I: pbuilder: network access will be disabled during build I: Current time: Sat Dec 14 15:28:38 +14 2024 I: pbuilder-time-stamp: 1734139718 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [mdtraj_1.10.1-2.dsc] I: copying [./mdtraj_1.10.1.orig.tar.gz] I: copying [./mdtraj_1.10.1-2.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Nov 11 19:58:43 2024 gpgv: using RSA key 13796755BBC72BB8ABE2AEB5FA9DEC5DE11C63F1 gpgv: issuer "eamanu@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.10.1-2.dsc: no acceptable signature found dpkg-source: info: extracting mdtraj in mdtraj-1.10.1 dpkg-source: info: unpacking mdtraj_1.10.1.orig.tar.gz dpkg-source: info: unpacking mdtraj_1.10.1-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying docs_use_local_mathjax.patch dpkg-source: info: applying build_dir_pybuild.patch dpkg-source: info: applying python_hashbang.patch dpkg-source: info: applying 32bit_skip_image_molecule.patch dpkg-source: info: applying test_relax_tol.patch dpkg-source: info: applying rename-mdconvert-mdtraj.patch dpkg-source: info: applying drop_notebook_in_docs.patch dpkg-source: info: applying test_increase_timeout.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/7091/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 Dec 14 01:28 /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/7091/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/7091/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]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.37(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=10 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=0b68f0b41e6c43a1bae21c827c82a592 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=7091 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.7mWDbeeO/pbuilderrc_1Hqr --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.7mWDbeeO/b2 --logfile b2/build.log mdtraj_1.10.1-2.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://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/7091/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, cython3, pandoc, python3-setuptools, python3-all-dev, python3-gsd, python3-numpy, python3-scipy, python3-nbsphinx, python3-nbsphinx-link, python3-netcdf4, python3-networkx, python3-pandas, python3-pyparsing, python3-sphinx, python3-tables, python3-versioneer, libjs-mathjax, python3-msmb-theme, python3-ipykernel, python3-jupyter-client, python3-matplotlib, python3-nbconvert, python3-nbformat, python3-numpydoc, python3-sklearn dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19952 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on pandoc; however: Package pandoc is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-gsd; however: Package python3-gsd is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-nbsphinx; however: Package python3-nbsphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-nbsphinx-link; however: Package python3-nbsphinx-link is not installed. pbuilder-satisfydepends-dummy depends on python3-netcdf4; however: Package python3-netcdf4 is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-pyparsing; however: Package python3-pyparsing is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-tables; however: Package python3-tables is not installed. pbuilder-satisfydepends-dummy depends on python3-versioneer; however: Package python3-versioneer is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax is not installed. pbuilder-satisfydepends-dummy depends on python3-msmb-theme; however: Package python3-msmb-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-ipykernel; however: Package python3-ipykernel is not installed. pbuilder-satisfydepends-dummy depends on python3-jupyter-client; however: Package python3-jupyter-client is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-nbconvert; however: Package python3-nbconvert is not installed. pbuilder-satisfydepends-dummy depends on python3-nbformat; however: Package python3-nbformat is not installed. pbuilder-satisfydepends-dummy depends on python3-numpydoc; however: Package python3-numpydoc is not installed. pbuilder-satisfydepends-dummy depends on python3-sklearn; however: Package python3-sklearn is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-font-awesome{a} fonts-lato{a} fonts-lyx{a} fonts-mathjax{a} gdb{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libbabeltrace1{a} libblas3{a} libblosc1{a} libblosc2-4{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdebhelper-perl{a} libdebuginfod-common{a} libdebuginfod1t64{a} libdeflate0{a} libdw1t64{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhdf5-310{a} libhdf5-hl-310{a} libicu72{a} libimagequant0{a} libipt2{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-c5{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblua5.4-0{a} liblzo2-2{a} libmagic-mgc{a} libmagic1t64{a} libnetcdf19t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnorm1t64{a} libnsl2{a} libnuma1{a} libopenjp2-7{a} libpgm-5.3-0t64{a} libpipeline1{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsnappy1v5{a} libsodium23{a} libsource-highlight-common{a} libsource-highlight4t64{a} libssh2-1t64{a} libsz2{a} libtcl8.6{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} libzmq5{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} pandoc{a} pandoc-data{a} po-debconf{a} procps{a} python-babel-localedata{a} python-matplotlib-data{a} python-tables-data{a} python-tinycss2-common{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-appdirs{a} python3-asttokens{a} python3-attr{a} python3-autocommand{a} python3-babel{a} python3-bleach{a} python3-brotli{a} python3-bs4{a} python3-certifi{a} python3-cffi-backend{a} python3-cftime{a} python3-chardet{a} python3-charset-normalizer{a} python3-comm{a} python3-contourpy{a} python3-coverage{a} python3-cpuinfo{a} python3-cycler{a} python3-dateutil{a} python3-debugpy{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-executing{a} python3-fastjsonschema{a} python3-fonttools{a} python3-fs{a} python3-gsd{a} python3-html5lib{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-ipykernel{a} python3-ipython{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jedi{a} python3-jinja2{a} python3-joblib{a} python3-jsonschema{a} python3-jsonschema-specifications{a} python3-jupyter-client{a} python3-jupyter-core{a} python3-jupyterlab-pygments{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-markupsafe{a} python3-matplotlib{a} python3-matplotlib-inline{a} python3-minimal{a} python3-mistune{a} python3-more-itertools{a} python3-mpmath{a} python3-msmb-theme{a} python3-nbclient{a} python3-nbconvert{a} python3-nbformat{a} python3-nbsphinx{a} python3-nbsphinx-link{a} python3-nest-asyncio{a} python3-netcdf4{a} python3-networkx{a} python3-numexpr{a} python3-numpy{a} python3-numpydoc{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pandocfilters{a} python3-parso{a} python3-pexpect{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-platformdirs{a} python3-prompt-toolkit{a} python3-psutil{a} python3-ptyprocess{a} python3-pure-eval{a} python3-py{a} python3-pygments{a} python3-pyparsing{a} python3-referencing{a} python3-requests{a} python3-roman{a} python3-rpds-py{a} python3-scipy{a} python3-setuptools{a} python3-sklearn{a} python3-sklearn-lib{a} python3-snowballstemmer{a} python3-soupsieve{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-sphinxcontrib.jquery{a} python3-stack-data{a} python3-sympy{a} python3-tables{a} python3-tables-lib{a} python3-tabulate{a} python3-threadpoolctl{a} python3-tinycss2{a} python3-tk{a} python3-tornado{a} python3-traitlets{a} python3-typeguard{a} python3-typeshed{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-urllib3{a} python3-versioneer{a} python3-wcwidth{a} python3-webencodings{a} python3-zipp{a} python3-zmq{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} python3.12-tk{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} python3.13-tk{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} tk8.6-blt2.5{a} tzdata{a} ucf{a} unicode-data{a} x11-common{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl isympy-common javascript-common krb5-locales libarchive-cpio-perl libc6-dbg libglib2.0-data libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-bottleneck python3-cssselect python3-gdal python3-json-pointer python3-odf python3-olefile python3-openpyxl python3-pooch python3-pydot python3-pygraphviz python3-pytest python3-rfc3987 python3-simplejson python3-sphinxcontrib.bibtex python3-uritemplate python3-webcolors python3-yaml shared-mime-info wget xdg-user-dirs 0 packages upgraded, 298 newly installed, 0 to remove and 0 not upgraded. Need to get 236 MB of archives. After unpacking 1248 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libproc2-0 i386 2:4.0.4-6 [65.7 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 procps i386 2:4.0.4-6 [876 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 ucf all 3.0045 [45.2 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 libdebuginfod-common all 0.192-4 [23.7 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 libpython3.12-minimal i386 3.12.8-3 [816 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.4-1 [107 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 python3.12-minimal i386 3.12.8-3 [2239 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.12.7-1 [26.8 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 tzdata all 2024b-4 [256 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.2~rc1-2 [24.0 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 18 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 libtirpc3t64 i386 1.3.4+ds-1.3+b1 [90.5 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 libnsl2 i386 1.3.0-3+b3 [42.7 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-6 [69.4 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-6 [173 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 libpython3.12-stdlib i386 3.12.8-3 [1968 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 python3.12 i386 3.12.8-3 [677 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.12.7-1 [9712 B] Get: 28 http://deb.debian.org/debian unstable/main i386 python3 i386 3.12.7-1 [27.8 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 libpython3.13-minimal i386 3.13.1-2 [858 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 python3.13-minimal i386 3.13.1-2 [2260 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 sgml-base all 1.31 [15.4 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 openssl i386 3.3.2-2 [1387 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 ca-certificates all 20240203 [158 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-6 [1198 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.2-12 [95.9 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-2 [723 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 libtcl8.6 i386 8.6.15+dfsg-2 [1103 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 libpng16-16t64 i386 1.6.44-3 [288 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 libfreetype6 i386 2.13.3+dfsg-1 [464 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 fontconfig-config i386 2.15.0-1.1+b1 [318 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 libfontconfig1 i386 2.15.0-1.1+b1 [402 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 libxau6 i386 1:1.0.11-1 [20.7 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 libxdmcp6 i386 1:1.1.5-1 [28.2 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 libxcb1 i386 1.17.0-2+b1 [148 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 libx11-data all 2:1.8.10-2 [337 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 libx11-6 i386 2:1.8.10-2 [834 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 libxrender1 i386 1:0.9.10-1.1+b2 [28.9 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 libxft2 i386 2.3.6-1+b2 [55.3 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 libxext6 i386 2:1.3.4-1+b2 [52.6 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 x11-common all 1:7.7+23.1 [216 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 libxss1 i386 1:1.2.3-1+b2 [17.3 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 libtk8.6 i386 8.6.15-1 [833 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 tk8.6-blt2.5 i386 2.5.3+dfsg-7 [616 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 blt i386 2.5.3+dfsg-7 [6024 B] Get: 69 http://deb.debian.org/debian unstable/main i386 cython3 i386 3.0.11+dfsg-1+b1 [3019 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-8 [517 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 76 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 debhelper all 13.20 [915 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 python3-inflect all 7.3.1-2 [32.4 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 90 http://deb.debian.org/debian unstable/main i386 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 python3-zipp all 3.21.0-1 [10.6 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 python3-setuptools all 75.2.0-1 [731 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 dh-python all 6.20241024 [109 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 xml-core all 0.19 [20.1 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 fonts-lyx all 2.4.2.1-1 [190 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 101 http://deb.debian.org/debian unstable/main i386 libdw1t64 i386 0.192-4 [284 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 libglib2.0-0t64 i386 2.82.4-1 [1572 kB] Get: 103 http://deb.debian.org/debian unstable/main i386 libbabeltrace1 i386 1.5.11-4+b1 [195 kB] Get: 104 http://deb.debian.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB] Get: 105 http://deb.debian.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB] Get: 106 http://deb.debian.org/debian unstable/main i386 libldap-2.5-0 i386 2.5.18+dfsg-3+b1 [200 kB] Get: 107 http://deb.debian.org/debian unstable/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB] Get: 108 http://deb.debian.org/debian unstable/main i386 libnghttp3-9 i386 1.6.0-2 [75.9 kB] Get: 109 http://deb.debian.org/debian unstable/main i386 libngtcp2-16 i386 1.9.1-1 [151 kB] Get: 110 http://deb.debian.org/debian unstable/main i386 libngtcp2-crypto-gnutls8 i386 1.9.1-1 [19.1 kB] Get: 111 http://deb.debian.org/debian unstable/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB] Get: 112 http://deb.debian.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB] Get: 113 http://deb.debian.org/debian unstable/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB] Get: 114 http://deb.debian.org/debian unstable/main i386 libcurl3t64-gnutls i386 8.11.1-1 [404 kB] Get: 115 http://deb.debian.org/debian unstable/main i386 libjson-c5 i386 0.18+ds-1 [48.7 kB] Get: 116 http://deb.debian.org/debian unstable/main i386 libdebuginfod1t64 i386 0.192-4 [33.9 kB] Get: 117 http://deb.debian.org/debian unstable/main i386 libipt2 i386 2.1.1-1 [56.7 kB] Get: 118 http://deb.debian.org/debian unstable/main i386 libpython3.12t64 i386 3.12.8-3 [2171 kB] Get: 119 http://deb.debian.org/debian unstable/main i386 libsource-highlight-common all 3.1.9-4.3 [77.5 kB] Get: 120 http://deb.debian.org/debian unstable/main i386 libsource-highlight4t64 i386 3.1.9-4.3+b1 [357 kB] Get: 121 http://deb.debian.org/debian unstable/main i386 gdb i386 15.2-1 [4537 kB] Get: 122 http://deb.debian.org/debian unstable/main i386 libaec0 i386 1.1.3-1+b1 [25.0 kB] Get: 123 http://deb.debian.org/debian unstable/main i386 libblas3 i386 3.12.0-4 [143 kB] Get: 124 http://deb.debian.org/debian unstable/main i386 libsnappy1v5 i386 1.2.1-1+b1 [31.3 kB] Get: 125 http://deb.debian.org/debian unstable/main i386 libblosc1 i386 1.21.5+ds-1+b2 [51.4 kB] Get: 126 http://deb.debian.org/debian unstable/main i386 libblosc2-4 i386 2.15.2+ds-1 [217 kB] Get: 127 http://deb.debian.org/debian unstable/main i386 libcurl4t64 i386 8.11.1-1 [393 kB] Get: 128 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.22-1 [48.1 kB] Get: 129 http://deb.debian.org/debian unstable/main i386 libexpat1-dev i386 2.6.4-1 [165 kB] Get: 130 http://deb.debian.org/debian unstable/main i386 libfribidi0 i386 1.0.16-1 [27.0 kB] Get: 131 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14.2.0-8 [735 kB] Get: 132 http://deb.debian.org/debian unstable/main i386 libgraphite2-3 i386 1.3.14-2+b1 [77.8 kB] Get: 133 http://deb.debian.org/debian unstable/main i386 libharfbuzz0b i386 10.1.0-1 [503 kB] Get: 134 http://deb.debian.org/debian unstable/main i386 libsz2 i386 1.1.3-1+b1 [8128 B] Get: 135 http://deb.debian.org/debian unstable/main i386 libhdf5-310 i386 1.14.5+repack-1 [1326 kB] Get: 136 http://deb.debian.org/debian unstable/main i386 libhdf5-hl-310 i386 1.14.5+repack-1 [81.3 kB] Get: 137 http://deb.debian.org/debian unstable/main i386 libimagequant0 i386 2.18.0-1+b2 [36.0 kB] Get: 138 http://deb.debian.org/debian unstable/main i386 libjbig0 i386 2.1-6.1+b2 [32.2 kB] Get: 139 http://deb.debian.org/debian unstable/main i386 libjpeg62-turbo i386 1:2.1.5-3+b1 [171 kB] Get: 140 http://deb.debian.org/debian unstable/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 141 http://deb.debian.org/debian unstable/main i386 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 142 http://deb.debian.org/debian unstable/main i386 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 143 http://deb.debian.org/debian unstable/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 144 http://deb.debian.org/debian unstable/main i386 libjs-sphinxdoc all 8.1.3-2 [30.3 kB] Get: 145 http://deb.debian.org/debian unstable/main i386 libjson-perl all 4.10000-1 [87.5 kB] Get: 146 http://deb.debian.org/debian unstable/main i386 liblapack3 i386 3.12.0-4 [2194 kB] Get: 147 http://deb.debian.org/debian unstable/main i386 liblbfgsb0 i386 3.0+dfsg.4-1+b2 [29.5 kB] Get: 148 http://deb.debian.org/debian unstable/main i386 liblcms2-2 i386 2.16-2 [171 kB] Get: 149 http://deb.debian.org/debian unstable/main i386 liblerc4 i386 4.0.0+ds-5 [191 kB] Get: 150 http://deb.debian.org/debian unstable/main i386 liblua5.4-0 i386 5.4.7-1+b1 [170 kB] Get: 151 http://deb.debian.org/debian unstable/main i386 liblzo2-2 i386 2.10-3+b1 [59.5 kB] Get: 152 http://deb.debian.org/debian unstable/main i386 libnetcdf19t64 i386 1:4.9.2-7+b1 [529 kB] Get: 153 http://deb.debian.org/debian unstable/main i386 libnorm1t64 i386 1.5.9+dfsg-3.1+b1 [239 kB] Get: 154 http://deb.debian.org/debian unstable/main i386 libnuma1 i386 2.0.18-1+b1 [23.9 kB] Get: 155 http://deb.debian.org/debian unstable/main i386 libopenjp2-7 i386 2.5.0-2+b4 [210 kB] Get: 156 http://deb.debian.org/debian unstable/main i386 libpgm-5.3-0t64 i386 5.3.128~dfsg-2.1+b1 [169 kB] Get: 157 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] Get: 158 http://deb.debian.org/debian unstable/main i386 libpython3.12-dev i386 3.12.8-3 [5296 kB] Get: 159 http://deb.debian.org/debian unstable/main i386 libpython3-dev i386 3.12.7-1 [9988 B] Get: 160 http://deb.debian.org/debian unstable/main i386 libpython3.13-stdlib i386 3.13.1-2 [1981 kB] Get: 161 http://deb.debian.org/debian unstable/main i386 libpython3.13 i386 3.13.1-2 [2199 kB] Get: 162 http://deb.debian.org/debian unstable/main i386 libpython3.13-dev i386 3.13.1-2 [5193 kB] Get: 163 http://deb.debian.org/debian unstable/main i386 libpython3-all-dev i386 3.12.7-1 [1072 B] Get: 164 http://deb.debian.org/debian unstable/main i386 libqhull-r8.0 i386 2020.2-6+b2 [259 kB] Get: 165 http://deb.debian.org/debian unstable/main i386 libraqm0 i386 0.10.2-1 [14.6 kB] Get: 166 http://deb.debian.org/debian unstable/main i386 libsharpyuv0 i386 1.4.0-0.1+b1 [113 kB] Get: 167 http://deb.debian.org/debian unstable/main i386 libsodium23 i386 1.0.18-1+b2 [186 kB] Get: 168 http://deb.debian.org/debian unstable/main i386 libwebp7 i386 1.4.0-0.1+b1 [322 kB] Get: 169 http://deb.debian.org/debian unstable/main i386 libtiff6 i386 4.5.1+git230720-5 [339 kB] Get: 170 http://deb.debian.org/debian unstable/main i386 libwebpdemux2 i386 1.4.0-0.1+b1 [111 kB] Get: 171 http://deb.debian.org/debian unstable/main i386 libwebpmux3 i386 1.4.0-0.1+b1 [125 kB] Get: 172 http://deb.debian.org/debian unstable/main i386 libxslt1.1 i386 1.1.35-1.1+b1 [243 kB] Get: 173 http://deb.debian.org/debian unstable/main i386 libyaml-0-2 i386 0.2.5-1+b2 [56.0 kB] Get: 174 http://deb.debian.org/debian unstable/main i386 libzmq5 i386 4.3.5-1+b3 [308 kB] Get: 175 http://deb.debian.org/debian unstable/main i386 pandoc-data all 3.1.11.1-3 [459 kB] Get: 176 http://deb.debian.org/debian unstable/main i386 pandoc i386 3.1.11.1+ds-2 [37.3 MB] Get: 177 http://deb.debian.org/debian unstable/main i386 python-babel-localedata all 2.16.0-1 [5696 kB] Get: 178 http://deb.debian.org/debian unstable/main i386 python-matplotlib-data all 3.8.3-3 [2731 kB] Get: 179 http://deb.debian.org/debian unstable/main i386 python-tables-data all 3.10.1-1 [49.5 kB] Get: 180 http://deb.debian.org/debian unstable/main i386 python-tinycss2-common all 1.4.0-1 [44.8 kB] Get: 181 http://deb.debian.org/debian unstable/main i386 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 182 http://deb.debian.org/debian unstable/main i386 python3.13 i386 3.13.1-2 [740 kB] Get: 183 http://deb.debian.org/debian unstable/main i386 python3-all i386 3.12.7-1 [1052 B] Get: 184 http://deb.debian.org/debian unstable/main i386 python3.12-dev i386 3.12.8-3 [505 kB] Get: 185 http://deb.debian.org/debian unstable/main i386 python3-dev i386 3.12.7-1 [26.1 kB] Get: 186 http://deb.debian.org/debian unstable/main i386 python3.13-dev i386 3.13.1-2 [505 kB] Get: 187 http://deb.debian.org/debian unstable/main i386 python3-all-dev i386 3.12.7-1 [1076 B] Get: 188 http://deb.debian.org/debian unstable/main i386 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 189 http://deb.debian.org/debian unstable/main i386 python3-asttokens all 3.0.0-1 [20.1 kB] Get: 190 http://deb.debian.org/debian unstable/main i386 python3-attr all 24.2.0-1 [68.4 kB] Get: 191 http://deb.debian.org/debian unstable/main i386 python3-babel all 2.16.0-1 [114 kB] Get: 192 http://deb.debian.org/debian unstable/main i386 python3-webencodings all 0.5.1-5 [11.1 kB] Get: 193 http://deb.debian.org/debian unstable/main i386 python3-html5lib all 1.2-1 [92.2 kB] Get: 194 http://deb.debian.org/debian unstable/main i386 python3-bleach all 6.2.0-1 [51.2 kB] Get: 195 http://deb.debian.org/debian unstable/main i386 python3-brotli i386 