Sun Feb 16 09:13:37 UTC 2025  I: starting to build mdtraj/trixie/i386 on jenkins on '2025-02-16 09:13'
Sun Feb 16 09:13:37 UTC 2025  I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_12/40004/console.log
Sun Feb 16 09:13:37 UTC 2025  I: Downloading source for trixie/mdtraj=1.10.3-2
--2025-02-16 09:13:38--  http://deb.debian.org/debian/pool/main/m/mdtraj/mdtraj_1.10.3-2.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2677 (2.6K) [text/prs.lines.tag]
Saving to: ‘mdtraj_1.10.3-2.dsc’

     0K ..                                                    100%  409M=0s

2025-02-16 09:13:38 (409 MB/s) - ‘mdtraj_1.10.3-2.dsc’ saved [2677/2677]

Sun Feb 16 09:13:38 UTC 2025  I: mdtraj_1.10.3-2.dsc
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Hash: SHA512

Format: 3.0 (quilt)
Source: mdtraj
Binary: python3-mdtraj, python-mdtraj-doc
Architecture: any-amd64 arm64 i386 all
Version: 1.10.3-2
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Uploaders: Drew Parsons <dparsons@debian.org>
Homepage: https://mdtraj.org/
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/debichem-team/mdtraj
Vcs-Git: https://salsa.debian.org/debichem-team/mdtraj.git
Testsuite: autopkgtest
Testsuite-Triggers: python3-gsd, python3-ipykernel, python3-jupyter-client, python3-matplotlib, python3-nbformat, python3-netcdf4, python3-pandas, python3-pytest, python3-sklearn
Build-Depends: debhelper-compat (= 13), dh-sequence-python3, cython3, python3-setuptools, python3-all-dev, python3-gsd, python3-numpy, python3-scipy, python3-nbsphinx, python3-nbsphinx-link, python3-netcdf4, python3-networkx, python3-pandas, python3-pyparsing, python3-sphinx, python3-tables, python3-versioneer, libjs-mathjax
Build-Depends-Indep: pandoc, python3-msmb-theme, python3-ipykernel, python3-jupyter-client, python3-matplotlib, python3-nbconvert, python3-nbformat, python3-numpydoc, python3-sklearn
Package-List:
 python-mdtraj-doc deb doc optional arch=all
 python3-mdtraj deb python optional arch=any-amd64,arm64,i386
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Files:
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Sun Feb 16 09:13:38 UTC 2025  I: Checking whether the package is not for us
Sun Feb 16 09:13:38 UTC 2025  I: Starting 1st build on remote node ionos12-i386.debian.net.
Sun Feb 16 09:13:38 UTC 2025  I: Preparing to do remote build '1' on ionos12-i386.debian.net.
Sun Feb 16 09:48:09 UTC 2025  I: Deleting $TMPDIR on ionos12-i386.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sat Feb 15 21:13:41 -12 2025
I: pbuilder-time-stamp: 1739697221
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: using eatmydata during job
I: Copying source file
I: copying [mdtraj_1.10.3-2.dsc]
I: copying [./mdtraj_1.10.3.orig.tar.gz]
I: copying [./mdtraj_1.10.3-2.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.10.3-2.dsc: unsupported subcommand
dpkg-source: info: extracting mdtraj in mdtraj-1.10.3
dpkg-source: info: unpacking mdtraj_1.10.3.orig.tar.gz
dpkg-source: info: unpacking mdtraj_1.10.3-2.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
dpkg-source: info: applying revert_flaky_PR1972.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/20968/tmp/hooks/D02_print_environment starting
I: set
  BUILDDIR='/build/reproducible-path'
  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
  BUILDUSERNAME='pbuilder1'
  BUILD_ARCH='i386'
  DEBIAN_FRONTEND='noninteractive'
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 '
  DISTRIBUTION='trixie'
  HOME='/root'
  HOST_ARCH='i386'
  IFS=' 	
  '
  INVOCATION_ID='5761b42422544fa5874b5122b7f2f774'
  LANG='C'
  LANGUAGE='en_US:en'
  LC_ALL='C'
  LD_LIBRARY_PATH='/usr/lib/libeatmydata'
  LD_PRELOAD='libeatmydata.so'
  MAIL='/var/mail/root'
  OPTIND='1'
  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
  PBCURRENTCOMMANDLINEOPERATION='build'
  PBUILDER_OPERATION='build'
  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
  PBUILDER_SYSCONFDIR='/etc'
  PPID='20968'
  PS1='# '
  PS2='> '
  PS4='+ '
  PWD='/'
  SHELL='/bin/bash'
  SHLVL='2'
  SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.LUHbQ27q/pbuilderrc_mb9J --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.LUHbQ27q/b1 --logfile b1/build.log mdtraj_1.10.3-2.dsc'
  SUDO_GID='112'
  SUDO_UID='107'
  SUDO_USER='jenkins'
  TERM='unknown'
  TZ='/usr/share/zoneinfo/Etc/GMT+12'
