 0.18.2-1 [689 kB] Get: 209 http://deb.debian.org/debian bookworm/main i386 python3-traitlets all 5.5.0-1 [92.4 kB] Get: 210 http://deb.debian.org/debian bookworm/main i386 python3-matplotlib-inline all 0.1.6-2 [8652 B] Get: 211 http://deb.debian.org/debian bookworm/main i386 python3-ptyprocess all 0.7.0-5 [14.7 kB] Get: 212 http://deb.debian.org/debian bookworm/main i386 python3-pexpect all 4.8.0-4 [52.9 kB] Get: 213 http://deb.debian.org/debian bookworm/main i386 python3-pickleshare all 0.7.5-5 [7600 B] Get: 214 http://deb.debian.org/debian bookworm/main i386 python3-wcwidth all 0.2.5+dfsg1-1.1 [21.4 kB] Get: 215 http://deb.debian.org/debian bookworm/main i386 python3-prompt-toolkit all 3.0.36-2 [276 kB] Get: 216 http://deb.debian.org/debian bookworm/main i386 python3-pygments all 2.14.0+dfsg-1 [783 kB] Get: 217 http://deb.debian.org/debian bookworm/main i386 python3-pure-eval all 0.2.2-1 [11.2 kB] Get: 218 http://deb.debian.org/debian bookworm/main i386 python3-stack-data all 0.6.2-3 [21.8 kB] Get: 219 http://deb.debian.org/debian bookworm/main i386 python3-setuptools all 66.1.1-1 [521 kB] Get: 220 http://deb.debian.org/debian bookworm/main i386 python3-ipython all 8.5.0-4 [517 kB] Get: 221 http://deb.debian.org/debian bookworm/main i386 python3-jupyter-core all 4.12.0-1 [27.3 kB] Get: 222 http://deb.debian.org/debian bookworm/main i386 python3-nest-asyncio all 1.5.4-1 [6248 B] Get: 223 http://deb.debian.org/debian bookworm/main i386 python3-tornado i386 6.2.0-3 [337 kB] Get: 224 http://deb.debian.org/debian bookworm/main i386 python3-py all 1.11.0-1 [89.2 kB] Get: 225 http://deb.debian.org/debian bookworm/main i386 python3-zmq i386 24.0.1-4+b1 [266 kB] Get: 226 http://deb.debian.org/debian bookworm/main i386 python3-jupyter-client all 7.4.9-2 [103 kB] Get: 227 http://deb.debian.org/debian bookworm/main i386 python3-packaging all 23.0-1 [32.5 kB] Get: 228 http://deb.debian.org/debian bookworm/main i386 python3-psutil i386 5.9.4-1+b1 [190 kB] Get: 229 http://deb.debian.org/debian bookworm/main i386 python3-ipykernel all 6.17.0-1 [109 kB] Get: 230 http://deb.debian.org/debian bookworm/main i386 python3-markupsafe i386 2.1.2-1+b1 [13.3 kB] Get: 231 http://deb.debian.org/debian bookworm/main i386 python3-jinja2 all 3.1.2-1 [119 kB] Get: 232 http://deb.debian.org/debian bookworm/main i386 python3-joblib all 1.2.0-4 [211 kB] Get: 233 http://deb.debian.org/debian bookworm/main i386 python3-pyrsistent i386 0.18.1-1+b3 [60.5 kB] Get: 234 http://deb.debian.org/debian bookworm/main i386 python3-jsonschema all 4.10.3-1 [67.9 kB] Get: 235 http://deb.debian.org/debian bookworm/main i386 python3-jupyterlab-pygments all 0.2.2-3 [6096 B] Get: 236 http://deb.debian.org/debian bookworm/main i386 python3-kiwisolver i386 1.4.4-1+b1 [63.0 kB] Get: 237 http://deb.debian.org/debian bookworm/main i386 python3-pil i386 9.4.0-1.1+b1 [473 kB] Get: 238 http://deb.debian.org/debian bookworm/main i386 python3-tk i386 3.11.2-3 [99.2 kB] Get: 239 http://deb.debian.org/debian bookworm/main i386 python3-pil.imagetk i386 9.4.0-1.1+b1 [74.7 kB] Get: 240 http://deb.debian.org/debian bookworm/main i386 python3-pyparsing all 3.0.9-1 [138 kB] Get: 241 http://deb.debian.org/debian bookworm/main i386 python3-matplotlib i386 3.6.3-1+b1 [6891 kB] Get: 242 http://deb.debian.org/debian bookworm/main i386 sphinx-rtd-theme-common all 1.2.0+dfsg-1 [997 kB] Get: 243 http://deb.debian.org/debian bookworm/main i386 sphinx-common all 5.3.0-4 [653 kB] Get: 244 http://deb.debian.org/debian bookworm/main i386 python3-urllib3 all 1.26.12-1 [117 kB] Get: 245 http://deb.debian.org/debian bookworm/main i386 python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get: 246 http://deb.debian.org/debian bookworm/main i386 python3-snowballstemmer all 2.2.0-2 [57.8 kB] Get: 247 http://deb.debian.org/debian bookworm/main i386 python3-sphinx all 5.3.0-4 [549 kB] Get: 248 http://deb.debian.org/debian bookworm/main i386 python3-sphinx-rtd-theme all 1.2.0+dfsg-1 [27.7 kB] Get: 249 http://deb.debian.org/debian bookworm/main i386 python3-msmb-theme all 1.2.0-3 [33.7 kB] Get: 250 http://deb.debian.org/debian bookworm/main i386 python3-nbformat all 5.5.0-1 [43.2 kB] Get: 251 http://deb.debian.org/debian bookworm/main i386 python3-nbclient all 0.7.2-1 [62.1 kB] Get: 252 http://deb.debian.org/debian bookworm/main i386 python3-pandocfilters all 1.5.0-1 [23.7 kB] Get: 253 http://deb.debian.org/debian bookworm/main i386 python3-tinycss2 all 1.2.1-2 [21.9 kB] Get: 254 http://deb.debian.org/debian bookworm/main i386 python3-nbconvert all 6.5.3-3 [163 kB] Get: 255 http://deb.debian.org/debian bookworm/main i386 python3-networkx all 2.8.8-1 [1425 kB] Get: 256 http://deb.debian.org/debian bookworm/main i386 python3-numexpr i386 2.8.4-1+b2 [95.2 kB] Get: 257 http://deb.debian.org/debian bookworm/main i386 python3-numpydoc all 1.5.0-1 [43.0 kB] Get: 258 http://deb.debian.org/debian bookworm/main i386 python3-pandas-lib i386 1.5.3+dfsg-2 [3382 kB] Get: 259 http://deb.debian.org/debian bookworm/main i386 python3-pandas all 1.5.3+dfsg-2 [2885 kB] Get: 260 http://deb.debian.org/debian bookworm/main i386 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 261 http://deb.debian.org/debian bookworm/main i386 python3-sklearn-lib i386 1.2.1+dfsg-1 [2395 kB] Get: 262 http://deb.debian.org/debian bookworm/main i386 python3-sklearn all 1.2.1+dfsg-1 [2103 kB] Get: 263 http://deb.debian.org/debian bookworm/main i386 python3-tables-lib i386 3.7.0-5+b1 [399 kB] Get: 264 http://deb.debian.org/debian bookworm/main i386 python3-tables all 3.7.0-5 [339 kB] Fetched 170 MB in 10s (17.0 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 ... 18156 files and directories currently installed.) Preparing to unpack .../0-fonts-lato_2.0-2.1_all.deb ... Unpacking fonts-lato (2.0-2.1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../1-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... 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_0.188-2.1_all.deb ... Unpacking libdebuginfod-common (0.188-2.1) ... Selecting previously unselected package libpython3.11-minimal:i386. Preparing to unpack .../4-libpython3.11-minimal_3.11.2-6_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.2-6) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../5-libexpat1_2.5.0-1_i386.deb ... Unpacking libexpat1:i386 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../6-python3.11-minimal_3.11.2-6_i386.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:i386 (3.11.2-6) ... Setting up libexpat1:i386 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... 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 ... 18583 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_i386.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:i386. Preparing to unpack .../3-libreadline8_8.2-1.3_i386.deb ... Unpacking libreadline8:i386 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_i386.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... 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 ... 19017 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_i386.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package tzdata. Preparing to unpack .../002-tzdata_2023c-5+deb12u1_all.deb ... Unpacking tzdata (2023c-5+deb12u1) ... Selecting previously unselected package libproc2-0:i386. Preparing to unpack .../003-libproc2-0_2%3a4.0.2-3_i386.deb ... Unpacking libproc2-0:i386 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../004-procps_2%3a4.0.2-3_i386.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.0.11-1~deb12u2_i386.deb ... Unpacking openssl (3.0.11-1~deb12u2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.44-3_i386.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../008-libmagic1_1%3a5.44-3_i386.deb ... Unpacking libmagic1:i386 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.44-3_i386.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.21-12_i386.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../011-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.22.4-10_i386.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.38.1-5+b1_i386.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../014-libpipeline1_1.5.7-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.11.2-2_i386.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../016-m4_1.4.19-3_i386.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../017-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../018-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../019-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 .../020-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libtcl8.6:i386. Preparing to unpack .../021-libtcl8.6_8.6.13+dfsg-2_i386.deb ... Unpacking libtcl8.6:i386 (8.6.13+dfsg-2) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../022-libbrotli1_1.0.9-2+b6_i386.deb ... Unpacking libbrotli1:i386 (1.0.9-2+b6) ... Selecting previously unselected package libpng16-16:i386. Preparing to unpack .../023-libpng16-16_1.6.39-2_i386.deb ... Unpacking libpng16-16:i386 (1.6.39-2) ... Selecting previously unselected package libfreetype6:i386. Preparing to unpack .../024-libfreetype6_2.12.1+dfsg-5_i386.deb ... Unpacking libfreetype6:i386 (2.12.1+dfsg-5) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../025-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../026-fontconfig-config_2.14.1-4_i386.deb ... Unpacking fontconfig-config (2.14.1-4) ... Selecting previously unselected package libfontconfig1:i386. Preparing to unpack .../027-libfontconfig1_2.14.1-4_i386.deb ... Unpacking libfontconfig1:i386 (2.14.1-4) ... Selecting previously unselected package libxau6:i386. Preparing to unpack .../028-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 .../029-libbsd0_0.11.7-2_i386.deb ... Unpacking libbsd0:i386 (0.11.7-2) ... Selecting previously unselected package libxdmcp6:i386. Preparing to unpack .../030-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 .../031-libxcb1_1.15-1_i386.deb ... Unpacking libxcb1:i386 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../032-libx11-data_2%3a1.8.4-2+deb12u2_all.deb ... Unpacking libx11-data (2:1.8.4-2+deb12u2) ... Selecting previously unselected package libx11-6:i386. Preparing to unpack .../033-libx11-6_2%3a1.8.4-2+deb12u2_i386.deb ... Unpacking libx11-6:i386 (2:1.8.4-2+deb12u2) ... Selecting previously unselected package libxrender1:i386. Preparing to unpack .../034-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 .../035-libxft2_2.3.6-1_i386.deb ... Unpacking libxft2:i386 (2.3.6-1) ... Selecting previously unselected package libxext6:i386. Preparing to unpack .../036-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 .../037-x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) ... Selecting previously unselected package libxss1:i386. Preparing to unpack .../038-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 .../039-libtk8.6_8.6.13-2_i386.deb ... Unpacking libtk8.6:i386 (8.6.13-2) ... Selecting previously unselected package tk8.6-blt2.5. Preparing to unpack .../040-tk8.6-blt2.5_2.5.3+dfsg-4.1_i386.deb ... Unpacking tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Selecting previously unselected package blt. Preparing to unpack .../041-blt_2.5.3+dfsg-4.1_i386.deb ... Unpacking blt (2.5.3+dfsg-4.1) ... Selecting previously unselected package cython3. Preparing to unpack .../042-cython3_0.29.32-2+b1_i386.deb ... Unpacking cython3 (0.29.32-2+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../043-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../044-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../045-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../046-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 .../047-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../048-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../049-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../050-libelf1_0.188-2.1_i386.deb ... Unpacking libelf1:i386 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../051-dwz_0.15-1_i386.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:i386. 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Setting up libpgm-5.3-0:i386 (5.3.128~dfsg-2) ... Setting up fonts-lyx (2.3.7-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:i386 (1.0.9-2+b6) ... Setting up libnorm1:i386 (1.5.9+dfsg-2) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:i386 (1.52.0-1+deb12u1) ... Setting up libmagic1:i386 (1:5.44-3) ... Setting up libdeflate0:i386 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up libqhull-r8.0:i386 (2020.2-5) ... Setting up liblzo2-2:i386 (2.10-2) ... Setting up file (1:5.44-3) ... Setting up libjbig0:i386 (2.1-6.1) ... Setting up libaec0:i386 (1.0.6-1+b1) ... Setting up libsource-highlight-common (3.1.9-4.2) ... Setting up python-babel-localedata (2.10.3-1) ... Setting up libsnappy1v5:i386 (1.1.9-3) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg-10) ... Setting up tzdata (2023c-5+deb12u1) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Jan 22 13:38:29 UTC 2024. Universal Time is now: Mon Jan 22 13:38:29 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.0.0-1) ... Setting up libxsimd-dev:i386 (8.1.0-7) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.11.0-2) ... 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 (2.5.0-1) ... Setting up libjpeg62-turbo:i386 (1:2.1.5-2) ... Setting up libx11-data (2:1.8.4-2+deb12u2) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libfribidi0:i386 (1.0.8-2.1) ... Setting up libboost-regex1.74.0:i386 (1.74.0+ds1-21) ... Setting up libimagequant0:i386 (2.17.0-1) ... Setting up libproc2-0:i386 (2:4.0.2-3) ... Setting up libpng16-16:i386 (1.6.39-2) ... Setting up libtcl8.6:i386 (8.6.13+dfsg-2) ... Setting up autopoint (0.21-12) ... Setting up libipt2 (2.0.5-1) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libsasl2-2:i386 (2.1.28+dfsg-10) ... Setting up libgfortran5:i386 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:i386 (1.2.4-0.2+deb12u1) ... Setting up zlib1g-dev:i386 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libtiff6:i386 (4.5.0-6+deb12u1) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up python-tinycss2-common (1.2.1-2) ... Setting up libjson-perl (4.10000-1) ... Setting up libblosc1:i386 (1.21.3+ds-1) ... Setting up libopenjp2-7:i386 (2.5.0-2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:i386 (1.10.0-3+b1) ... Setting up sgml-base (1.31) ... Setting up libboost-dev:i386 (1.74.0.3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.6.3-1) ... Setting up openssl (3.0.11-1~deb12u2) ... Setting up libwebpmux3:i386 (1.2.4-0.2+deb12u1) ... Setting up libbsd0:i386 (0.11.7-2) ... Setting up libelf1:i386 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3~deb12u1) ... Setting up python-tables-data (3.7.0-5) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (1.2.0+dfsg-1) ... Setting up libsz2:i386 (1.0.6-1+b1) ... Setting up libsource-highlight4v5:i386 (3.1.9-4.2+b3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libdw1:i386 (0.188-2.1) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up liblapack3:i386 (3.11.