1.1.0-2+b6 [319 kB] Get: 196 http://deb.debian.org/debian unstable/main i386 python3-soupsieve all 2.6-1 [38.3 kB] Get: 197 http://deb.debian.org/debian unstable/main i386 python3-bs4 all 4.12.3-3 [133 kB] Get: 198 http://deb.debian.org/debian unstable/main i386 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 199 http://deb.debian.org/debian unstable/main i386 python3-cffi-backend i386 1.17.1-2+b1 [95.5 kB] Get: 200 http://deb.debian.org/debian unstable/main i386 python3-numpy i386 1:1.26.4+ds-12 [4752 kB] Get: 201 http://deb.debian.org/debian unstable/main i386 python3-cftime i386 1.6.4-1+b2 [305 kB] Get: 202 http://deb.debian.org/debian unstable/main i386 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 203 http://deb.debian.org/debian unstable/main i386 python3-charset-normalizer i386 3.4.0-1+b1 [139 kB] Get: 204 http://deb.debian.org/debian unstable/main i386 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB] Get: 205 http://deb.debian.org/debian unstable/main i386 python3-comm all 0.2.1-1 [8104 B] Get: 206 http://deb.debian.org/debian unstable/main i386 python3-contourpy i386 1.3.1-1 [271 kB] Get: 207 http://deb.debian.org/debian unstable/main i386 python3-coverage i386 7.6.0+dfsg1-2+b1 [177 kB] Get: 208 http://deb.debian.org/debian unstable/main i386 python3-cpuinfo all 9.0.0+git20221119-2 [23.4 kB] Get: 209 http://deb.debian.org/debian unstable/main i386 python3-cycler all 0.12.1-1 [9496 B] Get: 210 http://deb.debian.org/debian unstable/main i386 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 211 http://deb.debian.org/debian unstable/main i386 python3-debugpy i386 1.8.8+ds-2 [1066 kB] Get: 212 http://deb.debian.org/debian unstable/main i386 python3-decorator all 5.1.1-5 [15.1 kB] Get: 213 http://deb.debian.org/debian unstable/main i386 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 214 http://deb.debian.org/debian unstable/main i386 python3-roman all 4.2-1 [10.4 kB] Get: 215 http://deb.debian.org/debian unstable/main i386 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 216 http://deb.debian.org/debian unstable/main i386 python3-executing all 2.1.0-0.1 [23.9 kB] Get: 217 http://deb.debian.org/debian unstable/main i386 python3-fastjsonschema all 2.20.0-1 [21.8 kB] Get: 218 http://deb.debian.org/debian unstable/main i386 python3-tz all 2024.1-2 [30.9 kB] Get: 219 http://deb.debian.org/debian unstable/main i386 python3-fs all 2.4.16-5 [95.1 kB] Get: 220 http://deb.debian.org/debian unstable/main i386 python3-lxml i386 5.3.0-1+b1 [1586 kB] Get: 221 http://deb.debian.org/debian unstable/main i386 python3-lz4 i386 4.4.0+dfsg-1 [25.5 kB] Get: 222 http://deb.debian.org/debian unstable/main i386 python3-scipy i386 1.14.1-3 [20.1 MB] Get: 223 http://deb.debian.org/debian unstable/main i386 python3-mpmath all 1.3.0-1 [419 kB] Get: 224 http://deb.debian.org/debian unstable/main i386 python3-sympy all 1.13.3-1 [4147 kB] Get: 225 http://deb.debian.org/debian unstable/main i386 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB] Get: 226 http://deb.debian.org/debian unstable/main i386 unicode-data all 15.1.0-1 [8547 kB] Get: 227 http://deb.debian.org/debian unstable/main i386 python3-fonttools i386 4.55.0-3 [1593 kB] Get: 228 http://deb.debian.org/debian unstable/main i386 python3-gsd i386 3.3.0-1+b2 [229 kB] Get: 229 http://deb.debian.org/debian unstable/main i386 python3-idna all 3.8-2 [41.6 kB] Get: 230 http://deb.debian.org/debian unstable/main i386 python3-imagesize all 1.4.1-1 [6688 B] Get: 231 http://deb.debian.org/debian unstable/main i386 python3-parso all 0.8.4-1 [67.8 kB] Get: 232 http://deb.debian.org/debian unstable/main i386 python3-typeshed all 0.0~git20231111.6764465-3 [1258 kB] Get: 233 http://deb.debian.org/debian unstable/main i386 python3-jedi all 0.19.1+ds1-1 [691 kB] Get: 234 http://deb.debian.org/debian unstable/main i386 python3-matplotlib-inline all 0.1.6-2 [8652 B] Get: 235 http://deb.debian.org/debian unstable/main i386 python3-wcwidth all 0.2.13+dfsg1-1 [24.9 kB] Get: 236 http://deb.debian.org/debian unstable/main i386 python3-prompt-toolkit all 3.0.48-1 [277 kB] Get: 237 http://deb.debian.org/debian unstable/main i386 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 238 http://deb.debian.org/debian unstable/main i386 python3-pure-eval all 0.2.3-1 [11.2 kB] Get: 239 http://deb.debian.org/debian unstable/main i386 python3-stack-data all 0.6.3-1 [21.6 kB] Get: 240 http://deb.debian.org/debian unstable/main i386 python3-ptyprocess all 0.7.0-6 [14.5 kB] Get: 241 http://deb.debian.org/debian unstable/main i386 python3-pexpect all 4.9-3 [55.6 kB] Get: 242 http://deb.debian.org/debian unstable/main i386 python3-ipython all 8.30.0-1 [568 kB] Get: 243 http://deb.debian.org/debian unstable/main i386 python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 244 http://deb.debian.org/debian unstable/main i386 python3-jupyter-core all 5.7.2-4 [35.1 kB] Get: 245 http://deb.debian.org/debian unstable/main i386 python3-psutil i386 5.9.8-2 [226 kB] Get: 246 http://deb.debian.org/debian unstable/main i386 python3-tornado i386 6.4.2-1 [349 kB] Get: 247 http://deb.debian.org/debian unstable/main i386 python3-py all 1.11.0-2 [88.7 kB] Get: 248 http://deb.debian.org/debian unstable/main i386 python3-zmq i386 24.0.1-5+b3 [345 kB] Get: 249 http://deb.debian.org/debian unstable/main i386 python3-jupyter-client all 8.6.3-1 [92.0 kB] Get: 250 http://deb.debian.org/debian unstable/main i386 python3-nest-asyncio all 1.5.4-1 [6248 B] Get: 251 http://deb.debian.org/debian unstable/main i386 python3-packaging all 24.2-1 [55.3 kB] Get: 252 http://deb.debian.org/debian unstable/main i386 python3-ipykernel all 6.29.5-1 [102 kB] Get: 253 http://deb.debian.org/debian unstable/main i386 python3-markupsafe i386 2.1.5-1+b2 [13.9 kB] Get: 254 http://deb.debian.org/debian unstable/main i386 python3-jinja2 all 3.1.3-1 [119 kB] Get: 255 http://deb.debian.org/debian unstable/main i386 python3-joblib all 1.3.2-5 [216 kB] Get: 256 http://deb.debian.org/debian unstable/main i386 python3-rpds-py i386 0.21.0-2 [313 kB] Get: 257 http://deb.debian.org/debian unstable/main i386 python3-referencing all 0.35.1-2 [23.5 kB] Get: 258 http://deb.debian.org/debian unstable/main i386 python3-jsonschema-specifications all 2023.12.1-2 [9020 B] Get: 259 http://deb.debian.org/debian unstable/main i386 python3-jsonschema all 4.19.2-5 [71.4 kB] Get: 260 http://deb.debian.org/debian unstable/main i386 python3-jupyterlab-pygments all 0.2.2-3 [6096 B] Get: 261 http://deb.debian.org/debian unstable/main i386 python3-kiwisolver i386 1.4.7-2+b1 [83.4 kB] Get: 262 http://deb.debian.org/debian unstable/main i386 python3-pil i386 10.4.0-1+b1 [513 kB] Get: 263 http://deb.debian.org/debian unstable/main i386 python3.12-tk i386 3.12.8-3 [113 kB] Get: 264 http://deb.debian.org/debian unstable/main i386 python3.13-tk i386 3.13.1-2 [104 kB] Get: 265 http://deb.debian.org/debian unstable/main i386 python3-tk i386 3.12.7-1 [9444 B] Get: 266 http://deb.debian.org/debian unstable/main i386 python3-pil.imagetk i386 10.4.0-1+b1 [80.1 kB] Get: 267 http://deb.debian.org/debian unstable/main i386 python3-pyparsing all 3.1.2-1 [146 kB] Get: 268 http://deb.debian.org/debian unstable/main i386 python3-matplotlib i386 3.8.3-3+b1 [5660 kB] Get: 269 http://deb.debian.org/debian unstable/main i386 python3-mistune all 3.0.2-2 [33.2 kB] Get: 270 http://deb.debian.org/debian unstable/main i386 sphinx-rtd-theme-common all 3.0.2+dfsg-1 [1023 kB] Get: 271 http://deb.debian.org/debian unstable/main i386 sphinx-common all 8.1.3-2 [616 kB] Get: 272 http://deb.debian.org/debian unstable/main i386 python3-urllib3 all 2.2.3-4 [112 kB] Get: 273 http://deb.debian.org/debian unstable/main i386 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 274 http://deb.debian.org/debian unstable/main i386 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 275 http://deb.debian.org/debian unstable/main i386 python3-sphinx all 8.1.3-2 [468 kB] Get: 276 http://deb.debian.org/debian unstable/main i386 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 277 http://deb.debian.org/debian unstable/main i386 python3-sphinx-rtd-theme all 3.0.2+dfsg-1 [29.5 kB] Get: 278 http://deb.debian.org/debian unstable/main i386 python3-msmb-theme all 1.2.0-4 [33.8 kB] Get: 279 http://deb.debian.org/debian unstable/main i386 python3-nbformat all 5.9.1-1 [45.1 kB] Get: 280 http://deb.debian.org/debian unstable/main i386 python3-nbclient all 0.8.0-2 [62.2 kB] Get: 281 http://deb.debian.org/debian unstable/main i386 python3-pandocfilters all 1.5.1-1 [23.7 kB] Get: 282 http://deb.debian.org/debian unstable/main i386 python3-tinycss2 all 1.4.0-1 [24.9 kB] Get: 283 http://deb.debian.org/debian unstable/main i386 python3-nbconvert all 7.16.4-2 [158 kB] Get: 284 http://deb.debian.org/debian unstable/main i386 python3-nbsphinx all 0.9.5+ds-1 [39.9 kB] Get: 285 http://deb.debian.org/debian unstable/main i386 python3-nbsphinx-link all 1.3.0-4 [6264 B] Get: 286 http://deb.debian.org/debian unstable/main i386 python3-netcdf4 i386 1.7.2-1+b1 [843 kB] Get: 287 http://deb.debian.org/debian unstable/main i386 python3-networkx all 3.2.1-5 [13.0 MB] Get: 288 http://deb.debian.org/debian unstable/main i386 python3-numexpr i386 2.10.2-1 [132 kB] Get: 289 http://deb.debian.org/debian unstable/main i386 python3-tabulate all 0.9.0-1 [45.9 kB] Get: 290 http://deb.debian.org/debian unstable/main i386 python3-numpydoc all 1.8.0-1 [51.4 kB] Get: 291 http://deb.debian.org/debian unstable/main i386 python3-pandas-lib i386 2.2.3+dfsg-5+b1 [6860 kB] Get: 292 http://deb.debian.org/debian unstable/main i386 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 293 http://deb.debian.org/debian unstable/main i386 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 294 http://deb.debian.org/debian unstable/main i386 python3-sklearn-lib i386 1.4.2+dfsg-7 [5795 kB] Get: 295 http://deb.debian.org/debian unstable/main i386 python3-sklearn all 1.4.2+dfsg-7 [2248 kB] Get: 296 http://deb.debian.org/debian unstable/main i386 python3-tables-lib i386 3.10.1-1+b2 [776 kB] Get: 297 http://deb.debian.org/debian unstable/main i386 python3-tables all 3.10.1-1 [355 kB] Get: 298 http://deb.debian.org/debian unstable/main i386 python3-versioneer all 0.29-1 [43.0 kB] Fetched 236 MB in 4s (59.6 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 ... 19952 files and directories currently installed.) Preparing to unpack .../0-fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libproc2-0:i386. Preparing to unpack .../1-libproc2-0_2%3a4.0.4-6_i386.deb ... Unpacking libproc2-0:i386 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../2-procps_2%3a4.0.4-6_i386.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../3-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package ucf. Preparing to unpack .../4-ucf_3.0045_all.deb ... Moving old data out of the way Unpacking ucf (3.0045) ... Selecting previously unselected package libdebuginfod-common. Preparing to unpack .../5-libdebuginfod-common_0.192-4_all.deb ... Unpacking libdebuginfod-common (0.192-4) ... Selecting previously unselected package libpython3.12-minimal:i386. Preparing to unpack .../6-libpython3.12-minimal_3.12.8-3_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.8-3) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../7-libexpat1_2.6.4-1_i386.deb ... Unpacking libexpat1:i386 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../8-python3.12-minimal_3.12.8-3_i386.deb ... Unpacking python3.12-minimal (3.12.8-3) ... Setting up libpython3.12-minimal:i386 (3.12.8-3) ... Setting up libexpat1:i386 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20545 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_i386.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-4_all.deb ... Unpacking tzdata (2024b-4) ... Selecting previously unselected package libkrb5support0:i386. Preparing to unpack .../04-libkrb5support0_1.21.3-3_i386.deb ... Unpacking libkrb5support0:i386 (1.21.3-3) ... Selecting previously unselected package libcom-err2:i386. Preparing to unpack .../05-libcom-err2_1.47.2~rc1-2_i386.deb ... Unpacking libcom-err2:i386 (1.47.2~rc1-2) ... Selecting previously unselected package libk5crypto3:i386. Preparing to unpack .../06-libk5crypto3_1.21.3-3_i386.deb ... Unpacking libk5crypto3:i386 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:i386. Preparing to unpack .../07-libkeyutils1_1.6.3-4_i386.deb ... Unpacking libkeyutils1:i386 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:i386. Preparing to unpack .../08-libkrb5-3_1.21.3-3_i386.deb ... Unpacking libkrb5-3:i386 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:i386. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_i386.deb ... Unpacking libgssapi-krb5-2:i386 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:i386. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3 to /lib/i386-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3.0.0 to /lib/i386-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:i386 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:i386. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_i386.deb ... Unpacking libnsl2:i386 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:i386. Preparing to unpack .../14-libreadline8t64_8.2-6_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-6) ... Selecting previously unselected package libpython3.12-stdlib:i386. Preparing to unpack .../15-libpython3.12-stdlib_3.12.8-3_i386.deb ... Unpacking libpython3.12-stdlib:i386 (3.12.8-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.8-3_i386.deb ... Unpacking python3.12 (3.12.8-3) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../17-libpython3-stdlib_3.12.7-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21608 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.7-1_i386.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package libpython3.13-minimal:i386. Preparing to unpack .../001-libpython3.13-minimal_3.13.1-2_i386.deb ... Unpacking libpython3.13-minimal:i386 (3.13.1-2) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../002-python3.13-minimal_3.13.1-2_i386.deb ... Unpacking python3.13-minimal (3.13.1-2) ... Selecting previously unselected package sgml-base. Preparing to unpack .../003-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.3.2-2_i386.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../007-libmagic1t64_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.45-3+b1_i386.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.22.5-2_i386.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../010-libuchardet0_0.0.8-1+b2_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.23.0-6_i386.deb ... Unpacking groff-base (1.23.0-6) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../012-bsdextrautils_2.40.2-12_i386.deb ... Unpacking bsdextrautils (2.40.2-12) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../013-libpipeline1_1.5.8-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../014-man-db_2.13.0-1_i386.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../015-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../016-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../017-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../018-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 .../019-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libtcl8.6:i386. Preparing to unpack .../020-libtcl8.6_8.6.15+dfsg-2_i386.deb ... Unpacking libtcl8.6:i386 (8.6.15+dfsg-2) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../021-libbrotli1_1.1.0-2+b6_i386.deb ... Unpacking libbrotli1:i386 (1.1.0-2+b6) ... Selecting previously unselected package libpng16-16t64:i386. Preparing to unpack .../022-libpng16-16t64_1.6.44-3_i386.deb ... Unpacking libpng16-16t64:i386 (1.6.44-3) ... Selecting previously unselected package libfreetype6:i386. Preparing to unpack .../023-libfreetype6_2.13.3+dfsg-1_i386.deb ... Unpacking libfreetype6:i386 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../024-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../025-fonts-dejavu-core_2.37-8_all.deb ... 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Setting up python3-babel (2.16.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-networkx (3.2.1-5) ... Setting up python3-fs (2.4.16-5) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-ipython (8.30.0-1) ... Setting up python3-zmq (24.0.1-5+b3) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up python3-jupyter-client (8.6.3-1) ... Setting up python3-contourpy (1.3.1-1) ... Setting up python3-jsonschema-specifications (2023.12.1-2) ... Setting up dh-python (6.20241024) ... Setting up python3-scipy (1.14.1-3) ... Setting up python3-tables-lib (3.10.1-1+b2) ... Setting up python3-pandas-lib:i386 (2.2.3+dfsg-5+b1) ... Setting up python3-sklearn-lib:i386 (1.4.2+dfsg-7) ... Setting up python3-gsd (3.3.0-1+b2) ... Setting up python3-jupyterlab-pygments (0.2.2-3) ... Setting up python3-pandas (2.2.3+dfsg-5) ... Setting up python3-jsonschema (4.19.2-5) ... Setting up python3-ipykernel (6.29.5-1) ... Setting up python3-sklearn (1.4.2+dfsg-7) ... Setting up python3-cftime (1.6.4-1+b2) ... Setting up python3-numexpr (2.10.2-1) ... Setting up python3-netcdf4 (1.7.2-1+b1) ... Setting up python3-nbformat (5.9.1-1) ... Setting up python3-tables (3.10.1-1) ... Setting up python3-nbclient (0.8.0-2) ... Setting up python3-nbconvert (7.16.4-2) ... Setting up python3-fonttools (4.55.0-3) ... Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... Setting up python3-matplotlib (3.8.3-3+b1) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.1.3-2) ... Setting up python3-nbsphinx (0.9.5+ds-1) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-numpydoc (1.8.0-1) ... Setting up python3-nbsphinx-link (1.3.0-4) ... Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-1) ... Setting up python3-msmb-theme (1.2.0-4) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/7091/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/7091/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/mdtraj-1.10.1/ && 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_1.10.1-2_source.changes dpkg-buildpackage: info: source package mdtraj dpkg-buildpackage: info: source version 1.10.1-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Emmanuel Arias dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 dpkg-source: info: using options from mdtraj-1.10.1/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild pybuild --clean -i python{version} -p "3.13 3.12" I: pybuild base:311: python3.13 setup.py clean Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-linux-gnu/14/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) /build/reproducible-path/mdtraj-1.10.1/basesetup.py:483: UserWarning: Unrecognized setuptools command ('clean'), proceeding with generating Cython sources and expanding templates warnings.warn( warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired. Possible solutions: 1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'make_whole' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired. Possible solutions: 1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired. Possible solutions: 1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE2 support... Compiler supports SSE2 Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx [ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 5/10] Cythonizing mdtraj/geometry/drid.pyx [ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx running clean removing '/build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build' (and everything under it) 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it I: pybuild base:311: python3.12 setup.py clean Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-linux-gnu/14/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) /build/reproducible-path/mdtraj-1.10.1/basesetup.py:483: UserWarning: Unrecognized setuptools command ('clean'), proceeding with generating Cython sources and expanding templates warnings.warn( warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired. Possible solutions: 1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'make_whole' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired. Possible solutions: 1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired. Possible solutions: 1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE2 support... Compiler supports SSE2 Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx [ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 5/10] Cythonizing mdtraj/geometry/drid.pyx [ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx running clean removing '/build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build' (and everything under it) 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/mdtraj-1.10.1' for f in mdtraj/formats/binpos/binpos.c \ mdtraj/formats/dcd/dcd.c \ mdtraj/formats/dtr/dtr.cpp \ mdtraj/formats/tng/tng.c \ mdtraj/formats/xtc/trr.c \ mdtraj/formats/xtc/xtc.c \ mdtraj/geometry/drid.cpp \ mdtraj/geometry/neighborlist.cpp \ mdtraj/geometry/neighbors.cpp \ mdtraj/geometry/src/_geometry.cpp \ mdtraj/rmsd/_lprmsd.cpp \ mdtraj/rmsd/_rmsd.cpp \ mdtraj/version.py; \ do rm -f $f; done rm -rf mdtraj/core/lib rm -rf docs/api/generated rm -rf __pycache__ .pybuild find . -name "lib*.a" -delete make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.10.1' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/python3-mdtraj.substvars debian/python-mdtraj-doc.substvars debian/files rm -fr -- debian/python3-mdtraj/ debian/tmp/ debian/python-mdtraj-doc/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --with sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild pybuild --configure -i python{version} -p "3.13 3.12" I: pybuild base:311: python3.13 setup.py config Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-linux-gnu/14/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) /build/reproducible-path/mdtraj-1.10.1/basesetup.py:483: UserWarning: Unrecognized setuptools command ('config'), proceeding with generating Cython sources and expanding templates warnings.warn( warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired. Possible solutions: 1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'make_whole' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired. Possible solutions: 1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired. Possible solutions: 1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE2 support... Compiler supports SSE2 Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx [ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 5/10] Cythonizing mdtraj/geometry/drid.pyx [ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx running config I: pybuild base:311: python3.12 setup.py config Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-linux-gnu/14/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) /build/reproducible-path/mdtraj-1.10.1/basesetup.py:483: UserWarning: Unrecognized setuptools command ('config'), proceeding with generating Cython sources and expanding templates warnings.warn( warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired. Possible solutions: 1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'make_whole' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired. Possible solutions: 1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired. Possible solutions: 1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE2 support... Compiler supports SSE2 Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx [ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 5/10] Cythonizing mdtraj/geometry/drid.pyx [ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx running config dh_auto_build -O--buildsystem=pybuild pybuild --build -i python{version} -p "3.13 3.12" I: pybuild base:311: /usr/bin/python3.13 setup.py build Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-linux-gnu/14/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired. Possible solutions: 1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'make_whole' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired. Possible solutions: 1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired. Possible solutions: 1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE2 support... Compiler supports SSE2 Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx [ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 5/10] Cythonizing mdtraj/geometry/drid.pyx [ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx running build running build_py creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj copying mdtraj/io.