  USER='root'
  _='/usr/bin/systemd-run'
  http_proxy='http://46.16.76.132:3128'
I: uname -a
  Linux ionos12-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) 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/20968/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 <pbuilder-maint@lists.alioth.debian.org>
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, 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, pandoc, 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 ... 19794 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 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 pandoc; however:
  Package pandoc 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} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgcrypt20{a} libgfortran5{a} libglib2.0-0t64{a} libgnutls30t64{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhdf5-310{a} libhdf5-hl-310{a} libicu72{a} libidn2-0{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} libldap2{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} libp11-kit0{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} libtasn1-6{a} libtcl8.6{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{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-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-pygments{a} python3-pyparsing{a} python3-pytz{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 libgpg-error-l10n 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-fqdn python3-gdal python3-isoduration python3-json-pointer python3-odf python3-olefile python3-openpyxl python3-pooch python3-pydot python3-pygraphviz python3-pytest python3-rfc3339-validator python3-rfc3986-validator python3-rfc3987 python3-sphinxcontrib.bibtex python3-uritemplate python3-webcolors python3-yaml shared-mime-info wget xdg-user-dirs 
0 packages upgraded, 307 newly installed, 0 to remove and 0 not upgraded.
Need to get 243 MB of archives. After unpacking 1287 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main i386 fonts-lato all 2.015-1 [2780 kB]
Get: 2 http://deb.debian.org/debian trixie/main i386 libtext-charwidth-perl i386 0.04-11+b4 [9656 B]
Get: 3 http://deb.debian.org/debian trixie/main i386 libtext-wrapi18n-perl all 0.06-10 [8808 B]
Get: 4 http://deb.debian.org/debian trixie/main i386 libproc2-0 i386 2:4.0.4-7 [66.0 kB]
Get: 5 http://deb.debian.org/debian trixie/main i386 procps i386 2:4.0.4-7 [876 kB]
Get: 6 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 7 http://deb.debian.org/debian trixie/main i386 ucf all 3.0049 [42.5 kB]
Get: 8 http://deb.debian.org/debian trixie/main i386 libdebuginfod-common all 0.192-4 [23.7 kB]
Get: 9 http://deb.debian.org/debian trixie/main i386 libpython3.13-minimal i386 3.13.2-1 [859 kB]
Get: 10 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB]
Get: 11 http://deb.debian.org/debian trixie/main i386 python3.13-minimal i386 3.13.2-1 [2266 kB]
Get: 12 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.13.1-2 [27.0 kB]
Get: 13 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB]
Get: 14 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB]
Get: 15 http://deb.debian.org/debian trixie/main i386 tzdata all 2024b-6 [257 kB]
Get: 16 http://deb.debian.org/debian trixie/main i386 libffi8 i386 3.4.6-1 [21.2 kB]
Get: 17 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-6 [69.4 kB]
Get: 18 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-6 [173 kB]
Get: 19 http://deb.debian.org/debian trixie/main i386 libpython3.13-stdlib i386 3.13.2-1 [1985 kB]
Get: 20 http://deb.debian.org/debian trixie/main i386 python3.13 i386 3.13.2-1 [745 kB]
Get: 21 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.13.1-2 [9952 B]
Get: 22 http://deb.debian.org/debian trixie/main i386 python3 i386 3.13.1-2 [28.0 kB]
Get: 23 http://deb.debian.org/debian trixie/main i386 libpython3.12-minimal i386 3.12.9-1 [816 kB]
Get: 24 http://deb.debian.org/debian trixie/main i386 python3.12-minimal i386 3.12.9-1 [2238 kB]
Get: 25 http://deb.debian.org/debian trixie/main i386 sgml-base all 1.31 [15.4 kB]
Get: 26 http://deb.debian.org/debian trixie/main i386 openssl i386 3.4.0-2 [1427 kB]
Get: 27 http://deb.debian.org/debian trixie/main i386 ca-certificates all 20241223 [164 kB]