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up libxcb1:i386 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libopenblas0-pthread:i386 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/i386-linux-gnu/libopenblas.so.0 (libopenblas.so.0-i386-linux-gnu) in auto mode Setting up libzmq5:i386 (4.3.4-6) ... Setting up libtool (2.4.7-5) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libwebpdemux2:i386 (1.2.4-0.2+deb12u1) ... Setting up libreadline8:i386 (8.2-1.3) ... Setting up libldap-2.5-0:i386 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:i386 (2.12.1+dfsg-5) ... Setting up ucf (3.0043+nmu1) ... Setting up libbabeltrace1:i386 (1.5.11-1+b2) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libopenblas0:i386 (0.3.21+ds-4) ... Setting up groff-base (1.22.4-10) ... Setting up xml-core (0.18+nmu1) ... Setting up libxslt1.1:i386 (1.1.35-1) ... Setting up libcurl4:i386 (7.88.1-10+deb12u4) ... Setting up libx11-6:i386 (2:1.8.4-2+deb12u2) ... Setting up libharfbuzz0b:i386 (6.0.0+dfsg-3) ... Setting up libfontconfig1:i386 (2.14.1-4) ... Setting up liblbfgsb0:i386 (3.0+dfsg.4-1) ... Setting up libopenblas-pthread-dev:i386 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) in auto mode update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/i386-linux-gnu/liblapack.so (liblapack.so-i386-linux-gnu) in auto mode update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/i386-linux-gnu/libopenblas.so (libopenblas.so-i386-linux-gnu) in auto mode Setting up libxrender1:i386 (1:0.9.10-1.1) ... Setting up libdebuginfod-common (0.188-2.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:i386 (3.11.2-6) ... Setting up libxext6:i386 (2:1.3.4-1+b1) ... Setting up libcurl3-gnutls:i386 (7.88.1-10+deb12u4) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libopenblas-dev:i386 (0.3.21+ds-4) ... Setting up libraqm0:i386 (0.7.0-4.1) ... Setting up sphinx-common (5.3.0-4) ... Setting up libhdf5-103-1:i386 (1.10.8+repack1-1) ... Setting up libxss1:i386 (1:1.2.3-1) ... Setting up libpython3-stdlib:i386 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libxft2:i386 (2.3.6-1) ... Setting up libpython3.11:i386 (3.11.2-6) ... Setting up libtk8.6:i386 (8.6.13-2) ... Setting up libdebuginfod1:i386 (0.188-2.1) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up python3-pandocfilters (1.5.0-1) ... Setting up python3-markupsafe (2.1.2-1+b1) ... Setting up python3-webencodings (0.5.1-5) ... Setting up python3-psutil (5.9.4-1+b1) ... Setting up python3-tz (2022.7.1-4) ... Setting up python3-six (1.16.0-4) ... Setting up python3-roman (3.3-3) ... Setting up python3-decorator (5.1.1-3) ... Setting up python3-jinja2 (3.1.2-1) ... Setting up python3-packaging (23.0-1) ... Setting up gdb (13.1-3) ... Setting up python3-wcwidth (0.2.5+dfsg1-1.1) ... Setting up python3-pyparsing (3.0.9-1) ... Setting up python3-certifi (2022.9.24-1) ... Setting up python3-snowballstemmer (2.2.0-2) ... Setting up libpython3.11-dev:i386 (3.11.2-6) ... Setting up python3-nest-asyncio (1.5.4-1) ... Setting up python3-brotli (1.0.9-2+b6) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-bytecode (0.14.0-2) ... Setting up python3-kiwisolver (1.4.4-1+b1) ... Setting up python3-idna (3.3-1) ... Setting up cython3 (0.29.32-2+b1) ... Setting up python3-html5lib (1.1-3) ... Setting up python3-pickleshare (0.7.5-5) ... Setting up python3-urllib3 (1.26.12-1) ... Setting up python3-fastjsonschema (2.16.3-2) ... Setting up python3-pyrsistent:i386 (0.18.1-1+b3) ... Setting up python3-lxml:i386 (4.9.2-1+b1) ... Setting up python3-traitlets (5.5.0-1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-appdirs (1.4.4-3) ... Setting up python3-soupsieve (2.3.2-1) ... Setting up python3-cffi-backend:i386 (1.15.1-5+b1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-ptyprocess (0.7.0-5) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-entrypoints (0.4-2) ... Setting up python3-prompt-toolkit (3.0.36-2) ... Setting up python3-distutils (3.11.2-3) ... Setting up dh-python (5.20230130+deb12u1) ... Setting up python3-sympy (1.11.1-1) ... Setting up python3-attr (22.2.0-1) ... Setting up python3-tornado (6.2.0-3) ... Setting up python3-pure-eval (0.2.2-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Setting up python3-astunparse (1.6.3-2) ... Setting up python3-tinycss2 (1.2.1-2) ... Setting up libpython3-dev:i386 (3.11.2-1+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-py (1.11.0-1) ... Setting up python3-backcall (0.2.0-4) ... Setting up python3-joblib (1.2.0-4) ... Setting up python3-parso (0.8.3-1) ... Setting up python3-babel (2.10.3-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-lz4 (4.0.2+dfsg-1+b2) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-asttokens (2.2.1-1) ... Setting up python3.11-dev (3.11.2-6) ... Setting up python3-charset-normalizer (3.0.1-2) ... Setting up python3-alabaster (0.7.12-1) ... Setting up blt (2.5.3+dfsg-4.1) ... Setting up python3-ply (3.11-5) ... Setting up python3-threadpoolctl (3.1.0-1) ... Setting up python3-gast (0.5.2-2) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-coverage (6.5.0+dfsg1-2+b1) ... Setting up python3-tk:i386 (3.11.2-3) ... Setting up python3-networkx (2.8.8-1) ... Setting up python3-bs4 (4.11.2-2) ... Setting up python3-bleach (5.0.1-2) ... Setting up python3-matplotlib-inline (0.1.6-2) ... Setting up python3-fs (2.4.16-2) ... Setting up python3-beniget (0.4.1-3) ... Setting up python3-pygments (2.14.0+dfsg-1) ... Setting up python3-chardet (5.1.0+dfsg-2) ... Setting up python3-jsonschema (4.10.3-1) ... Setting up python3-executing (1.2.0-2) ... Setting up libpython3-all-dev:i386 (3.11.2-1+b1) ... Setting up python3-pexpect (4.8.0-4) ... Setting up python3-zmq (24.0.1-4+b1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up python3-requests (2.28.1+dfsg-1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-contourpy (1.0.7-1+b1) ... Setting up python3-pydevd (2.9.5+ds-4) ... Setting up python3-stack-data (0.6.2-3) ... Setting up python3-jupyter-core (4.12.0-1) ... Setting up python3-all-dev (3.11.2-1+b1) ... Setting up python3-jedi (0.18.2-1) ... Setting up python3-tables-lib (3.7.0-5+b1) ... Setting up python3-pandas-lib:i386 (1.5.3+dfsg-2) ... Setting up python3-sklearn-lib:i386 (1.2.1+dfsg-1) ... Setting up python3-nbformat (5.5.0-1) ... Setting up python3-debugpy (1.6.6+ds-1) ... Setting up python3-jupyterlab-pygments (0.2.2-3) ... Setting up python3-pandas (1.5.3+dfsg-2) ... Setting up python3-ipython (8.5.0-4) ... Setting up python3-numexpr (2.8.4-1+b2) ... Setting up python3-pythran (0.11.0+ds-7) ... Setting up python3-jupyter-client (7.4.9-2) ... Setting up python3-scipy (1.10.1-2) ... Setting up python3-tables (3.7.0-5) ... Setting up python3-nbclient (0.7.2-1) ... Setting up python3-ipykernel (6.17.0-1) ... Setting up python3-sklearn (1.2.1+dfsg-1) ... Setting up python3-nbconvert (6.5.3-3) ... Setting up python3-fonttools (4.38.0-1+b1) ... Setting up python3-pil.imagetk:i386 (9.4.0-1.1+b1) ... Setting up python3-ufolib2 (0.14.0+dfsg1-1) ... Setting up python3-pil:i386 (9.4.0-1.1+b1) ... Setting up python3-matplotlib (3.6.3-1+b1) ... Processing triggers for libc-bin (2.36-9+deb12u3) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.19+dfsg-6) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.19+dfsg-6) ... Setting up python3-sphinx (5.3.0-4) ... Setting up python3-sphinx-rtd-theme (1.2.0+dfsg-1) ... Setting up python3-numpydoc (1.5.0-1) ... Setting up python3-msmb-theme (1.2.0-3) ... Processing triggers for ca-certificates (20230311) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.31-1.2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/13800/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bookworm I: user script /srv/workspace/pbuilder/13800/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/mdtraj-1.9.7/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../mdtraj_1.9.7-6_source.changes dpkg-buildpackage: info: source package mdtraj dpkg-buildpackage: info: source version 1.9.7-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Drew Parsons dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 dpkg-source: info: using options from mdtraj-1.9.7/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ fakeroot debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/mdtraj-1.9.7' dh_auto_clean || /bin/true I: pybuild base:240: python3.11 setup.py clean Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/12/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --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-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 12.2.0 (Debian 12.2.0-14) /build/reproducible-path/mdtraj-1.9.7/basesetup.py:431: UserWarning: Unrecognized setuptools command ('clean'), proceeding with generating Cython sources and expanding templates warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " /usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar. if not hasattr(numpy, method): /usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar. obj = getattr(themodule, elem) 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 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-1.9.7/.pybuild/cpython3_3.11_mdtraj/build' (and everything under it) 'build/bdist.linux-i386' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it 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__ make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.9.7' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build dh build --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py config Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/12/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --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-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 12.2.0 (Debian 12.2.0-14) /build/reproducible-path/mdtraj-1.9.7/basesetup.py:431: UserWarning: Unrecognized setuptools command ('config'), proceeding with generating Cython sources and expanding templates warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " /usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar. if not hasattr(numpy, method): /usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar. obj = getattr(themodule, elem) 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 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 debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/mdtraj-1.9.7' dh_auto_build I: pybuild base:240: /usr/bin/python3 setup.py build Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/12/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --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-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 12.2.0 (Debian 12.2.0-14) /usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar. if not hasattr(numpy, method): /usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar. obj = getattr(themodule, elem) 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 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 build running build_py creating /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj copying mdtraj/io.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj copying mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj copying mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj creating /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats copying mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing copying mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing copying mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing copying mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing copying mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing creating /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/six.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils creating /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core copying mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core copying mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core copying mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core copying mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core copying mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core copying mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/data running build_ext building 'mdtraj.formats.xtc' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC creating build creating build/temp.linux-i386-cpython-311 creating build/temp.linux-i386-cpython-311/mdtraj creating build/temp.linux-i386-cpython-311/mdtraj/formats creating build/temp.linux-i386-cpython-311/mdtraj/formats/xtc creating build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/src INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/src/xdr_seek.c INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile.c INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile_xtc.c INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/xtc.c 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 { | ^~ 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; | ^~~~~~ 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:778: /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/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write': mdtraj/formats/xtc/xtc.c:690:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 690 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:9539:7: note: '__pyx_v_status' was declared here 9539 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:8058:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8058 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6461:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 6461 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8054:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8054 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6461:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 6461 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8050:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8050 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6461:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 6461 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8010:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8010 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6457:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 6457 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7992:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7992 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6453:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 6453 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8068:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8068 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6449:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 6449 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8030:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8030 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6443:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 6443 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8026:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8026 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6443:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 6443 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8022:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8022 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6443:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 6443 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7645:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 7645 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6445:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 6445 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7641:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7641 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6445:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 6445 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ INFO: i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/xtc.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/xtc.