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj copying mdtraj/_version.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj copying mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats copying mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing copying mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing copying mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing copying mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing copying mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils copying mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils copying mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils copying mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils copying mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils copying mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils copying mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils copying mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core copying mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core copying mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core copying mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core copying mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core copying mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core copying mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/data UPDATING /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_version.py set /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_version.py to '1.10.1' running build_ext building 'mdtraj.formats.xtc' extension creating build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord': mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes': mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 119 | if (NULL == xd) | ^~ mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 122 | do { | ^~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/xtc.c:1263: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write' at mdtraj/formats/xtc/xtc.c:13728:16, inlined from '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write' at mdtraj/formats/xtc/xtc.c:13424:13: mdtraj/formats/xtc/xtc.c:1165:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 1165 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/xtc.c:25481:20: note: in expansion of macro 'PyInt_FromLong' 25481 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write': mdtraj/formats/xtc/xtc.c:13444:7: note: '__pyx_v_status' was declared here 13444 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:11491:10: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11491 | if (unlikely(__pyx_t_5 != -1)) { | ^ mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 10279 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11490:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11490 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 10279 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11856:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11856 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11860:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11860 | } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11864:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 11864 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11902:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11902 | } else if (unlikely(__pyx_t_41 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10283:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 10283 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11826:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11826 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10287:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 10287 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11844:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11844 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10291:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 10291 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11884:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11884 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11888:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11888 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11892:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 11892 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/xtc.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/xtc.cpython-313-i386-linux-gnu.so building 'mdtraj.formats.trr' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/trr.c:1265: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write' at mdtraj/formats/xtc/trr.c:15643:16, inlined from '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write' at mdtraj/formats/xtc/trr.c:15083:13: mdtraj/formats/xtc/trr.c:1167:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 1167 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/trr.c:27476:20: note: in expansion of macro 'PyInt_FromLong' 27476 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write': mdtraj/formats/xtc/trr.c:15111:7: note: '__pyx_v_status' was declared here 15111 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:12632:12: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12632 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 10939 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12631:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12631 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 10939 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12580:12: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12580 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 10955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12579:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12579 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 10955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12739:10: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12739 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 10959 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12738:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12738 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 10959 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12339:56: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12339 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:2533:95: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:12354:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 12354 | __pyx_v_frame_vel = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_vel.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_vel.diminfo[0].strides, __pyx_t_30, __pyx_pybuffernd_vel.diminfo[1].strides, __pyx_t_31, __pyx_pybuffernd_vel.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12345:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12345 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12349:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 12349 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_4 = 2; | ^ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12396:59: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12396 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:2533:95: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:12411:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 12411 | __pyx_v_frame_forces = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_forces.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_forces.diminfo[0].strides, __pyx_t_31, __pyx_pybuffernd_forces.diminfo[1].strides, __pyx_t_30, __pyx_pybuffernd_forces.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12402:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12402 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12406:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 12406 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_4 = 2; | ^ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/trr.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/trr.cpython-313-i386-linux-gnu.so building 'mdtraj.formats.dcd' extension creating build/temp.linux-i686-cpython-313/mdtraj/formats/dcd creating build/temp.linux-i686-cpython-313/mdtraj/formats/dcd/src i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-i686-cpython-313/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dcd/dcd.c:1260: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read' at mdtraj/formats/dcd/dcd.c:10190:17: mdtraj/formats/dcd/dcd.c:1162:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 1162 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/dcd/dcd.c:18997:20: note: in expansion of macro 'PyInt_FromLong' 18997 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:8994:7: note: '__pyx_v_i' was declared here 8994 | int __pyx_v_i; | ^~~~~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-i686-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/mdtraj/formats/dcd/dcd.o build/temp.linux-i686-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dcd.cpython-313-i386-linux-gnu.so building 'mdtraj.formats.dtr' extension creating build/temp.linux-i686-cpython-313/mdtraj/formats/dtr creating build/temp.linux-i686-cpython-313/mdtraj/formats/dtr/src i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-i686-cpython-313/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dtr/dtr.cpp:1279: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-i686-cpython-313/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/dtr/src/dtrplugin.cxx: In member function 'bool desres::molfile::Timekeys::init(const std::string&)': mdtraj/formats/dtr/src/dtrplugin.cxx:486:64: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %lld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format '%d' expects argument of type 'int', but argument 3 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %lld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:494:60: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 494 | "non-constant time interval at frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d mdtraj/formats/dtr/src/dtrplugin.cxx:499:60: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)': mdtraj/formats/dtr/src/dtrplugin.cxx:1301:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", | ~~^ | | | long int | %lld 1302 | 3*natoms, pos.count); | ~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:1310:71: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", | ~~^ | | | long int | %lld 1311 | 3*natoms, vel.count); | ~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)': mdtraj/formats/dtr/src/dtrplugin.cxx:1572:45: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", | ~~^ | | | long int | %lld 1573 | velblob.count, 3*natoms); | ~~~~~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 706 | sprintf(sub, "%03x/", i); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 706 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:970, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(subsub, "%03x", j); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 714 | sprintf(subsub, "%03x", j); | ^~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 4 and 9 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 667 | sprintf(answer, "%03x/", d1); | ^ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:667:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: '%03x' directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ In function 'std::string DDreldir(const std::string&, int, int)', inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:665:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 9 and 19 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/mdtraj/formats/dtr/dtr.o build/temp.linux-i686-cpython-313/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dtr.cpython-313-i386-linux-gnu.so building 'mdtraj._rmsd' extension creating build/temp.linux-i686-cpython-313/mdtraj/rmsd creating build/temp.linux-i686-cpython-313/mdtraj/rmsd/src i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/mdtraj/rmsd/_rmsd.o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/center.o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/rotation.o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_rmsd.cpython-313-i386-linux-gnu.so building 'mdtraj._lprmsd' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/_lprmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/rmsd/_lprmsd.cpp:1307: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/Munkres.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/fancy_index.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/mdtraj/rmsd/_lprmsd.o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/Munkres.o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/center.o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/fancy_index.o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/rotation.o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_lprmsd.cpython-313-i386-linux-gnu.so building 'mdtraj.core.lib.libtheobald' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -msse2 -mssse3 -O3 -funroll-loops --std=c++11 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/center.o -msse2 -mssse3 -O3 -funroll-loops --std=c++11 i686-linux-gnu-gcc-ar rcs /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/lib/libtheobald.a build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/center.o building 'mdtraj.geometry._geometry' extension creating build/temp.linux-i686-cpython-313/mdtraj/geometry/src i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/_geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/geometry/src/_geometry.cpp:1289: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/dssp.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/sasa.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/mdtraj/geometry/src/_geometry.o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/dssp.o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/geometry.o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/sasa.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/_geometry.cpython-313-i386-linux-gnu.so building 'mdtraj.geometry.drid' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/drid.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/drid.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/dridkernels.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/moments.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/mdtraj/geometry/drid.o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/dridkernels.o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/moments.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/drid.cpython-313-i386-linux-gnu.so building 'mdtraj.geometry.neighbors' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/mdtraj/geometry/neighbors.o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/neighbors.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighbors.cpython-313-i386-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/mdtraj/geometry/neighborlist.o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/neighborlist.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighborlist.cpython-313-i386-linux-gnu.so I: pybuild base:311: /usr/bin/python3 setup.py build Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-linux-gnu/14/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired. Possible solutions: 1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'make_whole' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired. Possible solutions: 1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired. Possible solutions: 1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE2 support... Compiler supports SSE2 Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx [ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 5/10] Cythonizing mdtraj/geometry/drid.pyx [ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx running build running build_py creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj copying mdtraj/io.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj copying mdtraj/_version.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj copying mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats copying mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts copying mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing copying mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils copying mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry copying mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core copying mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters copying mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr copying mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb copying mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit copying mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data copying mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data UPDATING /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py set /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py to '1.10.1' running build_ext building 'mdtraj.formats.xtc' extension creating build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord': mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes': mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 119 | if (NULL == xd) | ^~ mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 122 | do { | ^~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/xtc.c:1263: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write' at mdtraj/formats/xtc/xtc.c:13728:16, inlined from '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write' at mdtraj/formats/xtc/xtc.c:13424:13: mdtraj/formats/xtc/xtc.c:1165:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 1165 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/xtc.c:25481:20: note: in expansion of macro 'PyInt_FromLong' 25481 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write': mdtraj/formats/xtc/xtc.c:13444:7: note: '__pyx_v_status' was declared here 13444 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:11491:10: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11491 | if (unlikely(__pyx_t_5 != -1)) { | ^ mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 10279 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11490:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11490 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 10279 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11856:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11856 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11860:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11860 | } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11864:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 11864 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11902:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11902 | } else if (unlikely(__pyx_t_41 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10283:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 10283 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11826:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11826 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10287:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 10287 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11844:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11844 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10291:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 10291 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11884:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11884 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11888:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11888 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11892:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 11892 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/xtc.