Get: 28 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 29 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 30 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 31 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.23.1-1 [245 kB]
Get: 32 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 33 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 34 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.4-3 [96.2 kB]
Get: 35 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 36 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 37 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-5 [301 kB]
Get: 38 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB]
Get: 39 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 40 http://deb.debian.org/debian trixie/main i386 automake all 1:1.17-3 [862 kB]
Get: 41 http://deb.debian.org/debian trixie/main i386 autopoint all 0.23.1-1 [770 kB]
Get: 42 http://deb.debian.org/debian trixie/main i386 libtcl8.6 i386 8.6.16+dfsg-1 [1103 kB]
Get: 43 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB]
Get: 44 http://deb.debian.org/debian trixie/main i386 libpng16-16t64 i386 1.6.46-4 [292 kB]
Get: 45 http://deb.debian.org/debian trixie/main i386 libfreetype6 i386 2.13.3+dfsg-1 [464 kB]
Get: 46 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 47 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 48 http://deb.debian.org/debian trixie/main i386 fontconfig-config i386 2.15.0-2 [317 kB]
Get: 49 http://deb.debian.org/debian trixie/main i386 libfontconfig1 i386 2.15.0-2 [402 kB]
Get: 50 http://deb.debian.org/debian trixie/main i386 libxau6 i386 1:1.0.11-1 [20.7 kB]
Get: 51 http://deb.debian.org/debian trixie/main i386 libxdmcp6 i386 1:1.1.5-1 [28.2 kB]
Get: 52 http://deb.debian.org/debian trixie/main i386 libxcb1 i386 1.17.0-2+b1 [148 kB]
Get: 53 http://deb.debian.org/debian trixie/main i386 libx11-data all 2:1.8.10-2 [337 kB]
Get: 54 http://deb.debian.org/debian trixie/main i386 libx11-6 i386 2:1.8.10-2 [834 kB]
Get: 55 http://deb.debian.org/debian trixie/main i386 libxrender1 i386 1:0.9.10-1.1+b4 [28.8 kB]
Get: 56 http://deb.debian.org/debian trixie/main i386 libxft2 i386 2.3.6-1+b4 [55.3 kB]
Get: 57 http://deb.debian.org/debian trixie/main i386 libxext6 i386 2:1.3.4-1+b3 [52.5 kB]
Get: 58 http://deb.debian.org/debian trixie/main i386 x11-common all 1:7.7+24 [217 kB]
Get: 59 http://deb.debian.org/debian trixie/main i386 libxss1 i386 1:1.2.3-1+b3 [17.3 kB]
Get: 60 http://deb.debian.org/debian trixie/main i386 libtk8.6 i386 8.6.16-1 [834 kB]
Get: 61 http://deb.debian.org/debian trixie/main i386 tk8.6-blt2.5 i386 2.5.3+dfsg-7 [616 kB]
Get: 62 http://deb.debian.org/debian trixie/main i386 blt i386 2.5.3+dfsg-7 [6024 B]
Get: 63 http://deb.debian.org/debian trixie/main i386 cython3 i386 3.0.11+dfsg-2 [3020 kB]
Get: 64 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 65 http://deb.debian.org/debian trixie/main i386 libtool all 2.5.4-3 [539 kB]
Get: 66 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 67 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 68 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 69 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 70 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 71 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 72 http://deb.debian.org/debian trixie/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 73 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 74 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 75 http://deb.debian.org/debian trixie/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 76 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 77 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 78 http://deb.debian.org/debian trixie/main i386 debhelper all 13.24.1 [920 kB]
Get: 79 http://deb.debian.org/debian trixie/main i386 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 80 http://deb.debian.org/debian trixie/main i386 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 81 http://deb.debian.org/debian trixie/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 82 http://deb.debian.org/debian trixie/main i386 python3-typeguard all 4.4.1-1 [37.0 kB]
Get: 83 http://deb.debian.org/debian trixie/main i386 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 84 http://deb.debian.org/debian trixie/main i386 python3-jaraco.context all 6.0.0-1 [7984 B]