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.trr' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/src/xdr_seek.c INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile.c INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile_trr.c INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/trr.c 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; | ^~~~~~ 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:778: /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/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write': mdtraj/formats/xtc/trr.c:690:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 690 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:11065:7: note: '__pyx_v_status' was declared here 11065 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:8418:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8418 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 6955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8414:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8414 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 6955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1929:95: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1929 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 6955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8408:59: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8408 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 6955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8361:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8361 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 6971 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8357:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8357 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 6971 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1929:95: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1929 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 6971 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8351:56: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8351 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 6971 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8751:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8751 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6977:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 6977 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8747:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8747 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6977:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 6977 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8592:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8592 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6973:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 6973 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8588:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8588 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6973:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 6973 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8644:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8644 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6957:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 6957 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8640:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8640 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6957:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 6957 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ INFO: i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/trr.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/trr.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.tng' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC creating build/temp.linux-i386-cpython-311/mdtraj/formats/tng creating build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src creating build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression creating build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/lib INFO: compile options: '-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' INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/bwlzh.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/bwt.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/coder.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/dict.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/fixpoint.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/huffman.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/huffmem.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/lz77.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/merge_sort.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/mtf.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/rle.c 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) | ^~ 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]) | ^~ INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/tng_compress.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/vals16.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/warnmalloc.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/widemuldiv.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/xtc2.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/xtc3.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/lib/md5.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/lib/tng_io.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/tng.c 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 = | ^ 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:804: /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/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/tng.c: In function '__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__': mdtraj/formats/tng/tng.c:3692:104: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3692 | __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:3747:88: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3747 | __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:3779:90: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3779 | __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:3811:95: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3811 | __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:3881:113: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3881 | __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:3925:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3925 | __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:4721:106: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4721 | __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:4766:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4766 | __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:4873:115: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4873 | __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:4903:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4903 | __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:5031:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5031 | __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:5632:126: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5632 | __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:6042:152: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6042 | __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:6310:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6310 | __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:6412:304: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6412 | __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:8904:94: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8904 | __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:8936:75: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8936 | __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:8968:81: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8968 | __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:9291:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9291 | __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:9482:372: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9482 | __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:9534:378: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9534 | __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:9596:89: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9596 | __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); | ^~ 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); | ^~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: 'num_first_particle' may be used uninitialized [-Wmaybe-uninitialized] 5986 | for(j = num_first_particle; j < num_first_particle + n_particles; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 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; | ^~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: 'n_particles' may be used uninitialized [-Wmaybe-uninitialized] 5986 | for(j = num_first_particle; j < num_first_particle + n_particles; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 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; | ^~~~~~~~~~~ INFO: i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib/i386-linux-gnu -lz -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/tng.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.dcd' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC creating build/temp.linux-i386-cpython-311/mdtraj/formats/dcd creating build/temp.linux-i386-cpython-311/mdtraj/formats/dcd/src INFO: compile options: '-Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/formats/dcd/src/dcdplugin.c INFO: i686-linux-gnu-gcc: mdtraj/formats/dcd/dcd.c 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:776: /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/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:688:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 688 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c:5434:7: note: '__pyx_v_i' was declared here 5434 | int __pyx_v_i; | ^~~~~~~~~ INFO: i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/formats/dcd/dcd.o build/temp.linux-i386-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dcd.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.binpos' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC creating build/temp.linux-i386-cpython-311/mdtraj/formats/binpos creating build/temp.linux-i386-cpython-311/mdtraj/formats/binpos/src INFO: compile options: '-Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/formats/binpos/binpos.c INFO: i686-linux-gnu-gcc: mdtraj/formats/binpos/src/binposplugin.c 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:776: /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:4980:13: mdtraj/formats/binpos/binpos.c:5512:6: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 5512 | if (__pyx_t_2) { | ^ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:4992:7: note: '__pyx_v_status' was declared here 4992 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c:688:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 688 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c:4989:7: note: '__pyx_v_i' was declared here 4989 | int __pyx_v_i; | ^~~~~~~~~ INFO: i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/formats/binpos/binpos.o build/temp.linux-i386-cpython-311/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/binpos.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.dtr' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC creating build/temp.linux-i386-cpython-311/mdtraj/formats/dtr creating build/temp.linux-i386-cpython-311/mdtraj/formats/dtr/src INFO: compile options: '-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' extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/formats/dtr/dtr.cpp INFO: i686-linux-gnu-gcc: mdtraj/formats/dtr/src/dtrplugin.cxx 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:797: /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/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 ()); | ~~~~~~~~~~~~~~~~~ INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/formats/dtr/dtr.o build/temp.linux-i386-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dtr.cpython-311-i386-linux-gnu.so building 'mdtraj._rmsd' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC creating build/temp.linux-i386-cpython-311/mdtraj/rmsd creating build/temp.linux-i386-cpython-311/mdtraj/rmsd/src INFO: compile options: '-Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-fopenmp -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/rmsd/_rmsd.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/center.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/rotation.cpp INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/rmsd/_rmsd.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_rmsd.cpython-311-i386-linux-gnu.so building 'mdtraj._lprmsd' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-fopenmp -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/rmsd/_lprmsd.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/center.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/Munkres.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/rotation.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/fancy_index.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/euclidean_permutation.cpp 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:807: /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 " \ | ^~~~~~~ INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/rmsd/_lprmsd.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/Munkres.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/fancy_index.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_lprmsd.cpython-311-i386-linux-gnu.so building 'mdtraj.core.lib.libtheobald' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-mssse3 -O3 -funroll-loops --std=c++11' INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/center.cpp INFO: i686-linux-gnu-gcc-ar: adding 2 object files to /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/lib/libtheobald.a building 'mdtraj.geometry._geometry' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC creating build/temp.linux-i386-cpython-311/mdtraj/geometry creating build/temp.linux-i386-cpython-311/mdtraj/geometry/src INFO: compile options: '-Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-fopenmp -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/_geometry.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/dssp.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/sasa.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/geometry.cpp 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:809: /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:6085:224: warning: '__pyx_v_delta[2]' may be used uninitialized [-Wmaybe-uninitialized] 6085 | (__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:6006:9: note: '__pyx_v_delta[2]' was declared here 6006 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6099:277: warning: '__pyx_v_delta[1]' may be used uninitialized [-Wmaybe-uninitialized] 6099 | (__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:6006:9: note: '__pyx_v_delta[1]' was declared here 6006 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6099:277: warning: '__pyx_v_offset[1]' may be used uninitialized [-Wmaybe-uninitialized] 6099 | (__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:6005:9: note: '__pyx_v_offset[1]' was declared here 6005 | float __pyx_v_offset[3]; | ^~~~~~~~~~~~~~ INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/geometry/src/_geometry.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/dssp.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/geometry.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/sasa.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/_geometry.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry.drid' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-fopenmp -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/geometry/drid.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/dridkernels.