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-i386-linux-gnu.so building 'mdtraj.formats.trr' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/trr.c:1265: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write' at mdtraj/formats/xtc/trr.c:15643:16, inlined from '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write' at mdtraj/formats/xtc/trr.c:15083:13: mdtraj/formats/xtc/trr.c:1167:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 1167 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/trr.c:27476:20: note: in expansion of macro 'PyInt_FromLong' 27476 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write': mdtraj/formats/xtc/trr.c:15111:7: note: '__pyx_v_status' was declared here 15111 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:12632:12: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12632 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 10939 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12631:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12631 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 10939 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12580:12: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12580 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 10955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12579:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12579 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 10955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12739:10: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12739 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 10959 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12738:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12738 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 10959 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12339:56: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12339 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:2533:95: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:12354:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 12354 | __pyx_v_frame_vel = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_vel.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_vel.diminfo[0].strides, __pyx_t_30, __pyx_pybuffernd_vel.diminfo[1].strides, __pyx_t_31, __pyx_pybuffernd_vel.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12345:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12345 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12349:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 12349 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_4 = 2; | ^ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12396:59: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12396 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:2533:95: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:12411:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 12411 | __pyx_v_frame_forces = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_forces.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_forces.diminfo[0].strides, __pyx_t_31, __pyx_pybuffernd_forces.diminfo[1].strides, __pyx_t_30, __pyx_pybuffernd_forces.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12402:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12402 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12406:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 12406 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_4 = 2; | ^ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/trr.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so building 'mdtraj.formats.dcd' extension creating build/temp.linux-i686-cpython-312/mdtraj/formats/dcd creating build/temp.linux-i686-cpython-312/mdtraj/formats/dcd/src i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dcd/dcd.c:1260: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read' at mdtraj/formats/dcd/dcd.c:10190:17: mdtraj/formats/dcd/dcd.c:1162:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 1162 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/dcd/dcd.c:18997:20: note: in expansion of macro 'PyInt_FromLong' 18997 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:8994:7: note: '__pyx_v_i' was declared here 8994 | int __pyx_v_i; | ^~~~~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/dcd/dcd.o build/temp.linux-i686-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so building 'mdtraj.formats.dtr' extension creating build/temp.linux-i686-cpython-312/mdtraj/formats/dtr creating build/temp.linux-i686-cpython-312/mdtraj/formats/dtr/src i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-i686-cpython-312/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dtr/dtr.cpp:1279: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-i686-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/dtr/src/dtrplugin.cxx: In member function 'bool desres::molfile::Timekeys::init(const std::string&)': mdtraj/formats/dtr/src/dtrplugin.cxx:486:64: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %lld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format '%d' expects argument of type 'int', but argument 3 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %lld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:494:60: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 494 | "non-constant time interval at frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d mdtraj/formats/dtr/src/dtrplugin.cxx:499:60: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)': mdtraj/formats/dtr/src/dtrplugin.cxx:1301:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", | ~~^ | | | long int | %lld 1302 | 3*natoms, pos.count); | ~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:1310:71: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", | ~~^ | | | long int | %lld 1311 | 3*natoms, vel.count); | ~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)': mdtraj/formats/dtr/src/dtrplugin.cxx:1572:45: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", | ~~^ | | | long int | %lld 1573 | velblob.count, 3*natoms); | ~~~~~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 706 | sprintf(sub, "%03x/", i); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 706 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:970, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(subsub, "%03x", j); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 714 | sprintf(subsub, "%03x", j); | ^~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 4 and 9 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 667 | sprintf(answer, "%03x/", d1); | ^ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:667:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: '%03x' directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ In function 'std::string DDreldir(const std::string&, int, int)', inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:665:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 9 and 19 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/dtr/dtr.o build/temp.linux-i686-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-i386-linux-gnu.so building 'mdtraj._rmsd' extension creating build/temp.linux-i686-cpython-312/mdtraj/rmsd creating build/temp.linux-i686-cpython-312/mdtraj/rmsd/src i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/rmsd/_rmsd.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so building 'mdtraj._lprmsd' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/_lprmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/rmsd/_lprmsd.cpp:1307: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/Munkres.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/fancy_index.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/rmsd/_lprmsd.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/Munkres.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/fancy_index.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so building 'mdtraj.core.lib.libtheobald' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -msse2 -mssse3 -O3 -funroll-loops --std=c++11 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/center.o -msse2 -mssse3 -O3 -funroll-loops --std=c++11 i686-linux-gnu-gcc-ar rcs /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/libtheobald.a build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/center.o building 'mdtraj.geometry._geometry' extension creating build/temp.linux-i686-cpython-312/mdtraj/geometry/src i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/_geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/geometry/src/_geometry.cpp:1289: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/dssp.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/sasa.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/geometry/src/_geometry.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/dssp.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/geometry.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/sasa.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.drid' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/drid.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/drid.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/dridkernels.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/moments.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/geometry/drid.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/dridkernels.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/moments.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.neighbors' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/geometry/neighbors.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/neighbors.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/geometry/neighborlist.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/neighborlist.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so dh_auto_test -O--buildsystem=pybuild pybuild --test -i python{version} -p "3.13 3.12" I: pybuild base:311: cd /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build; python3.13 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN I: pybuild base:311: cd /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build; python3.12 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN rm -fr -- /tmp/dh-xdg-rundir-jDIDLqU_ create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild rm -f -- debian/python3-mdtraj.substvars debian/python-mdtraj-doc.substvars rm -fr -- debian/.debhelper/generated/python3-mdtraj/ debian/python3-mdtraj/ debian/tmp/ debian/.debhelper/generated/python-mdtraj-doc/ debian/python-mdtraj-doc/ dh_installdirs -O--buildsystem=pybuild install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples/data dh_auto_install -O--buildsystem=pybuild install -m0755 -d /build/reproducible-path/mdtraj-1.10.1/debian/tmp pybuild --install -i python{version} -p "3.13 3.12" --dest-dir /build/reproducible-path/mdtraj-1.10.1/debian/tmp I: pybuild base:311: /usr/bin/python3.13 setup.py install --root /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-linux-gnu/14/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired. Possible solutions: 1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'make_whole' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired. Possible solutions: 1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired. Possible solutions: 1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE2 support... Compiler supports SSE2 Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx [ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 5/10] Cythonizing mdtraj/geometry/drid.pyx [ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py UPDATING /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_version.py set /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_version.py to '1.10.1' running build_ext building 'mdtraj.formats.xtc' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord': mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes': mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 119 | if (NULL == xd) | ^~ mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 122 | do { | ^~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/xtc.c:1263: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write' at mdtraj/formats/xtc/xtc.c:13728:16, inlined from '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write' at mdtraj/formats/xtc/xtc.c:13424:13: mdtraj/formats/xtc/xtc.c:1165:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 1165 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/xtc.c:25481:20: note: in expansion of macro 'PyInt_FromLong' 25481 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write': mdtraj/formats/xtc/xtc.c:13444:7: note: '__pyx_v_status' was declared here 13444 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:11491:10: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11491 | if (unlikely(__pyx_t_5 != -1)) { | ^ mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 10279 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11490:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11490 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 10279 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11856:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11856 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11860:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11860 | } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11864:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 11864 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11902:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11902 | } else if (unlikely(__pyx_t_41 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10283:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 10283 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11826:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11826 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10287:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 10287 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11844:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11844 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10291:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 10291 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11884:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11884 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11888:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11888 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11892:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 11892 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/xtc.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/xtc.cpython-313-i386-linux-gnu.so building 'mdtraj.formats.trr' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/trr.c:1265: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write' at mdtraj/formats/xtc/trr.c:15643:16, inlined from '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write' at mdtraj/formats/xtc/trr.c:15083:13: mdtraj/formats/xtc/trr.c:1167:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 1167 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/trr.c:27476:20: note: in expansion of macro 'PyInt_FromLong' 27476 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write': mdtraj/formats/xtc/trr.c:15111:7: note: '__pyx_v_status' was declared here 15111 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:12632:12: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12632 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 10939 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12631:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12631 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 10939 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12580:12: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12580 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 10955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12579:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12579 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 10955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12739:10: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12739 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 10959 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12738:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12738 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 10959 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12339:56: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12339 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:2533:95: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:12354:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 12354 | __pyx_v_frame_vel = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_vel.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_vel.diminfo[0].strides, __pyx_t_30, __pyx_pybuffernd_vel.diminfo[1].strides, __pyx_t_31, __pyx_pybuffernd_vel.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12345:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12345 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12349:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 12349 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_4 = 2; | ^ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12396:59: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12396 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:2533:95: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:12411:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 12411 | __pyx_v_frame_forces = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_forces.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_forces.diminfo[0].strides, __pyx_t_31, __pyx_pybuffernd_forces.diminfo[1].strides, __pyx_t_30, __pyx_pybuffernd_forces.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12402:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12402 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12406:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 12406 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_4 = 2; | ^ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-i686-cpython-313/mdtraj/formats/xtc/trr.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/trr.cpython-313-i386-linux-gnu.so building 'mdtraj.formats.dcd' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-i686-cpython-313/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dcd/dcd.c:1260: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read' at mdtraj/formats/dcd/dcd.c:10190:17: mdtraj/formats/dcd/dcd.c:1162:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 1162 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/dcd/dcd.c:18997:20: note: in expansion of macro 'PyInt_FromLong' 18997 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:8994:7: note: '__pyx_v_i' was declared here 8994 | int __pyx_v_i; | ^~~~~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-i686-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/mdtraj/formats/dcd/dcd.o build/temp.linux-i686-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dcd.cpython-313-i386-linux-gnu.so building 'mdtraj.formats.dtr' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-i686-cpython-313/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dtr/dtr.cpp:1279: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-i686-cpython-313/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/dtr/src/dtrplugin.cxx: In member function 'bool desres::molfile::Timekeys::init(const std::string&)': mdtraj/formats/dtr/src/dtrplugin.cxx:486:64: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %lld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format '%d' expects argument of type 'int', but argument 3 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %lld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:494:60: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 494 | "non-constant time interval at frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d mdtraj/formats/dtr/src/dtrplugin.cxx:499:60: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)': mdtraj/formats/dtr/src/dtrplugin.cxx:1301:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", | ~~^ | | | long int | %lld 1302 | 3*natoms, pos.count); | ~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:1310:71: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", | ~~^ | | | long int | %lld 1311 | 3*natoms, vel.count); | ~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)': mdtraj/formats/dtr/src/dtrplugin.cxx:1572:45: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", | ~~^ | | | long int | %lld 1573 | velblob.count, 3*natoms); | ~~~~~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 706 | sprintf(sub, "%03x/", i); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 706 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:970, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(subsub, "%03x", j); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 714 | sprintf(subsub, "%03x", j); | ^~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 4 and 9 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 667 | sprintf(answer, "%03x/", d1); | ^ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:667:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: '%03x' directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ In function 'std::string DDreldir(const std::string&, int, int)', inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:665:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 9 and 19 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/mdtraj/formats/dtr/dtr.o build/temp.linux-i686-cpython-313/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dtr.cpython-313-i386-linux-gnu.so building 'mdtraj._rmsd' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/mdtraj/rmsd/_rmsd.o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/center.o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/rotation.o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_rmsd.cpython-313-i386-linux-gnu.so building 'mdtraj._lprmsd' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/_lprmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/rmsd/_lprmsd.cpp:1307: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/Munkres.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/fancy_index.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/mdtraj/rmsd/_lprmsd.o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/Munkres.o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/center.o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/fancy_index.o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/rotation.o build/temp.linux-i686-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_lprmsd.cpython-313-i386-linux-gnu.so building 'mdtraj.geometry._geometry' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/_geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/geometry/src/_geometry.cpp:1289: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/dssp.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/sasa.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/mdtraj/geometry/src/_geometry.o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/dssp.o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/geometry.o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/sasa.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/_geometry.cpython-313-i386-linux-gnu.so building 'mdtraj.geometry.drid' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/drid.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/drid.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/dridkernels.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/moments.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/mdtraj/geometry/drid.o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/dridkernels.o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/moments.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/drid.cpython-313-i386-linux-gnu.so building 'mdtraj.geometry.neighbors' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/mdtraj/geometry/neighbors.o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/neighbors.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighbors.cpython-313-i386-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/mdtraj/geometry/neighborlist.o build/temp.linux-i686-cpython-313/mdtraj/geometry/src/neighborlist.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighborlist.cpython-313-i386-linux-gnu.so running install_lib creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_rmsd.cpython-313-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/data creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbstructure.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbfile.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dcd.cpython-313-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/lammpstrj.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/registry.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/arc.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/xyzfile.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/pdbx.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/hdf5.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/netcdf.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/amberrst.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/psf.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/mdcrd.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/openmmxml.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/gro.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/hoomdxml.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/lh5.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/prmtop.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/mol2.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/gsd.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/xtc.cpython-313-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/trr.cpython-313-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dtr.cpython-313-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/io.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/__pycache__/docscrape.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/__pycache__/testing.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/__pycache__/docstrings.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/standard_dimensions.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_operators.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/unit.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/baseunit.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/mymatrix.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_definitions.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/quantity.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/basedimension.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/prefix.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/rotation.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/contextmanagers.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/validation.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/delay_import.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/singleton.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/unitcell.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/zipped.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/__pycache__/_version.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_lprmsd.cpython-313-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_version.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/_geometry.cpython-313-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/order.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/hbond.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/rdf.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/dihedral.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/distance.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/angle.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/thermodynamic_properties.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/sasa.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/rg.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/shape.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/contact.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/dssp.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighbors.cpython-313-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighborlist.cpython-313-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/drid.cpython-313-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__pycache__/selection.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__pycache__/trajectory.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__pycache__/residue_names.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__pycache__/element.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__pycache__/topology.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/lib/libtheobald.a -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/lib/center.h -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/lib/theobald_rmsd.h -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__pycache__/basereporter.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__pycache__/netcdfreporter.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__pycache__/xtcreporter.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__pycache__/dcdreporter.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__pycache__/hdf5reporter.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/__pycache__/shift_wrappers.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/__pycache__/scalar_couplings.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/arc.py to arc.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/pdbstructure.py to pdbstructure.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/pdbfile.py to pdbfile.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/mol2.py to mol2.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/amberrst.py to amberrst.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/gsd.py to gsd.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/psf.py to psf.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/lh5.py to lh5.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/hdf5.py to hdf5.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/registry.py to registry.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/gro.py to gro.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/prmtop.py to prmtop.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/netcdf.py to netcdf.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx.py to pdbx.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/io.py to io.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts/mdconvert.py to mdconvert.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/docscrape.py to docscrape.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/docstrings.py to docstrings.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/testing.py to testing.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/quantity.py to quantity.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/unit.py to unit.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/doctests.py to doctests.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/unit_operators.py to unit_operators.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/prefix.py to prefix.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/baseunit.py to baseunit.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/unit_math.py to unit_math.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/unit_definitions.py to unit_definitions.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/standard_dimensions.py to standard_dimensions.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/mymatrix.py to mymatrix.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/basedimension.py to basedimension.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/constants.py to constants.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unitcell.py to unitcell.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/validation.py to validation.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/zipped.py to zipped.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/delay_import.py to delay_import.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/singleton.py to singleton.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/rotation.py to rotation.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/_version.py to _version.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/hbond.py to hbond.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/alignment.py to alignment.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/sasa.py to sasa.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/shape.py to shape.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/order.py to order.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/rdf.py to rdf.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/angle.py to angle.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/thermodynamic_properties.py to thermodynamic_properties.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/dssp.py to dssp.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/distance.py to distance.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/contact.py to contact.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/internal.py to internal.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/rg.py to rg.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/trajectory.py to trajectory.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/residue_names.py to residue_names.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/element.py to element.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/topology.py to topology.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/selection.py to selection.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/shift_wrappers.py to shift_wrappers.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/scalar_couplings.py to scalar_couplings.cpython-313.pyc running install_egg_info running egg_info creating mdtraj.egg-info writing mdtraj.egg-info/PKG-INFO writing dependency_links to mdtraj.egg-info/dependency_links.txt writing entry points to mdtraj.egg-info/entry_points.txt writing requirements to mdtraj.egg-info/requires.txt writing top-level names to mdtraj.egg-info/top_level.txt writing manifest file 'mdtraj.egg-info/SOURCES.txt' dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative reading manifest file 'mdtraj.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching '__pycache__' no previously-included directories found matching '*.pyc' adding license file 'LICENSE' writing manifest file 'mdtraj.egg-info/SOURCES.txt' Copying mdtraj.egg-info to /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj-1.10.1.egg-info Skipping SOURCES.txt running install_scripts Installing mdconvert-mdtraj script to /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/bin Installing mdinspect script to /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/bin I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj Using built-in specs. COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-linux-gnu/14/lto-wrapper Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-8' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 14.2.0 (Debian 14.2.0-8) warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired. Possible solutions: 1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'make_whole' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired. Possible solutions: 1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned. performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired. Possible solutions: 1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned. C compiler: Attempting to autodetect OpenMP support... Compiler supports OpenMP Attempting to autodetect SSE2 support... Compiler supports SSE2 Attempting to autodetect SSE3 support... Compiler supports SSE3 Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1 Attempting to autodetect NEON support... Did not detect NEON support [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx [ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx [ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx [ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx [ 5/10] Cythonizing mdtraj/geometry/drid.pyx [ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py UPDATING /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py set /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py to '1.10.1' running build_ext building 'mdtraj.formats.xtc' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord': mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable] 66 | int i,j,result; | ^ mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes': mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 119 | if (NULL == xd) | ^~ mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 122 | do { | ^~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/xtc.c:1263: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write' at mdtraj/formats/xtc/xtc.c:13728:16, inlined from '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write' at mdtraj/formats/xtc/xtc.c:13424:13: mdtraj/formats/xtc/xtc.c:1165:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 1165 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/xtc.c:25481:20: note: in expansion of macro 'PyInt_FromLong' 25481 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write': mdtraj/formats/xtc/xtc.c:13444:7: note: '__pyx_v_status' was declared here 13444 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read': mdtraj/formats/xtc/xtc.c:11491:10: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11491 | if (unlikely(__pyx_t_5 != -1)) { | ^ mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here 10279 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11490:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11490 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here 10279 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11856:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11856 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11860:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11860 | } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11864:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 11864 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here 10277 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11902:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11902 | } else if (unlikely(__pyx_t_41 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10283:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here 10283 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11826:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11826 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10287:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here 10287 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11844:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11844 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10291:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here 10291 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11884:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 11884 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_5 = 0; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11888:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 11888 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_5 = 1; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/xtc.c:11892:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 11892 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_5 = 2; | ^ mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here 10295 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/xtc.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-i386-linux-gnu.so building 'mdtraj.formats.trr' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 788 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 785 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float': mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1016 | int errval=1; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable] 1305 | int smallnum, smaller, larger, i, is_smaller, run; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable] 1302 | int smallidx, minidx, maxidx; | ^~~~~~ mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double': mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable] 1509 | int errval=1; | ^~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/xtc/trr.c:1265: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write' at mdtraj/formats/xtc/trr.c:15643:16, inlined from '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write' at mdtraj/formats/xtc/trr.c:15083:13: mdtraj/formats/xtc/trr.c:1167:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized] 1167 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/xtc/trr.c:27476:20: note: in expansion of macro 'PyInt_FromLong' 27476 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write': mdtraj/formats/xtc/trr.c:15111:7: note: '__pyx_v_status' was declared here 15111 | int __pyx_v_status; | ^~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read': mdtraj/formats/xtc/trr.c:12632:12: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12632 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here 10939 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12631:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12631 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here 10939 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12580:12: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12580 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here 10955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12579:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12579 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here 10955 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12739:10: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12739 | if (unlikely(__pyx_t_4 != -1)) { | ^ mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here 10959 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12738:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12738 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here 10959 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12339:56: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12339 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:2533:95: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:12354:42: note: in expansion of macro '__Pyx_BufPtrCContig3d' 12354 | __pyx_v_frame_vel = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_vel.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_vel.diminfo[0].strides, __pyx_t_30, __pyx_pybuffernd_vel.diminfo[1].strides, __pyx_t_31, __pyx_pybuffernd_vel.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12345:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12345 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12349:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 12349 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_4 = 2; | ^ mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here 10953 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; | ^~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12396:59: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized] 12396 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:2533:95: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized] 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) | ^ mdtraj/formats/xtc/trr.c:12411:45: note: in expansion of macro '__Pyx_BufPtrCContig3d' 12411 | __pyx_v_frame_forces = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_forces.