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/moments.cpp INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/geometry/drid.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/dridkernels.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/moments.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/drid.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry.neighbors' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-fopenmp -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/geometry/neighbors.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/neighbors.cpp In file included from /usr/lib/gcc/i686-linux-gnu/12/include/emmintrin.h:31, from /usr/lib/gcc/i686-linux-gnu/12/include/pmmintrin.h:31, from mdtraj/geometry/include/vectorize.h:38, from mdtraj/geometry/src/neighbors.cpp:4: In function '__m128 _mm_mul_ps(__m128, __m128)', inlined from 'fvec4 fvec4::operator*(const fvec4&) const' at mdtraj/geometry/include/vectorize_sse.h:167:37, inlined from 'std::vector _compute_neighbors(float*, int, float, const std::vector&, const std::vector&, float*)' at mdtraj/geometry/src/neighbors.cpp:55:52: /usr/lib/gcc/i686-linux-gnu/12/include/xmmintrin.h:198:45: warning: 'box_size.fvec4::val' may be used uninitialized [-Wmaybe-uninitialized] 198 | return (__m128) ((__v4sf)__A * (__v4sf)__B); | ^ mdtraj/geometry/src/neighbors.cpp: In function 'std::vector _compute_neighbors(float*, int, float, const std::vector&, const std::vector&, float*)': mdtraj/geometry/src/neighbors.cpp:19:11: note: 'box_size.fvec4::val' was declared here 19 | fvec4 box_size, inv_box_size, box_vec1, box_vec2, box_vec3; | ^~~~~~~~ INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/geometry/neighbors.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/neighbors.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighbors.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-fopenmp -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/neighborlist.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/neighborlist.cpp 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]; | ^~~~~~~~~~~~~~~~~~ INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/geometry/neighborlist.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/neighborlist.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighborlist.cpython-311-i386-linux-gnu.so cp -a /build/reproducible-path/mdtraj-1.9.7/examples /build/reproducible-path/mdtraj-1.9.7/examples.orig mkdir -p /build/reproducible-path/mdtraj-1.9.7/build/html/examples/iterload ln -s /build/reproducible-path/mdtraj-1.9.7/examples/data /build/reproducible-path/mdtraj-1.9.7/build/html/examples/iterload/data sed "s|http://www.rcsb.org/pdb/files|/build/reproducible-path/mdtraj-1.9.7/debian/external|g" -i /build/reproducible-path/mdtraj-1.9.7/examples/*.ipynb PYTHONPATH=/build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build \ MPLCONFIGDIR=/build/reproducible-path/mdtraj-1.9.7/build/matplotlib \ make -C docs BUILDDIR=/build/reproducible-path/mdtraj-1.9.7/build html make[2]: Entering directory '/build/reproducible-path/mdtraj-1.9.7/docs' sphinx-build -b html -d /build/reproducible-path/mdtraj-1.9.7/build/doctrees . /build/reproducible-path/mdtraj-1.9.7/build/html Running Sphinx v5.3.0 [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-1.9.7/docs/api/generated/mdtraj.Topology.rst, /build/reproducible-path/mdtraj-1.9.7/docs/api/generated/mdtraj.Trajectory.rst, /build/reproducible-path/mdtraj-1.9.7/docs/api/generated/mdtraj.Trajectory.superpose.rst, /build/reproducible-path/mdtraj-1.9.7/docs/api/generated/mdtraj.acylindricity.rst, /build/reproducible-path/mdtraj-1.9.7/docs/api/generated/mdtraj.asphericity.rst, /build/reproducible-path/mdtraj-1.9.7/docs/api/generated/mdtraj.baker_hubbard.rst, /build/reproducible-path/mdtraj-1.9.7/docs/api/generated/mdtraj.chemical_shifts_ppm.rst, /build/reproducible-path/mdtraj-1.9.7/docs/api/generated/mdtraj.chemical_shifts_shiftx2.rst, /build/reproducible-path/mdtraj-1.9.7/docs/api/generated/mdtraj.chemical_shifts_spartaplus.rst, /build/reproducible-path/mdtraj-1.9.7/docs/api/generated/mdtraj.compute_J3_HN_C.rst, ..., /build/reproducible-path/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.check_random_state.rst, /build/reproducible-path/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.ensure_type.rst, /build/reproducible-path/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.ilen.rst, /build/reproducible-path/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.import_.rst, /build/reproducible-path/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.in_units_of.rst, /build/reproducible-path/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors.rst, /build/reproducible-path/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.rotation_matrix_from_quaternion.rst, /build/reproducible-path/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.timing.rst, /build/reproducible-path/mdtraj-1.9.7/docs/api/generated/mdtraj.utils.uniform_quaternion.rst, /build/reproducible-path/mdtraj-1.9.7/docs/api/generated/mdtraj.wernet_nilsson.rst building [mo]: targets for 0 po files that are out of date building [html]: targets for 29 source files that are out of date updating environment: [new config] 127 added, 0 changed, 0 removed reading sources... [ 0%] analysis reading sources... [ 1%] api/generated/mdtraj.Topology /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: 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-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/topology.py. warn(msg) /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: 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-1.9.7/.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... [ 3%] api/generated/mdtraj.acylindricity reading sources... [ 4%] api/generated/mdtraj.asphericity reading sources... [ 5%] api/generated/mdtraj.baker_hubbard reading sources... [ 6%] api/generated/mdtraj.chemical_shifts_ppm reading sources... [ 7%] api/generated/mdtraj.chemical_shifts_shiftx2 reading sources... [ 7%] api/generated/mdtraj.chemical_shifts_spartaplus reading sources... [ 8%] api/generated/mdtraj.compute_J3_HN_C reading sources... [ 9%] api/generated/mdtraj.compute_J3_HN_CB reading sources... [ 10%] api/generated/mdtraj.compute_J3_HN_HA reading sources... [ 11%] api/generated/mdtraj.compute_angles reading sources... [ 11%] api/generated/mdtraj.compute_center_of_mass reading sources... [ 12%] api/generated/mdtraj.compute_chi1 reading sources... [ 13%] api/generated/mdtraj.compute_chi2 reading sources... [ 14%] api/generated/mdtraj.compute_chi3 reading sources... [ 14%] api/generated/mdtraj.compute_chi4 reading sources... [ 15%] api/generated/mdtraj.compute_contacts reading sources... [ 16%] api/generated/mdtraj.compute_dihedrals reading sources... [ 17%] api/generated/mdtraj.compute_directors reading sources... [ 18%] api/generated/mdtraj.compute_displacements reading sources... [ 18%] api/generated/mdtraj.compute_distances reading sources... [ 19%] api/generated/mdtraj.compute_drid reading sources... [ 20%] api/generated/mdtraj.compute_dssp reading sources... [ 21%] api/generated/mdtraj.compute_gyration_tensor reading sources... [ 22%] api/generated/mdtraj.compute_inertia_tensor reading sources... [ 22%] api/generated/mdtraj.compute_neighbors reading sources... [ 23%] api/generated/mdtraj.compute_nematic_order reading sources... [ 24%] api/generated/mdtraj.compute_omega reading sources... [ 25%] api/generated/mdtraj.compute_phi reading sources... [ 25%] api/generated/mdtraj.compute_psi reading sources... [ 26%] api/generated/mdtraj.compute_rdf reading sources... [ 27%] api/generated/mdtraj.compute_rg reading sources... [ 28%] api/generated/mdtraj.density reading sources... [ 29%] api/generated/mdtraj.dipole_moments reading sources... [ 29%] api/generated/mdtraj.formats.AmberNetCDFRestartFile reading sources... [ 30%] api/generated/mdtraj.formats.AmberRestartFile reading sources... [ 31%] api/generated/mdtraj.formats.ArcTrajectoryFile reading sources... [ 32%] api/generated/mdtraj.formats.BINPOSTrajectoryFile reading sources... [ 33%] api/generated/mdtraj.formats.DCDTrajectoryFile reading sources... [ 33%] api/generated/mdtraj.formats.DTRTrajectoryFile reading sources... [ 34%] api/generated/mdtraj.formats.GroTrajectoryFile reading sources... [ 35%] api/generated/mdtraj.formats.HDF5TrajectoryFile reading sources... [ 36%] api/generated/mdtraj.formats.LAMMPSTrajectoryFile reading sources... [ 37%] api/generated/mdtraj.formats.LH5TrajectoryFile reading sources... [ 37%] api/generated/mdtraj.formats.MDCRDTrajectoryFile reading sources... [ 38%] api/generated/mdtraj.formats.NetCDFTrajectoryFile reading sources... [ 39%] api/generated/mdtraj.formats.PDBTrajectoryFile reading sources... [ 40%] api/generated/mdtraj.formats.TRRTrajectoryFile reading sources... [ 40%] api/generated/mdtraj.formats.XTCTrajectoryFile reading sources... [ 41%] api/generated/mdtraj.formats.XYZTrajectoryFile reading sources... [ 42%] api/generated/mdtraj.geometry.squareform reading sources... [ 43%] api/generated/mdtraj.isothermal_compressability_kappa_T reading sources... [ 44%] api/generated/mdtraj.iterload reading sources... [ 44%] api/generated/mdtraj.join reading sources... [ 45%] api/generated/mdtraj.kabsch_sander reading sources... [ 46%] api/generated/mdtraj.load reading sources... [ 47%] api/generated/mdtraj.load_arc reading sources... [ 48%] api/generated/mdtraj.load_binpos reading sources... [ 48%] api/generated/mdtraj.load_dcd reading sources... [ 49%] api/generated/mdtraj.load_dtr reading sources... [ 50%] api/generated/mdtraj.load_frame reading sources... [ 51%] api/generated/mdtraj.load_hdf5 reading sources... [ 51%] api/generated/mdtraj.load_hoomdxml reading sources... [ 52%] api/generated/mdtraj.load_lammpstrj reading sources... [ 53%] api/generated/mdtraj.load_lh5 reading sources... [ 54%] api/generated/mdtraj.load_netcdf reading sources... [ 55%] api/generated/mdtraj.load_pdb reading sources... [ 55%] api/generated/mdtraj.load_prmtop reading sources... [ 56%] api/generated/mdtraj.load_trr reading sources... [ 57%] api/generated/mdtraj.load_xml reading sources... [ 58%] api/generated/mdtraj.load_xtc reading sources... [ 59%] api/generated/mdtraj.load_xyz reading sources... [ 59%] api/generated/mdtraj.lprmsd reading sources... [ 60%] api/generated/mdtraj.open reading sources... [ 61%] api/generated/mdtraj.principal_moments reading sources... [ 62%] api/generated/mdtraj.reindex_dataframe_by_atoms reading sources... [ 62%] api/generated/mdtraj.relative_shape_antisotropy reading sources... [ 63%] api/generated/mdtraj.reporters.DCDReporter reading sources... [ 64%] api/generated/mdtraj.reporters.HDF5Reporter reading sources... [ 65%] api/generated/mdtraj.reporters.NetCDFReporter reading sources... [ 66%] api/generated/mdtraj.rmsd reading sources... [ 66%] api/generated/mdtraj.rmsf reading sources... [ 67%] api/generated/mdtraj.shrake_rupley reading sources... [ 68%] api/generated/mdtraj.static_dielectric reading sources... [ 69%] api/generated/mdtraj.thermal_expansion_alpha_P reading sources... [ 70%] api/generated/mdtraj.utils.box_vectors_to_lengths_and_angles reading sources... [ 70%] api/generated/mdtraj.utils.check_random_state reading sources... [ 71%] api/generated/mdtraj.utils.ensure_type reading sources... [ 72%] api/generated/mdtraj.utils.ilen reading sources... [ 73%] api/generated/mdtraj.utils.import_ reading sources... [ 74%] api/generated/mdtraj.utils.in_units_of reading sources... [ 74%] api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors reading sources... [ 75%] api/generated/mdtraj.utils.rotation_matrix_from_quaternion reading sources... [ 76%] api/generated/mdtraj.utils.timing reading sources... [ 77%] api/generated/mdtraj.utils.uniform_quaternion reading sources... [ 77%] api/generated/mdtraj.wernet_nilsson reading sources... [ 78%] api/reporters reading sources... [ 79%] api/trajectory_files reading sources... [ 80%] api/utils reading sources... [ 81%] atom_selection reading sources... [ 81%] building_docs reading sources... [ 82%] examples/atom-selection reading sources... [ 83%] examples/centroids reading sources... [ 84%] examples/clustering reading sources... [ 85%] examples/hbonds reading sources... [ 85%] examples/index reading sources... [ 86%] examples/introduction reading sources... [ 87%] examples/iterload reading sources... [ 88%] examples/native-contact reading sources... [ 88%] examples/nmr reading sources... [ 89%] examples/openmm reading sources... [ 90%] examples/pca reading sources... [ 91%] examples/ramachandran-plot reading sources... [ 92%] examples/rmsd-benchmark reading sources... [ 92%] examples/solvent-accessible-surface-area reading sources... [ 93%] examples/two-pass-clustering reading sources... [ 94%] faq reading sources... [ 95%] hdf5_format reading sources... [ 96%] index reading sources... [ 96%] installation reading sources... [ 97%] load_functions reading sources... [ 98%] mdconvert reading sources... [ 99%] new_to_python reading sources... [100%] whatsnew /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.asphericity:4: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:4: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/mdtraj-1.9.7/.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-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:40: 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-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:4: WARNING: Block quote ends without a blank line; unexpected unindent. docstring of mdtraj._rmsd.rmsf:41: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/rotation.py:docstring of mdtraj.utils.rotation.uniform_quaternion:32: 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-1.9.7/docs/examples/atom-selection.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/atom-selection.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.7/docs/examples/centroids.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/centroids.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.7/docs/examples/clustering.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/clustering.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.7/docs/examples/hbonds.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/hbonds.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.7/docs/examples/iterload.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/iterload.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.7/docs/examples/native-contact.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/native-contact.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.7/docs/examples/nmr.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/nmr.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.7/docs/examples/openmm.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/simulation-with-openmm.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.7/docs/examples/pca.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/principal-components.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.7/docs/examples/ramachandran-plot.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/ramachandran-plot.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.7/docs/examples/rmsd-benchmark.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/rmsd-benchmark.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.7/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-1.9.7/docs/examples/two-pass-clustering.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/two-pass-clustering.ipynb :skip_exceptions: /build/reproducible-path/mdtraj-1.9.7/docs/installation.rst:1: WARNING: malformed hyperlink target. /build/reproducible-path/mdtraj-1.9.7/docs/mdconvert.rst:2: WARNING: Title underline too short. ``mdconvert`` (``mdconvert-mdtraj``) ============= /build/reproducible-path/mdtraj-1.9.7/docs/whatsnew.rst:7: 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-1.9.7/docs/building_docs.rst: WARNING: document isn't included in any toctree /build/reproducible-path/mdtraj-1.9.7/docs/faq.