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_forces.diminfo[0].strides, __pyx_t_31, __pyx_pybuffernd_forces.diminfo[1].strides, __pyx_t_30, __pyx_pybuffernd_forces.diminfo[2].strides)))); | ^~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12402:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized] 12402 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_4 = 1; | ^ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ mdtraj/formats/xtc/trr.c:12406:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized] 12406 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_4 = 2; | ^ mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here 10937 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; | ^~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-i686-cpython-312/mdtraj/formats/xtc/trr.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so building 'mdtraj.formats.dcd' extension i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dcd/dcd.c:1260: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ In function '__Pyx_PyInt_From_int', inlined from '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read' at mdtraj/formats/dcd/dcd.c:10190:17: mdtraj/formats/dcd/dcd.c:1162:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized] 1162 | #define PyInt_FromLong PyLong_FromLong | ^ mdtraj/formats/dcd/dcd.c:18997:20: note: in expansion of macro 'PyInt_FromLong' 18997 | return PyInt_FromLong((long) value); | ^~~~~~~~~~~~~~ mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read': mdtraj/formats/dcd/dcd.c:8994:7: note: '__pyx_v_i' was declared here 8994 | int __pyx_v_i; | ^~~~~~~~~ i686-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-i686-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/dcd/dcd.o build/temp.linux-i686-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so building 'mdtraj.formats.dtr' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-i686-cpython-312/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/formats/dtr/dtr.cpp:1279: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-i686-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare mdtraj/formats/dtr/src/dtrplugin.cxx: In member function 'bool desres::molfile::Timekeys::init(const std::string&)': mdtraj/formats/dtr/src/dtrplugin.cxx:486:64: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %lld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format '%d' expects argument of type 'int', but argument 3 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 487 | printf("size %d framesize %d\n\n", | ~^ | | | int | %lld 488 | keys[i].size(), m_framesize); | ~~~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:494:60: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 494 | "non-constant time interval at frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d mdtraj/formats/dtr/src/dtrplugin.cxx:499:60: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); | ~~^ ~ | | | | | size_t {aka unsigned int} | long int | %d mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)': mdtraj/formats/dtr/src/dtrplugin.cxx:1301:69: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", | ~~^ | | | long int | %lld 1302 | 3*natoms, pos.count); | ~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx:1310:71: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", | ~~^ | | | long int | %lld 1311 | 3*natoms, vel.count); | ~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)': mdtraj/formats/dtr/src/dtrplugin.cxx:1572:45: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", | ~~^ | | | long int | %lld 1573 | velblob.count, 3*natoms); | ~~~~~~~~~~~~~ | | | uint64_t {aka long long unsigned int} mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 706 | sprintf(sub, "%03x/", i); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 706 | sprintf(sub, "%03x/", i); | ^~~~~~~ In file included from /usr/include/stdio.h:970, from mdtraj/formats/dtr/include/molfile_plugin.h:35, from mdtraj/formats/dtr/include/dtrplugin.hxx:46, from mdtraj/formats/dtr/src/dtrplugin.cxx:42: In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'void DDmkdir(const std::string&, mode_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(subsub, "%03x", j); | ^~~~ mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 714 | sprintf(subsub, "%03x", j); | ^~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void DDmkdir(const std::string&, mode_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 4 and 9 bytes into a destination of size 6 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 667 | sprintf(answer, "%03x/", d1); | ^ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:667:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mdtraj/formats/dtr/src/dtrplugin.cxx: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: '%03x' directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~ In function 'std::string DDreldir(const std::string&, int, int)', inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 665 | sprintf(answer, "%03x/%03x/", d1, d2); | ^~~~~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'std::string DDreldir(const std::string&, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:665:13, inlined from 'std::string framefile(const std::string&, size_t, size_t, int, int)' at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: /usr/include/i386-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 9 and 19 bytes into a destination of size 9 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/formats/dtr/dtr.o build/temp.linux-i686-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/i386-linux-gnu -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-i386-linux-gnu.so building 'mdtraj._rmsd' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/rmsd/_rmsd.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so building 'mdtraj._lprmsd' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/_lprmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/rmsd/_lprmsd.cpp:1307: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/Munkres.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/fancy_index.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/rmsd/_lprmsd.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/Munkres.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/fancy_index.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-i686-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry._geometry' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/_geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from mdtraj/geometry/src/_geometry.cpp:1289: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/dssp.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/geometry.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/sasa.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/geometry/src/_geometry.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/dssp.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/geometry.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/sasa.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.drid' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/drid.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/drid.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/dridkernels.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/moments.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/geometry/drid.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/dridkernels.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/moments.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.neighbors' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/geometry/neighbors.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/neighbors.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so building 'mdtraj.geometry.neighborlist' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/mdtraj/geometry/neighborlist.o build/temp.linux-i686-cpython-312/mdtraj/geometry/src/neighborlist.o -L/usr/lib/i386-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so running install_lib creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbfile.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbstructure.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/psf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/xyzfile.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/hdf5.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/gsd.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/openmmxml.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/lammpstrj.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/amberrst.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/lh5.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/netcdf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/prmtop.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/pdbx.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/mdcrd.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/mol2.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/registry.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/gro.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/hoomdxml.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/arc.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/io.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/testing.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/docstrings.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/docscrape.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/baseunit.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/quantity.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_operators.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/mymatrix.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/standard_dimensions.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/prefix.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/basedimension.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_definitions.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/rotation.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/unitcell.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/singleton.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/zipped.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/delay_import.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/contextmanagers.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/validation.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__pycache__/_version.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/order.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/dihedral.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/dssp.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/sasa.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/contact.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/distance.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/angle.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/thermodynamic_properties.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/rg.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/shape.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/hbond.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/rdf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/element.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/trajectory.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/selection.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/residue_names.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/topology.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/libtheobald.a -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/center.h -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/theobald_rmsd.h -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/basereporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/netcdfreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/xtcreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/hdf5reporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/dcdreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr creating /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/scalar_couplings.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/shift_wrappers.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__ copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr copying /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/arc.py to arc.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/pdbstructure.py to pdbstructure.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/pdbfile.py to pdbfile.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/mol2.py to mol2.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/amberrst.py to amberrst.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/gsd.py to gsd.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/psf.py to psf.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/lh5.py to lh5.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/hdf5.py to hdf5.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/registry.py to registry.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/gro.py to gro.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/prmtop.py to prmtop.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/netcdf.py to netcdf.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdbx.py to pdbx.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/io.py to io.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/mdconvert.py to mdconvert.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/docscrape.py to docscrape.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/docstrings.py to docstrings.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/testing.py to testing.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/quantity.py to quantity.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/unit.py to unit.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/doctests.py to doctests.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/unit_operators.py to unit_operators.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/prefix.py to prefix.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/baseunit.py to baseunit.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/unit_math.py to unit_math.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/unit_definitions.py to unit_definitions.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/standard_dimensions.py to standard_dimensions.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/mymatrix.py to mymatrix.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/basedimension.py to basedimension.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/constants.py to constants.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unitcell.py to unitcell.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/validation.py to validation.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/zipped.py to zipped.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/delay_import.py to delay_import.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/singleton.py to singleton.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/rotation.py to rotation.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/_version.py to _version.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/hbond.py to hbond.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/alignment.py to alignment.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/sasa.py to sasa.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/shape.py to shape.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/order.py to order.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/rdf.py to rdf.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/angle.py to angle.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/thermodynamic_properties.py to thermodynamic_properties.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/dssp.py to dssp.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/distance.py to distance.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/contact.py to contact.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/internal.py to internal.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/rg.py to rg.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/trajectory.py to trajectory.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/residue_names.py to residue_names.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/element.py to element.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/topology.py to topology.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/selection.py to selection.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/shift_wrappers.py to shift_wrappers.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/scalar_couplings.py to scalar_couplings.cpython-312.pyc running install_egg_info running egg_info writing mdtraj.egg-info/PKG-INFO writing dependency_links to mdtraj.egg-info/dependency_links.txt writing entry points to mdtraj.egg-info/entry_points.txt writing requirements to mdtraj.egg-info/requires.txt writing top-level names to mdtraj.egg-info/top_level.txt dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative reading manifest file 'mdtraj.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching '__pycache__' no previously-included directories found matching '*.pyc' adding license file 'LICENSE' writing manifest file 'mdtraj.egg-info/SOURCES.txt' Copying mdtraj.egg-info to /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj-1.10.1.egg-info Skipping SOURCES.txt running install_scripts Installing mdconvert-mdtraj script to /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/bin Installing mdinspect script to /build/reproducible-path/mdtraj-1.10.1/debian/python3-mdtraj/usr/bin debian/rules execute_after_dh_auto_install-indep make[1]: Entering directory '/build/reproducible-path/mdtraj-1.10.1' cp -a /build/reproducible-path/mdtraj-1.10.1/examples /build/reproducible-path/mdtraj-1.10.1/examples.orig mkdir -p /build/reproducible-path/mdtraj-1.10.1/build/html/examples/iterload ln -s /build/reproducible-path/mdtraj-1.10.1/examples/data /build/reproducible-path/mdtraj-1.10.1/build/html/examples/iterload/data sed "s|http://www.rcsb.org/pdb/files|/build/reproducible-path/mdtraj-1.10.1/debian/external|g" -i /build/reproducible-path/mdtraj-1.10.1/examples/*.ipynb PYTHONPATH=/build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build \ MPLCONFIGDIR=/build/reproducible-path/mdtraj-1.10.1/build/matplotlib \ make -C docs BUILDDIR=/build/reproducible-path/mdtraj-1.10.1/build html make[2]: Entering directory '/build/reproducible-path/mdtraj-1.10.1/docs' sphinx-build -b html -d /build/reproducible-path/mdtraj-1.10.1/build/doctrees . /build/reproducible-path/mdtraj-1.10.1/build/html Running Sphinx v8.1.3 WARNING: Calling get_html_theme_path is deprecated. If you are calling it to define html_theme_path, you are safe to remove that code. loading translations [en]... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. [autosummary] generating autosummary for: analysis.rst, api/reporters.rst, api/trajectory_files.rst, api/utils.rst, atom_selection.rst, building_docs.rst, examples/atom-selection.rst, examples/centroids.rst, examples/clustering.rst, examples/hbonds.rst, ..., notebook-examples/iterload.nblink, notebook-examples/native-contact.nblink, notebook-examples/openmm.nblink, notebook-examples/pca.nblink, notebook-examples/ramachandran-plot.nblink, notebook-examples/rmsd-benchmark.nblink, notebook-examples/rmsd-drift.nblink, notebook-examples/solvent-accessible-surface-area.nblink, notebook-examples/two-pass-clustering.nblink, whatsnew.rst [autosummary] generating autosummary for: /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.Topology.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.Trajectory.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.Trajectory.superpose.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.acylindricity.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.asphericity.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.baker_hubbard.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.chemical_shifts_ppm.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.chemical_shifts_shiftx2.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.chemical_shifts_spartaplus.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.compute_J3_HN_C.rst, ..., /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.check_random_state.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.ensure_type.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.ilen.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.import_.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.in_units_of.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.rotation_matrix_from_quaternion.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.timing.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.utils.uniform_quaternion.rst, /build/reproducible-path/mdtraj-1.10.1/docs/api/generated/mdtraj.wernet_nilsson.rst Writing evaluated template result to /build/reproducible-path/mdtraj-1.10.1/build/html/_static/nbsphinx-code-cells.css building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 44 source files that are out of date updating environment: [new config] 140 added, 0 changed, 0 removed reading sources... [ 1%] analysis reading sources... [ 1%] api/generated/mdtraj.Topology /usr/lib/python3/dist-packages/numpydoc/docscrape.py:203: UserWarning: potentially wrong underline length... Returns ---------- in Get the indices of biologically-relevant groups by name. ... in the docstring of select_atom_indices in /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/topology.py. while not self._is_at_section() and not self._doc.eof(): reading sources... [ 2%] api/generated/mdtraj.Trajectory reading sources... [ 3%] api/generated/mdtraj.Trajectory.superpose reading sources... [ 4%] api/generated/mdtraj.acylindricity reading sources... [ 4%] api/generated/mdtraj.asphericity reading sources... [ 5%] api/generated/mdtraj.baker_hubbard reading sources... [ 6%] api/generated/mdtraj.chemical_shifts_ppm reading sources... [ 6%] api/generated/mdtraj.chemical_shifts_shiftx2 reading sources... [ 7%] api/generated/mdtraj.chemical_shifts_spartaplus reading sources... [ 8%] api/generated/mdtraj.compute_J3_HN_C reading sources... [ 9%] api/generated/mdtraj.compute_J3_HN_CB reading sources... [ 9%] api/generated/mdtraj.compute_J3_HN_HA reading sources... [ 10%] api/generated/mdtraj.compute_angles reading sources... [ 11%] api/generated/mdtraj.compute_center_of_mass reading sources... [ 11%] api/generated/mdtraj.compute_chi1 reading sources... [ 12%] api/generated/mdtraj.compute_chi2 reading sources... [ 13%] api/generated/mdtraj.compute_chi3 reading sources... [ 14%] api/generated/mdtraj.compute_chi4 reading sources... [ 14%] api/generated/mdtraj.compute_contacts reading sources... [ 15%] api/generated/mdtraj.compute_dihedrals reading sources... [ 16%] api/generated/mdtraj.compute_directors reading sources... [ 16%] api/generated/mdtraj.compute_displacements reading sources... [ 17%] api/generated/mdtraj.compute_distances reading sources... [ 18%] api/generated/mdtraj.compute_drid reading sources... [ 19%] api/generated/mdtraj.compute_dssp reading sources... [ 19%] api/generated/mdtraj.compute_gyration_tensor reading sources... [ 20%] api/generated/mdtraj.compute_inertia_tensor reading sources... [ 21%] api/generated/mdtraj.compute_neighbors reading sources... [ 21%] api/generated/mdtraj.compute_nematic_order reading sources... [ 22%] api/generated/mdtraj.compute_omega reading sources... [ 23%] api/generated/mdtraj.compute_phi reading sources... [ 24%] api/generated/mdtraj.compute_psi reading sources... [ 24%] api/generated/mdtraj.compute_rdf reading sources... [ 25%] api/generated/mdtraj.compute_rg reading sources... [ 26%] api/generated/mdtraj.density reading sources... [ 26%] api/generated/mdtraj.dipole_moments reading sources... [ 27%] api/generated/mdtraj.formats.AmberNetCDFRestartFile reading sources... [ 28%] api/generated/mdtraj.formats.AmberRestartFile reading sources... [ 29%] api/generated/mdtraj.formats.ArcTrajectoryFile reading sources... [ 29%] api/generated/mdtraj.formats.DCDTrajectoryFile reading sources... [ 30%] api/generated/mdtraj.formats.DTRTrajectoryFile reading sources... [ 31%] api/generated/mdtraj.formats.GroTrajectoryFile reading sources... [ 31%] api/generated/mdtraj.formats.HDF5TrajectoryFile reading sources... [ 32%] api/generated/mdtraj.formats.LAMMPSTrajectoryFile reading sources... [ 33%] api/generated/mdtraj.formats.LH5TrajectoryFile reading sources... [ 34%] api/generated/mdtraj.formats.MDCRDTrajectoryFile reading sources... [ 34%] api/generated/mdtraj.formats.NetCDFTrajectoryFile reading sources... [ 35%] api/generated/mdtraj.formats.PDBTrajectoryFile reading sources... [ 36%] api/generated/mdtraj.formats.TRRTrajectoryFile reading sources... [ 36%] api/generated/mdtraj.formats.XTCTrajectoryFile reading sources... [ 37%] api/generated/mdtraj.formats.XYZTrajectoryFile reading sources... [ 38%] api/generated/mdtraj.geometry.squareform reading sources... [ 39%] api/generated/mdtraj.isothermal_compressability_kappa_T reading sources... [ 39%] api/generated/mdtraj.iterload reading sources... [ 40%] api/generated/mdtraj.join reading sources... [ 41%] api/generated/mdtraj.kabsch_sander reading sources... [ 41%] api/generated/mdtraj.load reading sources... [ 42%] api/generated/mdtraj.load_arc reading sources... [ 43%] api/generated/mdtraj.load_dcd reading sources... [ 44%] api/generated/mdtraj.load_dtr reading sources... [ 44%] api/generated/mdtraj.load_frame reading sources... [ 45%] api/generated/mdtraj.load_hdf5 reading sources... [ 46%] api/generated/mdtraj.load_hoomdxml reading sources... [ 46%] api/generated/mdtraj.load_lammpstrj reading sources... [ 47%] api/generated/mdtraj.load_lh5 reading sources... [ 48%] api/generated/mdtraj.load_netcdf reading sources... [ 49%] api/generated/mdtraj.load_pdb reading sources... [ 49%] api/generated/mdtraj.load_prmtop reading sources... [ 50%] api/generated/mdtraj.load_trr reading sources... [ 51%] api/generated/mdtraj.load_xml reading sources... [ 51%] api/generated/mdtraj.load_xtc reading sources... [ 52%] api/generated/mdtraj.load_xyz reading sources... [ 53%] api/generated/mdtraj.lprmsd reading sources... [ 54%] api/generated/mdtraj.open reading sources... [ 54%] api/generated/mdtraj.principal_moments reading sources... [ 55%] api/generated/mdtraj.reindex_dataframe_by_atoms reading sources... [ 56%] api/generated/mdtraj.relative_shape_antisotropy reading sources... [ 56%] api/generated/mdtraj.reporters.DCDReporter reading sources... [ 57%] api/generated/mdtraj.reporters.HDF5Reporter reading sources... [ 58%] api/generated/mdtraj.reporters.NetCDFReporter reading sources... [ 59%] api/generated/mdtraj.rmsd reading sources... [ 59%] api/generated/mdtraj.rmsf reading sources... [ 60%] api/generated/mdtraj.shrake_rupley reading sources... [ 61%] api/generated/mdtraj.static_dielectric reading sources... [ 61%] api/generated/mdtraj.thermal_expansion_alpha_P reading sources... [ 62%] api/generated/mdtraj.utils.box_vectors_to_lengths_and_angles reading sources... [ 63%] api/generated/mdtraj.utils.check_random_state reading sources... [ 64%] api/generated/mdtraj.utils.ensure_type reading sources... [ 64%] api/generated/mdtraj.utils.ilen reading sources... [ 65%] api/generated/mdtraj.utils.import_ reading sources... [ 66%] api/generated/mdtraj.utils.in_units_of reading sources... [ 66%] api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors reading sources... [ 67%] api/generated/mdtraj.utils.rotation_matrix_from_quaternion reading sources... [ 68%] api/generated/mdtraj.utils.timing reading sources... [ 69%] api/generated/mdtraj.utils.uniform_quaternion reading sources... [ 69%] api/generated/mdtraj.wernet_nilsson reading sources... [ 70%] api/reporters reading sources... [ 71%] api/trajectory_files reading sources... [ 71%] api/utils reading sources... [ 72%] atom_selection reading sources... [ 73%] building_docs reading sources... [ 74%] examples/atom-selection reading sources... [ 74%] examples/centroids reading sources... [ 75%] examples/clustering reading sources... [ 76%] examples/hbonds reading sources... [ 76%] examples/index reading sources... [ 77%] examples/introduction reading sources... [ 78%] examples/iterload reading sources... [ 79%] examples/native-contact reading sources... [ 79%] examples/nmr reading sources... [ 80%] examples/openmm reading sources... [ 81%] examples/pca reading sources... [ 81%] examples/ramachandran-plot reading sources... [ 82%] examples/rmsd-benchmark reading sources... [ 83%] examples/solvent-accessible-surface-area reading sources... [ 84%] examples/two-pass-clustering reading sources... [ 84%] faq reading sources... [ 85%] hdf5_format reading sources... [ 86%] index reading sources... [ 86%] installation reading sources... [ 87%] load_functions reading sources... [ 88%] mdconvert reading sources... [ 89%] new_to_python reading sources... [ 89%] notebook-examples/atom-selection reading sources... [ 90%] notebook-examples/centroids reading sources... [ 91%] notebook-examples/clustering reading sources... [ 91%] notebook-examples/hbonds reading sources... [ 92%] notebook-examples/index reading sources... [ 93%] notebook-examples/introduction reading sources... [ 94%] notebook-examples/iterload reading sources... [ 94%] notebook-examples/native-contact reading sources... [ 95%] notebook-examples/openmm reading sources... [ 96%] notebook-examples/pca reading sources... [ 96%] notebook-examples/ramachandran-plot reading sources... [ 97%] notebook-examples/rmsd-benchmark reading sources... [ 98%] notebook-examples/rmsd-drift reading sources... [ 99%] notebook-examples/solvent-accessible-surface-area reading sources... [ 99%] notebook-examples/two-pass-clustering reading sources... [100%] whatsnew /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.asphericity:9: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:9: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:36: ERROR: Unexpected indentation. [docutils] /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:45: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] docstring of mdtraj.formats.dtr.load_dtr:7: ERROR: Unexpected indentation. [docutils] /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:9: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:11: ERROR: Unexpected indentation. [docutils] /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:12: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:14: WARNING: Definition list ends without a blank line; unexpected unindent. [docutils] /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:15: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] /build/reproducible-path/mdtraj-1.10.1/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/rotation.py:docstring of mdtraj.utils.rotation.uniform_quaternion:39: ERROR: Error in "rubric" directive: no content permitted. .. rubric:: References .. [R17e8d31e726c-1] K. Shoemake. Uniform random rotations. In D. Kirk, editor, Graphics Gems III, pages 124-132. Academic, New York, 1992. .. [R17e8d31e726c-2] http://planning.cs.uiuc.edu/node198.html [docutils] /build/reproducible-path/mdtraj-1.10.1/docs/examples/atom-selection.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/atom-selection.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.10.1/docs/examples/centroids.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/centroids.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.10.1/docs/examples/clustering.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/clustering.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.10.1/docs/examples/hbonds.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/hbonds.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.10.1/docs/examples/iterload.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/iterload.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.10.1/docs/examples/native-contact.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/native-contact.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.10.1/docs/examples/nmr.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/nmr.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.10.1/docs/examples/openmm.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/simulation-with-openmm.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.10.1/docs/examples/pca.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/principal-components.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.10.1/docs/examples/ramachandran-plot.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/ramachandran-plot.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.10.1/docs/examples/rmsd-benchmark.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/rmsd-benchmark.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.10.1/docs/examples/solvent-accessible-surface-area.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/solvent-accessible-surface-area.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.10.1/docs/examples/two-pass-clustering.rst:4: ERROR: Unknown directive type "notebook". .. notebook:: examples/two-pass-clustering.ipynb :skip_exceptions: [docutils] /build/reproducible-path/mdtraj-1.10.1/docs/index.rst:26: WARNING: toctree contains reference to nonexisting document '.. examples/index' [toc.not_readable] /build/reproducible-path/mdtraj-1.10.1/docs/installation.rst:1: WARNING: malformed hyperlink target. [docutils] /build/reproducible-path/mdtraj-1.10.1/docs/mdconvert.rst:2: WARNING: Title underline too short. ``mdconvert`` (``mdconvert-mdtraj``) ============= [docutils] /build/reproducible-path/mdtraj-1.10.1/docs/whatsnew.rst:60: WARNING: Title underline too short. v1.9.9 (July 22, 2023) --------------------- [docutils] /build/reproducible-path/mdtraj-1.10.1/docs/whatsnew.rst:60: WARNING: Title underline too short. v1.9.9 (July 22, 2023) --------------------- [docutils] /build/reproducible-path/mdtraj-1.10.1/docs/whatsnew.rst:115: WARNING: Title underline too short. v1.9.7 (November 12, 2021) ----------------------- [docutils] /build/reproducible-path/mdtraj-1.10.1/docs/whatsnew.rst:115: WARNING: Title underline too short. v1.9.7 (November 12, 2021) ----------------------- [docutils] looking for now-outdated files... none found pickling environment... 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Writing evaluated template result to /build/reproducible-path/mdtraj-1.10.1/build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/mdtraj-1.10.1/build/html/_static/basic.css Writing evaluated template result to /build/reproducible-path/mdtraj-1.10.1/build/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/mdtraj-1.10.1/build/html/_static/js/versions.js copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 1%] 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... [ 4%] api/generated/mdtraj.acylindricity writing output... [ 4%] api/generated/mdtraj.asphericity writing output... [ 5%] api/generated/mdtraj.baker_hubbard writing output... 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[ 99%] notebook-examples/two-pass-clustering writing output... [100%] whatsnew generating indices... genindex done copying linked files... copying notebooks ... [ 8%] notebook-examples/atom-selection.ipynb copying notebooks ... [ 15%] notebook-examples/centroids.ipynb copying notebooks ... [ 23%] notebook-examples/clustering.ipynb copying notebooks ... [ 31%] notebook-examples/hbonds.ipynb copying notebooks ... [ 38%] notebook-examples/iterload.ipynb copying notebooks ... [ 46%] notebook-examples/native-contact.ipynb copying notebooks ... [ 54%] notebook-examples/openmm.ipynb copying notebooks ... [ 62%] notebook-examples/pca.ipynb copying notebooks ... [ 69%] notebook-examples/ramachandran-plot.ipynb copying notebooks ... [ 77%] notebook-examples/rmsd-benchmark.ipynb copying notebooks ... [ 85%] notebook-examples/rmsd-drift.ipynb copying notebooks ... [ 92%] notebook-examples/solvent-accessible-surface-area.ipynb copying notebooks ... 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[ 72%] mdtraj.geometry.shape highlighting module code... [ 74%] mdtraj.geometry.thermodynamic_properties highlighting module code... [ 77%] mdtraj.nmr.scalar_couplings highlighting module code... [ 79%] mdtraj.nmr.shift_wrappers highlighting module code... [ 81%] mdtraj.reporters.dcdreporter highlighting module code... [ 83%] mdtraj.reporters.hdf5reporter highlighting module code... [ 85%] mdtraj.reporters.netcdfreporter highlighting module code... [ 87%] mdtraj.utils highlighting module code... [ 89%] mdtraj.utils.contextmanagers highlighting module code... [ 91%] mdtraj.utils.delay_import highlighting module code... [ 94%] mdtraj.utils.rotation highlighting module code... [ 96%] mdtraj.utils.unit highlighting module code... [ 98%] mdtraj.utils.unitcell highlighting module code... [100%] mdtraj.utils.validation writing additional pages... search done copying images... [ 11%] ../build/doctrees/nbsphinx/notebook-examples_clustering_11_0.png copying images... [ 22%] ../build/doctrees/nbsphinx/notebook-examples_hbonds_9_1.png copying images... [ 33%] ../build/doctrees/nbsphinx/notebook-examples_native-contact_6_0.png copying images... [ 44%] ../build/doctrees/nbsphinx/notebook-examples_pca_9_0.png copying images... [ 56%] ../build/doctrees/nbsphinx/notebook-examples_pca_12_0.png copying images... [ 67%] ../build/doctrees/nbsphinx/notebook-examples_ramachandran-plot_7_1.png copying images... [ 78%] ../build/doctrees/nbsphinx/notebook-examples_rmsd-drift_7_1.png copying images... [ 89%] ../build/doctrees/nbsphinx/notebook-examples_solvent-accessible-surface-area_8_0.png copying images... [100%] ../build/doctrees/nbsphinx/notebook-examples_solvent-accessible-surface-area_10_0.png dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 54 warnings. The HTML pages are in ../build/html. Build finished. The HTML pages are in /build/reproducible-path/mdtraj-1.10.1/build/html. make[2]: Leaving directory '/build/reproducible-path/mdtraj-1.10.1/docs' for img in `find /build/reproducible-path/mdtraj-1.10.1/build/html/examples -name *.png`; do \ mv $img /build/reproducible-path/mdtraj-1.10.1/build/html/examples; \ done sed "s|/build/reproducible-path/mdtraj-1.10.1/build/html/examples/|./|g; s|.ipynb|.ipynb.gz|g" -i /build/reproducible-path/mdtraj-1.10.1/build/html/examples/*.html sed "s|/build/reproducible-path/mdtraj-1.10.1/debian/external|http://www.rcsb.org/pdb/files|g" -i /build/reproducible-path/mdtraj-1.10.1/build/html/examples/*.html rm /build/reproducible-path/mdtraj-1.10.1/build/html/examples/iterload/data rm -rf /build/reproducible-path/mdtraj-1.10.1/examples mv /build/reproducible-path/mdtraj-1.10.1/examples.orig /build/reproducible-path/mdtraj-1.10.1/examples make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.10.1' dh_install -O--buildsystem=pybuild install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples/data cp --reflink=auto -a ./debian/external/2EQQ.pdb ./debian/external/2MI7.pdb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples/data/ install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doi-10.1016_j.bpj.2015.08.015-blue.svg cp --reflink=auto -a ./debian/external/doi-10.1016_j.bpj.2015.08.015-blue.svg debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doi-10.1016_j.bpj.2015.08.015-blue.svg/ dh_installdocs -O--buildsystem=pybuild dh_installdocs: warning: Cannot auto-detect main package for python-mdtraj-doc. If the default is wrong, please use --doc-main-package install -m0755 -d debian/python3-mdtraj/usr/share/doc/python3-mdtraj install -p -m0644 debian/copyright debian/python3-mdtraj/usr/share/doc/python3-mdtraj/copyright install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc cd './build/html/..' && find 'html' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/mdtraj-1.10.1/debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc cp --reflink=auto -a ./README.md debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc chmod -R u\+rw,go=rX debian/python-mdtraj-doc/usr/share/doc install -p -m0644 debian/copyright debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/copyright install -m0755 -d debian/python-mdtraj-doc/usr/share/doc-base/ install -p -m0644 debian/python-mdtraj-doc.doc-base debian/python-mdtraj-doc/usr/share/doc-base/python-mdtraj-doc.mdtraj debian/rules override_dh_sphinxdoc-indep make[1]: Entering directory '/build/reproducible-path/mdtraj-1.10.1' dh_sphinxdoc -i ln -sf ../../../../../sphinx_rtd_theme/static/css/theme.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css ln -sf ../../../../../sphinx_rtd_theme/static/css/badge_only.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css ln -sf ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Regular.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Bold.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.ttf 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debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.woff2 ln -sf ../../../../../sphinx_rtd_theme/static/js/theme.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/theme.js ln -sf ../../../../javascript/sphinxdoc/1.0/doctools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js ln -sf ../../../../javascript/sphinxdoc/1.0/language_data.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/language_data.js ln -sf ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/searchtools.js ln -sf ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/sphinx_highlight.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/.buildinfo mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars sed "s|src=\"https://img.shields.io/badge/DOI-10.1016%2Fj.bpj.2015.08.015-blue.svg\"|src=\"_static/doi-10.1016_j.bpj.2015.08.015-blue.svg\"|g" -i debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/index.html make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.10.1' dh_sphinxdoc -O--buildsystem=pybuild -Npython-mdtraj-doc dh_sphinxdoc: warning: Sphinx documentation not found dh_installchangelogs -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/usr/share/doc/python3-mdtraj install -p -m0644 debian/.debhelper/generated/python3-mdtraj/dh_installchangelogs.dch.trimmed debian/python3-mdtraj/usr/share/doc/python3-mdtraj/changelog.Debian install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc install -p -m0644 debian/.debhelper/generated/python-mdtraj-doc/dh_installchangelogs.dch.trimmed debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/changelog.Debian dh_installexamples -O--buildsystem=pybuild dh_installexamples: warning: Cannot auto-detect main package for python-mdtraj-doc. If the default is wrong, please use --doc-main-package install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/1vii_3frames.pdb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/ala2.h5 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/atom-selection.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/centroids.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/clustering.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/data debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/hbonds.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/iterload.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/native-contact.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/nmr.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/principal-components.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/ramachandran-plot.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/rmsd-benchmark.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/rmsd-drift.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/simulation-with-openmm.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/solvent-accessible-surface-area.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/test_examples.py debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples cp --reflink=auto -a ./examples/two-pass-clustering.