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 0%] analysis writing output... [ 1%] api/generated/mdtraj.Topology writing output... [ 2%] api/generated/mdtraj.Trajectory writing output... [ 3%] api/generated/mdtraj.Trajectory.superpose writing output... [ 3%] api/generated/mdtraj.acylindricity writing output... [ 4%] api/generated/mdtraj.asphericity writing output... [ 5%] 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... [ 7%] api/generated/mdtraj.chemical_shifts_spartaplus writing output... [ 8%] 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... [ 11%] api/generated/mdtraj.compute_center_of_mass writing output... [ 12%] api/generated/mdtraj.compute_chi1 writing output... [ 13%] api/generated/mdtraj.compute_chi2 writing output... [ 14%] api/generated/mdtraj.compute_chi3 writing output... [ 14%] api/generated/mdtraj.compute_chi4 writing output... [ 15%] api/generated/mdtraj.compute_contacts writing output... [ 16%] api/generated/mdtraj.compute_dihedrals writing output... [ 17%] api/generated/mdtraj.compute_directors writing output... [ 18%] api/generated/mdtraj.compute_displacements writing output... [ 18%] api/generated/mdtraj.compute_distances writing output... [ 19%] 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... [ 22%] api/generated/mdtraj.compute_neighbors writing output... [ 23%] api/generated/mdtraj.compute_nematic_order writing output... [ 24%] api/generated/mdtraj.compute_omega writing output... [ 25%] api/generated/mdtraj.compute_phi writing output... [ 25%] api/generated/mdtraj.compute_psi writing output... [ 26%] api/generated/mdtraj.compute_rdf writing output... [ 27%] api/generated/mdtraj.compute_rg writing output... [ 28%] api/generated/mdtraj.density writing output... [ 29%] api/generated/mdtraj.dipole_moments writing output... [ 29%] api/generated/mdtraj.formats.AmberNetCDFRestartFile writing output... [ 30%] 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... [ 33%] api/generated/mdtraj.formats.DTRTrajectoryFile writing output... [ 34%] api/generated/mdtraj.formats.GroTrajectoryFile writing output... [ 35%] api/generated/mdtraj.formats.HDF5TrajectoryFile writing output... [ 36%] api/generated/mdtraj.formats.LAMMPSTrajectoryFile writing output... [ 37%] api/generated/mdtraj.formats.LH5TrajectoryFile writing output... [ 37%] api/generated/mdtraj.formats.MDCRDTrajectoryFile writing output... [ 38%] api/generated/mdtraj.formats.NetCDFTrajectoryFile writing output... [ 39%] api/generated/mdtraj.formats.PDBTrajectoryFile writing output... [ 40%] api/generated/mdtraj.formats.TRRTrajectoryFile writing output... [ 40%] api/generated/mdtraj.formats.XTCTrajectoryFile writing output... [ 41%] api/generated/mdtraj.formats.XYZTrajectoryFile writing output... [ 42%] api/generated/mdtraj.geometry.squareform writing output... [ 43%] api/generated/mdtraj.isothermal_compressability_kappa_T writing output... [ 44%] api/generated/mdtraj.iterload writing output... [ 44%] api/generated/mdtraj.join writing output... [ 45%] 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... [ 48%] api/generated/mdtraj.load_dcd writing output... [ 49%] api/generated/mdtraj.load_dtr writing output... [ 50%] api/generated/mdtraj.load_frame writing output... [ 51%] api/generated/mdtraj.load_hdf5 writing output... [ 51%] api/generated/mdtraj.load_hoomdxml writing output... [ 52%] api/generated/mdtraj.load_lammpstrj writing output... [ 53%] api/generated/mdtraj.load_lh5 writing output... [ 54%] api/generated/mdtraj.load_netcdf writing output... [ 55%] api/generated/mdtraj.load_pdb writing output... [ 55%] api/generated/mdtraj.load_prmtop writing output... [ 56%] api/generated/mdtraj.load_trr writing output... [ 57%] api/generated/mdtraj.load_xml writing output... [ 58%] api/generated/mdtraj.load_xtc writing output... [ 59%] api/generated/mdtraj.load_xyz writing output... [ 59%] api/generated/mdtraj.lprmsd writing output... [ 60%] api/generated/mdtraj.open writing output... [ 61%] api/generated/mdtraj.principal_moments writing output... [ 62%] api/generated/mdtraj.reindex_dataframe_by_atoms writing output... [ 62%] api/generated/mdtraj.relative_shape_antisotropy writing output... [ 63%] api/generated/mdtraj.reporters.DCDReporter writing output... [ 64%] api/generated/mdtraj.reporters.HDF5Reporter writing output... [ 65%] api/generated/mdtraj.reporters.NetCDFReporter writing output... [ 66%] api/generated/mdtraj.rmsd writing output... [ 66%] api/generated/mdtraj.rmsf writing output... [ 67%] api/generated/mdtraj.shrake_rupley writing output... [ 68%] api/generated/mdtraj.static_dielectric writing output... [ 69%] api/generated/mdtraj.thermal_expansion_alpha_P writing output... [ 70%] api/generated/mdtraj.utils.box_vectors_to_lengths_and_angles writing output... [ 70%] api/generated/mdtraj.utils.check_random_state writing output... [ 71%] api/generated/mdtraj.utils.ensure_type writing output... [ 72%] api/generated/mdtraj.utils.ilen writing output... [ 73%] api/generated/mdtraj.utils.import_ writing output... [ 74%] api/generated/mdtraj.utils.in_units_of writing output... [ 74%] api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors writing output... [ 75%] api/generated/mdtraj.utils.rotation_matrix_from_quaternion writing output... [ 76%] api/generated/mdtraj.utils.timing writing output... [ 77%] api/generated/mdtraj.utils.uniform_quaternion writing output... [ 77%] api/generated/mdtraj.wernet_nilsson writing output... [ 78%] api/reporters writing output... [ 79%] api/trajectory_files writing output... [ 80%] api/utils writing output... [ 81%] atom_selection writing output... [ 81%] building_docs writing output... [ 82%] examples/atom-selection writing output... [ 83%] examples/centroids writing output... [ 84%] examples/clustering writing output... [ 85%] examples/hbonds writing output... [ 85%] examples/index writing output... [ 86%] examples/introduction writing output... [ 87%] examples/iterload writing output... [ 88%] examples/native-contact writing output... [ 88%] examples/nmr writing output... [ 89%] examples/openmm writing output... [ 90%] examples/pca writing output... [ 91%] examples/ramachandran-plot writing output... [ 92%] examples/rmsd-benchmark writing output... [ 92%] examples/solvent-accessible-surface-area writing output... [ 93%] examples/two-pass-clustering writing output... [ 94%] faq writing output... [ 95%] hdf5_format writing output... [ 96%] index writing output... [ 96%] installation writing output... [ 97%] 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 copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 26 warnings. The HTML pages are in ../build/html. Build finished. The HTML pages are in /build/reproducible-path/mdtraj-1.9.7/build/html. make[2]: Leaving directory '/build/reproducible-path/mdtraj-1.9.7/docs' for img in `find /build/reproducible-path/mdtraj-1.9.7/build/html/examples -name *.png`; do \ mv $img /build/reproducible-path/mdtraj-1.9.7/build/html/examples; \ done sed "s|/build/reproducible-path/mdtraj-1.9.7/build/html/examples/|./|g; s|.ipynb|.ipynb.gz|g" -i /build/reproducible-path/mdtraj-1.9.7/build/html/examples/*.html sed "s|/build/reproducible-path/mdtraj-1.9.7/debian/external|http://www.rcsb.org/pdb/files|g" -i /build/reproducible-path/mdtraj-1.9.7/build/html/examples/*.html rm /build/reproducible-path/mdtraj-1.9.7/build/html/examples/iterload/data rm -rf /build/reproducible-path/mdtraj-1.9.7/examples mv /build/reproducible-path/mdtraj-1.9.7/examples.orig /build/reproducible-path/mdtraj-1.9.7/examples make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.9.7' dh_auto_build -O--buildsystem=pybuild -Npython-mdtraj-doc I: pybuild base:240: /usr/bin/python3 setup.py build Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/12/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --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-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 12.2.0 (Debian 12.2.0-14) /usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar. if not hasattr(numpy, method): /usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar. obj = getattr(themodule, elem) 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 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 build running build_py copying mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj running build_ext building 'mdtraj.formats.xtc' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/src/xdr_seek.c INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile.c INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile_xtc.c INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/xtc.c 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 { | ^~ 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; | ^~~~~~ 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:778: /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/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write': mdtraj/formats/xtc/xtc.c:690:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 690 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:9539:7: note: '__pyx_v_status' was declared here 9539 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:8058:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8058 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6461:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 6461 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8054:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8054 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6461:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 6461 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8050:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8050 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6461:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 6461 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8010:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8010 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6457:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 6457 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7992:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7992 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6453:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 6453 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8068:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8068 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6449:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 6449 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8030:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8030 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6443:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 6443 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8026:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8026 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6443:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 6443 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8022:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8022 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6443:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 6443 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7645:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 7645 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6445:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 6445 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7641:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7641 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6445:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 6445 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ INFO: i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/xtc.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/xtc.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.trr' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/src/xdr_seek.c INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile.c INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile_trr.c INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/trr.c 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; | ^~~~~~ 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:778: /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/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write': mdtraj/formats/xtc/trr.c:690:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 690 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:11065:7: note: '__pyx_v_status' was declared here 11065 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:8418:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8418 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 6955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8414:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8414 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 6955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1929:95: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1929 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 6955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8408:59: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8408 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 6955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8361:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8361 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 6971 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8357:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8357 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 6971 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1929:95: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1929 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 6971 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8351:56: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8351 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 6971 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8751:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8751 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6977:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 6977 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8747:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8747 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6977:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 6977 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8592:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8592 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6973:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 6973 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8588:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8588 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6973:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 6973 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8644:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8644 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6957:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 6957 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8640:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8640 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6957:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 6957 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ INFO: i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/trr.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/trr.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.tng' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-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' INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/bwlzh.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/bwt.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/coder.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/dict.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/huffman.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/fixpoint.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/huffmem.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/lz77.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/merge_sort.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/mtf.c 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) | ^~ INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/rle.c 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]) | ^~ INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/tng_compress.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/vals16.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/warnmalloc.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/widemuldiv.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/xtc2.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/xtc3.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/lib/md5.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/lib/tng_io.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/tng.c 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 = | ^ 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:804: /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:3692:104: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3692 | __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:3747:88: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3747 | __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:3779:90: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3779 | __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:3811:95: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3811 | __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:3881:113: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3881 | __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:3925:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3925 | __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:4721:106: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4721 | __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:4766:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4766 | __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:4873:115: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4873 | __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:4903:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4903 | __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:5031:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5031 | __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:5632:126: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5632 | __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:6042:152: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6042 | __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:6310:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6310 | __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:6412:304: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6412 | __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:8904:94: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8904 | __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:8936:75: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8936 | __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:8968:81: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8968 | __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:9291:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9291 | __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:9482:372: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9482 | __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:9534:378: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9534 | __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:9596:89: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9596 | __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); | ^~ 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); | ^~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: 'num_first_particle' may be used uninitialized [-Wmaybe-uninitialized] 5986 | for(j = num_first_particle; j < num_first_particle + n_particles; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 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; | ^~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: 'n_particles' may be used uninitialized [-Wmaybe-uninitialized] 5986 | for(j = num_first_particle; j < num_first_particle + n_particles; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 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; | ^~~~~~~~~~~ INFO: i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib/i386-linux-gnu -lz -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/tng.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.dcd' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/formats/dcd/dcd.c INFO: i686-linux-gnu-gcc: mdtraj/formats/dcd/src/dcdplugin.c 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:776: /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/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:688:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 688 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c:5434:7: note: '__pyx_v_i' was declared here 5434 | int __pyx_v_i; | ^~~~~~~~~ INFO: i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/formats/dcd/dcd.o build/temp.linux-i386-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dcd.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.binpos' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/formats/binpos/binpos.c INFO: i686-linux-gnu-gcc: mdtraj/formats/binpos/src/binposplugin.c 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:776: /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:4980:13: mdtraj/formats/binpos/binpos.c:5512:6: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 5512 | if (__pyx_t_2) { | ^ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:4992:7: note: '__pyx_v_status' was declared here 4992 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c:688:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 688 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c:4989:7: note: '__pyx_v_i' was declared here 4989 | int __pyx_v_i; | ^~~~~~~~~ INFO: i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/formats/binpos/binpos.o build/temp.linux-i386-cpython-311/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/binpos.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.dtr' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-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' extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/formats/dtr/dtr.cpp INFO: i686-linux-gnu-gcc: mdtraj/formats/dtr/src/dtrplugin.cxx 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:797: /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/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 ()); | ~~~~~~~~~~~~~~~~~ INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/formats/dtr/dtr.o build/temp.linux-i386-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dtr.cpython-311-i386-linux-gnu.so building 'mdtraj._rmsd' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-fopenmp -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/rmsd/_rmsd.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/center.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/rotation.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/rmsd/_rmsd.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_rmsd.cpython-311-i386-linux-gnu.so building 'mdtraj._lprmsd' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-fopenmp -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/rmsd/_lprmsd.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/Munkres.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/center.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/euclidean_permutation.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/fancy_index.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/rotation.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp 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:807: /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 " \ | ^~~~~~~ INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/rmsd/_lprmsd.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/Munkres.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/fancy_index.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_lprmsd.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry._geometry' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-fopenmp -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/_geometry.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/dssp.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/geometry.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/sasa.cpp 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:809: /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:6085:224: warning: '__pyx_v_delta[2]' may be used uninitialized [-Wmaybe-uninitialized] 6085 | (__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:6006:9: note: '__pyx_v_delta[2]' was declared here 6006 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6099:277: warning: '__pyx_v_delta[1]' may be used uninitialized [-Wmaybe-uninitialized] 6099 | (__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:6006:9: note: '__pyx_v_delta[1]' was declared here 6006 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6099:277: warning: '__pyx_v_offset[1]' may be used uninitialized [-Wmaybe-uninitialized] 6099 | (__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:6005:9: note: '__pyx_v_offset[1]' was declared here 6005 | float __pyx_v_offset[3]; | ^~~~~~~~~~~~~~ INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/geometry/src/_geometry.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/dssp.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/geometry.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/sasa.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/_geometry.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry.drid' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-fopenmp -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/geometry/drid.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/dridkernels.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/moments.cpp INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/geometry/drid.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/dridkernels.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/moments.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/drid.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry.neighbors' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-fopenmp -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/geometry/neighbors.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/neighbors.cpp In file included from /usr/lib/gcc/i686-linux-gnu/12/include/emmintrin.h:31, from /usr/lib/gcc/i686-linux-gnu/12/include/pmmintrin.h:31, from mdtraj/geometry/include/vectorize.h:38, from mdtraj/geometry/src/neighbors.cpp:4: In function '__m128 _mm_mul_ps(__m128, __m128)', inlined from 'fvec4 fvec4::operator*(const fvec4&) const' at mdtraj/geometry/include/vectorize_sse.h:167:37, inlined from 'std::vector _compute_neighbors(float*, int, float, const std::vector&, const std::vector&, float*)' at mdtraj/geometry/src/neighbors.cpp:55:52: /usr/lib/gcc/i686-linux-gnu/12/include/xmmintrin.h:198:45: warning: 'box_size.fvec4::val' may be used uninitialized [-Wmaybe-uninitialized] 198 | return (__m128) ((__v4sf)__A * (__v4sf)__B); | ^ mdtraj/geometry/src/neighbors.cpp: In function 'std::vector _compute_neighbors(float*, int, float, const std::vector&, const std::vector&, float*)': mdtraj/geometry/src/neighbors.cpp:19:11: note: 'box_size.fvec4::val' was declared here 19 | fvec4 box_size, inv_box_size, box_vec1, box_vec2, box_vec3; | ^~~~~~~~ INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/geometry/neighbors.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/neighbors.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighbors.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-fopenmp -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/geometry/neighborlist.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/neighborlist.cpp 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]; | ^~~~~~~~~~~~~~~~~~ INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/geometry/neighborlist.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/neighborlist.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighborlist.cpython-311-i386-linux-gnu.so dh_auto_test -O--buildsystem=pybuild I: pybuild base:240: cd /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build; python3.11 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s OK create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3,sphinxdoc --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_installdirs -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/12/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --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-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 12.2.0 (Debian 12.2.0-14) /usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar. if not hasattr(numpy, method): /usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar. obj = getattr(themodule, elem) 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 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 install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py copying mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj running build_ext building 'mdtraj.formats.xtc' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/src/xdr_seek.c INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile.c INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/xtc.c INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile_xtc.c 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 { | ^~ 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; | ^~~~~~ 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:778: /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/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write': mdtraj/formats/xtc/xtc.c:690:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 690 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:9539:7: note: '__pyx_v_status' was declared here 9539 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:8058:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8058 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6461:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 6461 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8054:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8054 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6461:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 6461 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8050:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8050 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6461:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 6461 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8010:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8010 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6457:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 6457 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7992:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7992 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6453:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 6453 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8068:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8068 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6449:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 6449 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8030:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8030 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; | ^ mdtraj/formats/xtc/xtc.c:6443:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 6443 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8026:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8026 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6443:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 6443 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:8022:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8022 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6443:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 6443 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7645:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 7645 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; | ^ mdtraj/formats/xtc/xtc.c:6445:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 6445 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:7641:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 7641 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; | ^ mdtraj/formats/xtc/xtc.c:6445:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 6445 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ INFO: i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/xtc.