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples dh_installman -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/usr/share/man/man1/ install -p -m0644 ./debian/mdconvert-mdtraj.1 debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1 install -m0755 -d debian/python3-mdtraj/usr/share/man/man1/ install -p -m0644 ./debian/mdinspect.1 debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 man-recode --to-code UTF-8 --suffix .dh-new debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1 man-recode --to-code UTF-8 --suffix .dh-new debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 mv debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1.dh-new debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1 chmod 0644 -- debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1 mv debian/python3-mdtraj/usr/share/man/man1/mdinspect.1.dh-new debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 chmod 0644 -- debian/python3-mdtraj/usr/share/man/man1/mdinspect.1 dh_python3 -O--buildsystem=pybuild D: dh_python3 dh_python3:180: version: 6.20241024 D: dh_python3 dh_python3:181: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:182: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=['--buildsystem=pybuild']) D: dh_python3 dh_python3:183: supported Python versions: 3.12,3.13 (default=3.12) D: dh_python3 debhelper:166: skipping package python-mdtraj-doc (missing ${python3:Depends} in Depends/Recommends) D: dh_python3 debhelper:174: source=mdtraj, binary packages=['python3-mdtraj'] D: dh_python3 dh_python3:205: processing package python3-mdtraj... D: dh_python3 fs:50: moving files from debian/python3-mdtraj/usr/lib/python3.12/dist-packages to debian/python3-mdtraj/usr/lib/python3/dist-packages/ D: dh_python3 fs:50: moving files from debian/python3-mdtraj/usr/lib/python3.13/dist-packages to debian/python3-mdtraj/usr/lib/python3/dist-packages/ D: dh_python3 fs:338: package python3-mdtraj details = {'requires.txt': {'debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.10.1.egg-info/requires.txt'}, 'egg-info': {'debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.10.1.egg-info/PKG-INFO'}, 'dist-info': set(), 'nsp.txt': set(), 'shebangs': {/usr/bin/python3, /usr/bin/python3}, 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': {Version('3.12'), Version('3.13')}, 'ext_no_version': set()} D: dh_python3 depends:103: generating dependencies for package python3-mdtraj D: dh_python3 pydist:175: trying to find dependency for numpy<2.0.0a0,>=1.23 (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:284: dependency: included in build-deps D: dh_python3 pydist:175: trying to find dependency for packaging (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:284: dependency: included in build-deps D: dh_python3 pydist:175: trying to find dependency for pyparsing (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:284: dependency: included in build-deps D: dh_python3 pydist:175: trying to find dependency for scipy (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:284: dependency: included in build-deps D: dh_python3 depends:253: D={'python3:any', 'python3-pyparsing', 'python3-scipy', 'python3 (>= 3.12~)', 'python3-packaging', 'python3-numpy', 'python3 (<< 3.14)'}; R=[]; S=[]; E=[], B=[]; RT=[] rm -f debian/python-mdtraj-doc.debhelper.log debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/mdtraj-1.10.1' dh_numpy3 mv debian/python3-mdtraj.substvars.new debian/python3-mdtraj.substvars mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars # setup.py builds the static lib libtheobald.a for each python version # but dh_python3 can't tell the difference between the different builds, # since py3.11 compiles libtheobald.o with -fwrapv, where py3.12 uses -fno-strict-overflow # So clean up manually (assume the binary difference is not an issue) rm -f debian/python3-mdtraj/usr/lib/python3.*/dist-packages/mdtraj/core/lib/libtheobald.a for d in debian/python3-mdtraj/usr/lib/python3.*/dist-packages/mdtraj/core/lib; do if [-d $d]; then rmdir -p --ignore-fail-on-non-empty $d; fi; done /bin/sh: line 1: [-d: command not found make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.10.1' dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/theme.js ln -s ../../../../../sphinx_rtd_theme/static/js/theme.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/theme.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.svg ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.svg debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.svg rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.eot ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.eot debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.eot rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.ttf ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.ttf rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Bold.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Bold.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Regular.woff2 ln -s ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Regular.woff2 rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css ln -s ../../../../../sphinx_rtd_theme/static/css/badge_only.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css ln -s ../../../../../sphinx_rtd_theme/static/css/theme.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/language_data.js ln -s ../../../../javascript/sphinxdoc/1.0/language_data.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/language_data.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/searchtools.js ln -s ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/searchtools.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/sphinx_highlight.js ln -s ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/sphinx_highlight.js rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js ln -s ../../../../javascript/sphinxdoc/1.0/doctools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js dh_strip_nondeterminism -O--buildsystem=pybuild Using 1731351154 as canonical time Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_ramachandran-plot_7_1.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_hbonds_9_1.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/file.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/minus.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/plus.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_pca_9_0.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/mdtraj_logo-small.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_native-contact_6_0.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_solvent-accessible-surface-area_10_0.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_solvent-accessible-surface-area_8_0.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_rmsd-drift_7_1.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_pca_12_0.png using File::StripNondeterminism::handlers::png Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_clustering_11_0.png using File::StripNondeterminism::handlers::png dh_compress -O--buildsystem=pybuild cd debian/python-mdtraj-doc cd debian/python3-mdtraj chmod a-x usr/share/doc/python3-mdtraj/changelog.Debian usr/share/man/man1/mdconvert-mdtraj.1 usr/share/man/man1/mdinspect.1 gzip -9nf usr/share/doc/python3-mdtraj/changelog.Debian usr/share/man/man1/mdconvert-mdtraj.1 usr/share/man/man1/mdinspect.1 cd '/build/reproducible-path/mdtraj-1.10.1' chmod a-x usr/share/doc/python-mdtraj-doc/changelog.Debian usr/share/doc/python-mdtraj-doc/html/_static/example-trajectoryview-data.json usr/share/doc/python-mdtraj-doc/html/_static/mdtraj_logo.xcf usr/share/doc/python-mdtraj-doc/html/notebook-examples/atom-selection.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/clustering.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/hbonds.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/iterload.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/native-contact.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/openmm.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/pca.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/ramachandran-plot.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/rmsd-benchmark.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/rmsd-drift.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/solvent-accessible-surface-area.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/two-pass-clustering.ipynb gzip -9nf usr/share/doc/python-mdtraj-doc/changelog.Debian usr/share/doc/python-mdtraj-doc/html/_static/example-trajectoryview-data.json usr/share/doc/python-mdtraj-doc/html/_static/mdtraj_logo.xcf usr/share/doc/python-mdtraj-doc/html/notebook-examples/atom-selection.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/clustering.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/hbonds.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/iterload.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/native-contact.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/openmm.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/pca.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/ramachandran-plot.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/rmsd-benchmark.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/rmsd-drift.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/solvent-accessible-surface-area.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/two-pass-clustering.ipynb cd '/build/reproducible-path/mdtraj-1.10.1' dh_fixperms -O--buildsystem=pybuild find debian/python3-mdtraj ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python-mdtraj-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python3-mdtraj/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-mdtraj/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python-mdtraj-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/python-mdtraj-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-mdtraj/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/python-mdtraj-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/python3-mdtraj/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python-mdtraj-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-mdtraj -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-mdtraj/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/python3-mdtraj/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/usr/lib/debug/.dwz/i386-linux-gnu dwz -mdebian/python3-mdtraj/usr/lib/debug/.dwz/i386-linux-gnu/python3-mdtraj.debug -M/usr/lib/debug/.dwz/i386-linux-gnu/python3-mdtraj.debug -- debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-i386-linux-gnu.so objcopy --compress-debug-sections debian/python3-mdtraj/usr/lib/debug/.dwz/i386-linux-gnu/python3-mdtraj.debug chmod 0644 -- debian/python3-mdtraj/usr/lib/debug/.dwz/i386-linux-gnu/python3-mdtraj.debug dh_strip -a -O--buildsystem=pybuild install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/1b objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/1b/b90976b46f8d6969248815195e3f1b0b7a4d24.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/1b/b90976b46f8d6969248815195e3f1b0b7a4d24.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/1b/b90976b46f8d6969248815195e3f1b0b7a4d24.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/63 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/63/e47d38fb0eef0fa6e77958cc1346e9b58516bf.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/63/e47d38fb0eef0fa6e77958cc1346e9b58516bf.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/63/e47d38fb0eef0fa6e77958cc1346e9b58516bf.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/44 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/44/5b9033430cc4dc6638149dc269d1c3e4d45b9f.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/44/5b9033430cc4dc6638149dc269d1c3e4d45b9f.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/44/5b9033430cc4dc6638149dc269d1c3e4d45b9f.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/19 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/19/2e2965697f2de45a25988ed87b5901c268648e.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/19/2e2965697f2de45a25988ed87b5901c268648e.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/19/2e2965697f2de45a25988ed87b5901c268648e.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/71 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/71/1470224becdef48002069fcec71ae44994efc2.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/71/1470224becdef48002069fcec71ae44994efc2.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/71/1470224becdef48002069fcec71ae44994efc2.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6f objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6f/dd37847f304c194afb8783f2a692fe17d1235b.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6f/dd37847f304c194afb8783f2a692fe17d1235b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6f/dd37847f304c194afb8783f2a692fe17d1235b.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e7 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e7/5c1060836a8dbb753244a746ac29bd84ef296b.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e7/5c1060836a8dbb753244a746ac29bd84ef296b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e7/5c1060836a8dbb753244a746ac29bd84ef296b.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/11 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/11/7b7f2f8f78dac8fa0a1be9559b7f438737d1a5.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/11/7b7f2f8f78dac8fa0a1be9559b7f438737d1a5.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/11/7b7f2f8f78dac8fa0a1be9559b7f438737d1a5.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/8b objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/8b/6bdd7b30d0dd5d28ac6271ba88f116ede35d1e.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/8b/6bdd7b30d0dd5d28ac6271ba88f116ede35d1e.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/8b/6bdd7b30d0dd5d28ac6271ba88f116ede35d1e.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/8e objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/8e/6dd2d3f9fb178487347a06540ab7b72ea0dfab.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/8e/6dd2d3f9fb178487347a06540ab7b72ea0dfab.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/8e/6dd2d3f9fb178487347a06540ab7b72ea0dfab.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/18 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/18/2a8cb7dbed19e6f16d9ae1061ebaff9d00759e.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/18/2a8cb7dbed19e6f16d9ae1061ebaff9d00759e.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/18/2a8cb7dbed19e6f16d9ae1061ebaff9d00759e.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/ca objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/ca/313a93c34f98bfde55cdd29cd6ce7ba45662a7.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/ca/313a93c34f98bfde55cdd29cd6ce7ba45662a7.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/ca/313a93c34f98bfde55cdd29cd6ce7ba45662a7.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c5 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c5/0edb1a84658333c73757bb891e850291eb35a5.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c5/0edb1a84658333c73757bb891e850291eb35a5.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c5/0edb1a84658333c73757bb891e850291eb35a5.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/56 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/56/44123b74732619ee69c08f8146723592535a06.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/56/44123b74732619ee69c08f8146723592535a06.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/56/44123b74732619ee69c08f8146723592535a06.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c6 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c6/b7439cc093b8e65ef1da05e1326cd6363e3567.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c6/b7439cc093b8e65ef1da05e1326cd6363e3567.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c6/b7439cc093b8e65ef1da05e1326cd6363e3567.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/5a objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/5a/a545766dd065bd1b9f3e5c7b48738176dbd9ce.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/5a/a545766dd065bd1b9f3e5c7b48738176dbd9ce.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/5a/a545766dd065bd1b9f3e5c7b48738176dbd9ce.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c9 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c9/386e112d0ac395601e7775fb0dbc64ae68fdb0.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c9/386e112d0ac395601e7775fb0dbc64ae68fdb0.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c9/386e112d0ac395601e7775fb0dbc64ae68fdb0.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c2 objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c2/6ade6073ecc2ac574b6836802441b173b6c8f7.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c2/6ade6073ecc2ac574b6836802441b173b6c8f7.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/c2/6ade6073ecc2ac574b6836802441b173b6c8f7.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6c objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6c/e222844782e36471e1f6e1551ec73abb2b508c.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6c/e222844782e36471e1f6e1551ec73abb2b508c.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6c/e222844782e36471e1f6e1551ec73abb2b508c.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/9a objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/9a/af2f0eb2fd5aa9c5b21ff878443ebee6a85db5.debug chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/9a/af2f0eb2fd5aa9c5b21ff878443ebee6a85db5.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/9a/af2f0eb2fd5aa9c5b21ff878443ebee6a85db5.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-i386-linux-gnu.so strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives -R .gnu.lto_\* -R .gnu.debuglto_\* -N __gnu_lto_slim -N __gnu_lto_v1 debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/core/lib/libtheobald.a install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/python3-mdtraj/usr/lib/debug/.dwz/i386-linux-gnu debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/python3-mdtraj/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/python3-mdtraj/usr/lib/debug install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/share/doc ln -s python3-mdtraj debian/.debhelper/python3-mdtraj/dbgsym-root/usr/share/doc/python3-mdtraj-dbgsym install -m0755 -d debian/.debhelper/python3-mdtraj dh_makeshlibs -a -O--buildsystem=pybuild rm -f debian/python3-mdtraj/DEBIAN/shlibs dh_shlibdeps -a -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/DEBIAN dpkg-shlibdeps -Tdebian/python3-mdtraj.substvars debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-i386-linux-gnu.so dh_installdeb -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/DEBIAN printf '#!/bin/sh\nset -e\n' > debian/python3-mdtraj/DEBIAN/postinst cat debian/python3-mdtraj.postinst.debhelper >> debian/python3-mdtraj/DEBIAN/postinst chmod 0755 -- debian/python3-mdtraj/DEBIAN/postinst printf '#!/bin/sh\nset -e\n' > debian/python3-mdtraj/DEBIAN/prerm cat debian/python3-mdtraj.prerm.debhelper >> debian/python3-mdtraj/DEBIAN/prerm chmod 0755 -- debian/python3-mdtraj/DEBIAN/prerm install -m0755 -d debian/python-mdtraj-doc/DEBIAN dh_gencontrol -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/DEBIAN echo misc:Depends= >> debian/python3-mdtraj.substvars echo misc:Pre-Depends= >> debian/python3-mdtraj.substvars install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN dpkg-gencontrol -ppython3-mdtraj -ldebian/changelog -Tdebian/python3-mdtraj.substvars -cdebian/control -Pdebian/.debhelper/python3-mdtraj/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=python3-mdtraj-dbgsym "-DDepends=python3-mdtraj (= \${binary:Version})" "-DDescription=debug symbols for python3-mdtraj" "-DBuild-Ids=117b7f2f8f78dac8fa0a1be9559b7f438737d1a5 182a8cb7dbed19e6f16d9ae1061ebaff9d00759e 192e2965697f2de45a25988ed87b5901c268648e 1bb90976b46f8d6969248815195e3f1b0b7a4d24 445b9033430cc4dc6638149dc269d1c3e4d45b9f 5644123b74732619ee69c08f8146723592535a06 5aa545766dd065bd1b9f3e5c7b48738176dbd9ce 63e47d38fb0eef0fa6e77958cc1346e9b58516bf 6ce222844782e36471e1f6e1551ec73abb2b508c 6fdd37847f304c194afb8783f2a692fe17d1235b 711470224becdef48002069fcec71ae44994efc2 8b6bdd7b30d0dd5d28ac6271ba88f116ede35d1e 8e6dd2d3f9fb178487347a06540ab7b72ea0dfab 9aaf2f0eb2fd5aa9c5b21ff878443ebee6a85db5 c26ade6073ecc2ac574b6836802441b173b6c8f7 c50edb1a84658333c73757bb891e850291eb35a5 c6b7439cc093b8e65ef1da05e1326cd6363e3567 c9386e112d0ac395601e7775fb0dbc64ae68fdb0 ca313a93c34f98bfde55cdd29cd6ce7ba45662a7 e75c1060836a8dbb753244a746ac29bd84ef296b" -DSection=debug -UMulti-Arch -UReplaces -UBreaks install -m0755 -d debian/python-mdtraj-doc/DEBIAN echo misc:Depends= >> debian/python-mdtraj-doc.substvars echo misc:Pre-Depends= >> debian/python-mdtraj-doc.substvars dpkg-gencontrol -ppython-mdtraj-doc -ldebian/changelog -Tdebian/python-mdtraj-doc.substvars -cdebian/control -Pdebian/python-mdtraj-doc chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN/control dpkg-gencontrol -ppython3-mdtraj -ldebian/changelog -Tdebian/python3-mdtraj.substvars -cdebian/control -Pdebian/python3-mdtraj dpkg-gencontrol: warning: package python-mdtraj-doc: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package python-mdtraj-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined chmod 0644 -- debian/python-mdtraj-doc/DEBIAN/control chmod 0644 -- debian/python3-mdtraj/DEBIAN/control dh_md5sums -O--buildsystem=pybuild install -m0755 -d debian/python3-mdtraj/DEBIAN install -m0755 -d debian/python-mdtraj-doc/DEBIAN cd debian/python3-mdtraj >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/python-mdtraj-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/python3-mdtraj/DEBIAN/md5sums install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN cd debian/.debhelper/python3-mdtraj/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/python-mdtraj-doc/DEBIAN/md5sums dh_builddeb -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/python3-mdtraj .. dpkg-deb --root-owner-group --build debian/python-mdtraj-doc .. dpkg-deb --root-owner-group --build debian/.debhelper/python3-mdtraj/dbgsym-root .. dpkg-deb: building package 'python3-mdtraj' in '../python3-mdtraj_1.10.1-2_i386.deb'. dpkg-deb: building package 'python-mdtraj-doc' in '../python-mdtraj-doc_1.10.1-2_all.deb'. dpkg-deb: building package 'python3-mdtraj-dbgsym' in '../python3-mdtraj-dbgsym_1.10.1-2_i386.deb'. dpkg-genbuildinfo --build=binary -O../mdtraj_1.10.1-2_i386.buildinfo dpkg-genchanges --build=binary -O../mdtraj_1.10.1-2_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from mdtraj-1.10.1/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/7091/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/7091/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/7091 and its subdirectories I: Current time: Sat Dec 14 15:52:06 +14 2024 I: pbuilder-time-stamp: 1734141126