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/xtc.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.trr' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile.c INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/src/xdr_seek.c INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile_trr.c INFO: i686-linux-gnu-gcc: mdtraj/formats/xtc/trr.c 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; | ^~~~~~ 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:778: /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/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write': mdtraj/formats/xtc/trr.c:690:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 690 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:11065:7: note: '__pyx_v_status' was declared here 11065 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:8418:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8418 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 6955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8414:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8414 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 6955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1929:95: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1929 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 6955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8408:59: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8408 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:6955:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 6955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8361:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 8361 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 6971 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8357:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8357 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 6971 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:1929:95: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 1929 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 6971 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8351:56: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8351 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:6971:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 6971 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8751:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8751 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6977:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 6977 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8747:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8747 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6977:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 6977 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8592:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8592 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6973:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 6973 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8588:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8588 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6973:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 6973 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8644:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 8644 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/trr.c:6957:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 6957 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:8640:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 8640 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/trr.c:6957:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 6957 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ INFO: i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-i386-cpython-311/mdtraj/formats/xtc/trr.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/trr.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.tng' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-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' INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/bwlzh.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/bwt.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/coder.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/dict.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/fixpoint.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/huffman.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/huffmem.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/lz77.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/merge_sort.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/mtf.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/rle.c 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]) | ^~ 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) | ^~ INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/tng_compress.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/vals16.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/warnmalloc.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/widemuldiv.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/xtc2.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/compression/xtc3.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/lib/md5.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/src/lib/tng_io.c INFO: i686-linux-gnu-gcc: mdtraj/formats/tng/tng.c 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 = | ^ 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:804: /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:3692:104: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3692 | __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:3747:88: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3747 | __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:3779:90: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3779 | __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:3811:95: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3811 | __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:3881:113: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3881 | __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:3925:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 3925 | __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:4721:106: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4721 | __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:4766:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4766 | __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:4873:115: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4873 | __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:4903:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 4903 | __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:5031:105: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5031 | __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:5632:126: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 5632 | __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:6042:152: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6042 | __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:6310:108: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6310 | __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:6412:304: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 6412 | __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:8904:94: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8904 | __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:8936:75: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8936 | __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:8968:81: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 8968 | __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:9291:77: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9291 | __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:9482:372: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9482 | __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:9534:378: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9534 | __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:9596:89: warning: comparison between 'tng_function_status' and 'enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status' [-Wenum-compare] 9596 | __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); | ^~ 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); | ^~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c: In function 'tng_data_block_write.isra': mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: 'num_first_particle' may be used uninitialized [-Wmaybe-uninitialized] 5986 | for(j = num_first_particle; j < num_first_particle + n_particles; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 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; | ^~~~~~~~~~~~~~~~~~ mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: 'n_particles' may be used uninitialized [-Wmaybe-uninitialized] 5986 | for(j = num_first_particle; j < num_first_particle + n_particles; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 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; | ^~~~~~~~~~~ INFO: i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-i386-cpython-311/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib/i386-linux-gnu -lz -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/tng.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.dcd' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/formats/dcd/dcd.c INFO: i686-linux-gnu-gcc: mdtraj/formats/dcd/src/dcdplugin.c 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:776: /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/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:688:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 688 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c:5434:7: note: '__pyx_v_i' was declared here 5434 | int __pyx_v_i; | ^~~~~~~~~ INFO: i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/formats/dcd/dcd.o build/temp.linux-i386-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dcd.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.binpos' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/formats/binpos/binpos.c INFO: i686-linux-gnu-gcc: mdtraj/formats/binpos/src/binposplugin.c 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:776: /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:4980:13: mdtraj/formats/binpos/binpos.c:5512:6: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 5512 | if (__pyx_t_2) { | ^ mdtraj/formats/binpos/binpos.c: In function '__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read': mdtraj/formats/binpos/binpos.c:4992:7: note: '__pyx_v_status' was declared here 4992 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c:688:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 688 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ mdtraj/formats/binpos/binpos.c:4989:7: note: '__pyx_v_i' was declared here 4989 | int __pyx_v_i; | ^~~~~~~~~ INFO: i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/formats/binpos/binpos.o build/temp.linux-i386-cpython-311/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/binpos.cpython-311-i386-linux-gnu.so building 'mdtraj.formats.dtr' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-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' extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/formats/dtr/dtr.cpp INFO: i686-linux-gnu-gcc: mdtraj/formats/dtr/src/dtrplugin.cxx 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:797: /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/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 ()); | ~~~~~~~~~~~~~~~~~ INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/formats/dtr/dtr.o build/temp.linux-i386-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dtr.cpython-311-i386-linux-gnu.so building 'mdtraj._rmsd' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-fopenmp -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/rmsd/_rmsd.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/center.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/rotation.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/rmsd/_rmsd.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_rmsd.cpython-311-i386-linux-gnu.so building 'mdtraj._lprmsd' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-fopenmp -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/rmsd/_lprmsd.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/center.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/Munkres.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/euclidean_permutation.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/fancy_index.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp INFO: i686-linux-gnu-gcc: mdtraj/rmsd/src/rotation.cpp 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:807: /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 " \ | ^~~~~~~ INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/rmsd/_lprmsd.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/Munkres.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/fancy_index.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-i386-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_lprmsd.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry._geometry' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-fopenmp -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/_geometry.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/dssp.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/geometry.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/sasa.cpp 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:809: /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:6085:224: warning: '__pyx_v_delta[2]' may be used uninitialized [-Wmaybe-uninitialized] 6085 | (__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:6006:9: note: '__pyx_v_delta[2]' was declared here 6006 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6099:277: warning: '__pyx_v_delta[1]' may be used uninitialized [-Wmaybe-uninitialized] 6099 | (__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:6006:9: note: '__pyx_v_delta[1]' was declared here 6006 | float __pyx_v_delta[3]; | ^~~~~~~~~~~~~ mdtraj/geometry/src/_geometry.cpp:6099:277: warning: '__pyx_v_offset[1]' may be used uninitialized [-Wmaybe-uninitialized] 6099 | (__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:6005:9: note: '__pyx_v_offset[1]' was declared here 6005 | float __pyx_v_offset[3]; | ^~~~~~~~~~~~~~ INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/geometry/src/_geometry.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/dssp.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/geometry.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/sasa.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/_geometry.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry.drid' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-fopenmp -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/geometry/drid.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/moments.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/dridkernels.cpp INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/geometry/drid.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/dridkernels.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/moments.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/drid.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry.neighbors' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-fopenmp -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/geometry/neighbors.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/neighbors.cpp In file included from /usr/lib/gcc/i686-linux-gnu/12/include/emmintrin.h:31, from /usr/lib/gcc/i686-linux-gnu/12/include/pmmintrin.h:31, from mdtraj/geometry/include/vectorize.h:38, from mdtraj/geometry/src/neighbors.cpp:4: In function '__m128 _mm_mul_ps(__m128, __m128)', inlined from 'fvec4 fvec4::operator*(const fvec4&) const' at mdtraj/geometry/include/vectorize_sse.h:167:37, inlined from 'std::vector _compute_neighbors(float*, int, float, const std::vector&, const std::vector&, float*)' at mdtraj/geometry/src/neighbors.cpp:55:52: /usr/lib/gcc/i686-linux-gnu/12/include/xmmintrin.h:198:45: warning: 'box_size.fvec4::val' may be used uninitialized [-Wmaybe-uninitialized] 198 | return (__m128) ((__v4sf)__A * (__v4sf)__B); | ^ mdtraj/geometry/src/neighbors.cpp: In function 'std::vector _compute_neighbors(float*, int, float, const std::vector&, const std::vector&, float*)': mdtraj/geometry/src/neighbors.cpp:19:11: note: 'box_size.fvec4::val' was declared here 19 | fvec4 box_size, inv_box_size, box_vec1, box_vec2, box_vec3; | ^~~~~~~~ INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/geometry/neighbors.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/neighbors.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighbors.cpython-311-i386-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension INFO: C compiler: 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-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c' extra options: '-fopenmp -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare' INFO: i686-linux-gnu-gcc: mdtraj/geometry/neighborlist.cpp INFO: i686-linux-gnu-gcc: mdtraj/geometry/src/neighborlist.cpp 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]; | ^~~~~~~~~~~~~~~~~~ INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.9.7=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/mdtraj/geometry/neighborlist.o build/temp.linux-i386-cpython-311/mdtraj/geometry/src/neighborlist.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighborlist.cpython-311-i386-linux-gnu.so running install_lib creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11 creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_lprmsd.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/trr.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/xtc.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/data creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbstructure.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbfile.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/netcdf.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/mol2.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/hdf5.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/mdcrd.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/psf.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/hoomdxml.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/gro.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/xyzfile.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/openmmxml.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/amberrst.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/registry.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/gsd.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/lh5.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/arc.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/prmtop.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__pycache__/lammpstrj.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/tng.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/binpos.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dcd.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/dtr.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/io.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/__pycache__/testing.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/__pycache__/docstrings.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/__pycache__/docscrape.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/standard_dimensions.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/baseunit.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/unit.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_operators.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/prefix.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/quantity.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/mymatrix.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/basedimension.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_definitions.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/six.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/validation.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/zipped.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/rotation.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/singleton.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/contextmanagers.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/unitcell.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__pycache__/delay_import.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/six.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/__pycache__/version.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/_rmsd.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/drid.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighbors.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/neighborlist.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/distance.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/rdf.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/rg.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/dihedral.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/thermodynamic_properties.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/hbond.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/contact.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/sasa.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/angle.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/dssp.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/order.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__pycache__/shape.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/_geometry.cpython-311-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/version.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/selection.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/topology.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/element.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/trajectory.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__pycache__/residue_names.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/lib/libtheobald.a -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/lib/center.h -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/lib/theobald_rmsd.h -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/dcdreporter.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/basereporter.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/netcdfreporter.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/hdf5reporter.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__pycache__/xtcreporter.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/__pycache__/scalar_couplings.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/__pycache__/shift_wrappers.cpython-311.pyc -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.9.7/.pybuild/cpython3_3.11_mdtraj/build/mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/arc.py to arc.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/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-1.9.7/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-1.9.7/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-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/mol2.py to mol2.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/amberrst.py to amberrst.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/gsd.py to gsd.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/psf.py to psf.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/lh5.py to lh5.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/hdf5.py to hdf5.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/registry.py to registry.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/gro.py to gro.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/prmtop.py to prmtop.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/formats/netcdf.py to netcdf.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/io.py to io.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts/mdconvert.py to mdconvert.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/scripts/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/docscrape.py to docscrape.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/docstrings.py to docstrings.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/testing/testing.py to testing.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/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-1.9.7/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-1.9.7/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-1.9.7/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-1.9.7/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-1.9.7/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-1.9.7/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-1.9.7/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-1.9.7/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-1.9.7/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-1.9.7/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-1.9.7/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-1.9.7/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-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/unitcell.py to unitcell.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/validation.py to validation.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/zipped.py to zipped.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/six.py to six.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/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-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/singleton.py to singleton.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/rotation.py to rotation.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/hbond.py to hbond.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/alignment.py to alignment.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/sasa.py to sasa.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/shape.py to shape.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/order.py to order.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/rdf.py to rdf.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/angle.py to angle.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/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-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/dssp.py to dssp.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/distance.py to distance.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/contact.py to contact.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/internal.py to internal.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/geometry/rg.py to rg.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/version.py to version.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/trajectory.py to trajectory.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/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-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/element.py to element.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/topology.py to topology.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/core/selection.py to selection.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/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-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj/nmr/scalar_couplings.py to scalar_couplings.cpython-311.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' 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-1.9.7/debian/python3-mdtraj/usr/lib/python3.11/dist-packages/mdtraj-1.9.7.egg-info Skipping SOURCES.txt running install_scripts Installing mdconvert-mdtraj script to /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/bin Installing mdinspect script to /build/reproducible-path/mdtraj-1.9.7/debian/python3-mdtraj/usr/bin debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/mdtraj-1.9.7' dh_install dh_numpy3 make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.9.7' 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 debian/rules override_dh_sphinxdoc-indep make[1]: Entering directory '/build/reproducible-path/mdtraj-1.9.7' dh_sphinxdoc -i dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/versions.js 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-1.9.7' dh_sphinxdoc -O--buildsystem=pybuild -Npython-mdtraj-doc dh_sphinxdoc: warning: Sphinx documentation not found dh_installchangelogs -O--buildsystem=pybuild 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 dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild 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 dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-mdtraj-dbgsym' in '../python3-mdtraj-dbgsym_1.9.7-6_i386.deb'. dpkg-deb: building package 'python-mdtraj-doc' in '../python-mdtraj-doc_1.9.7-6_all.deb'. dpkg-deb: building package 'python3-mdtraj' in '../python3-mdtraj_1.9.7-6_i386.deb'. dpkg-genbuildinfo --build=binary -O../mdtraj_1.9.7-6_i386.buildinfo dpkg-genchanges --build=binary -O../mdtraj_1.9.7-6_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from mdtraj-1.9.7/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/13800/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/13800/tmp/hooks/B01_cleanup finished 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/13800 and its subdirectories I: Current time: Tue Jan 23 03:58:57 +14 2024 I: pbuilder-time-stamp: 1705931937