Get: 85 http://deb.debian.org/debian trixie/main i386 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 86 http://deb.debian.org/debian trixie/main i386 python3-pkg-resources all 75.6.0-1 [222 kB]
Get: 87 http://deb.debian.org/debian trixie/main i386 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 88 http://deb.debian.org/debian trixie/main i386 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 89 http://deb.debian.org/debian trixie/main i386 python3-setuptools all 75.6.0-1 [720 kB]
Get: 90 http://deb.debian.org/debian trixie/main i386 dh-python all 6.20250108 [113 kB]
Get: 91 http://deb.debian.org/debian trixie/main i386 xml-core all 0.19 [20.1 kB]
Get: 92 http://deb.debian.org/debian trixie/main i386 docutils-common all 0.21.2+dfsg-2 [128 kB]
Get: 93 http://deb.debian.org/debian trixie/main i386 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB]
Get: 94 http://deb.debian.org/debian trixie/main i386 fonts-lyx all 2.4.3-1 [190 kB]
Get: 95 http://deb.debian.org/debian trixie/main i386 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB]
Get: 96 http://deb.debian.org/debian trixie/main i386 libdw1t64 i386 0.192-4 [284 kB]
Get: 97 http://deb.debian.org/debian trixie/main i386 libglib2.0-0t64 i386 2.83.3-2 [1581 kB]
Get: 98 http://deb.debian.org/debian trixie/main i386 libbabeltrace1 i386 1.5.11-4+b1 [195 kB]
Get: 99 http://deb.debian.org/debian trixie/main i386 libidn2-0 i386 2.3.7-2+b1 [130 kB]
Get: 100 http://deb.debian.org/debian trixie/main i386 libp11-kit0 i386 0.25.5-3 [423 kB]
Get: 101 http://deb.debian.org/debian trixie/main i386 libtasn1-6 i386 4.19.0-3+b3 [51.1 kB]
Get: 102 http://deb.debian.org/debian trixie/main i386 libgnutls30t64 i386 3.8.9-2 [1462 kB]
Get: 103 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.21.3-4 [35.0 kB]
Get: 104 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.2-1 [24.3 kB]
Get: 105 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.21.3-4 [83.7 kB]
Get: 106 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-4 [9600 B]
Get: 107 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.21.3-4 [354 kB]
Get: 108 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.21.3-4 [149 kB]
Get: 109 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8+b1 [20.9 kB]
Get: 110 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-8+b1 [61.3 kB]
Get: 111 http://deb.debian.org/debian trixie/main i386 libldap2 i386 2.6.9+dfsg-1 [205 kB]
Get: 112 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB]
Get: 113 http://deb.debian.org/debian trixie/main i386 libnghttp3-9 i386 1.6.0-2 [75.9 kB]
Get: 114 http://deb.debian.org/debian trixie/main i386 libngtcp2-16 i386 1.9.1-1 [151 kB]
Get: 115 http://deb.debian.org/debian trixie/main i386 libngtcp2-crypto-gnutls8 i386 1.9.1-1 [19.1 kB]
Get: 116 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB]
Get: 117 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB]
Get: 118 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB]
Get: 119 http://deb.debian.org/debian trixie/main i386 libcurl3t64-gnutls i386 8.12.0+git20250209.89ed161+ds-1 [411 kB]
Get: 120 http://deb.debian.org/debian trixie/main i386 libjson-c5 i386 0.18+ds-1 [48.7 kB]
Get: 121 http://deb.debian.org/debian trixie/main i386 libdebuginfod1t64 i386 0.192-4 [33.9 kB]
Get: 122 http://deb.debian.org/debian trixie/main i386 libipt2 i386 2.1.2-1 [56.8 kB]
Get: 123 http://deb.debian.org/debian trixie/main i386 libpython3.13 i386 3.13.2-1 [2199 kB]
Get: 124 http://deb.debian.org/debian trixie/main i386 libsource-highlight-common all 3.1.9-4.3 [77.5 kB]
Get: 125 http://deb.debian.org/debian trixie/main i386 libsource-highlight4t64 i386 3.1.9-4.3+b1 [357 kB]
Get: 126 http://deb.debian.org/debian trixie/main i386 gdb i386 16.2-1 [7624 kB]
Get: 127 http://deb.debian.org/debian trixie/main i386 libaec0 i386 1.1.3-1+b1 [25.0 kB]
Get: 128 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.1-2 [150 kB]
Get: 129 http://deb.debian.org/debian trixie/main i386 libsnappy1v5 i386 1.2.1-1+b1 [31.3 kB]
Get: 130 http://deb.debian.org/debian trixie/main i386 libblosc1 i386 1.21.5+ds-1+b2 [51.4 kB]
Get: 131 http://deb.debian.org/debian trixie/main i386 libblosc2-4 i386 2.15.2+ds-6 [218 kB]
Get: 132 http://deb.debian.org/debian trixie/main i386 libcurl4t64 i386 8.12.0+git20250209.89ed161+ds-1 [398 kB]
Get: 133 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.23-1+b1 [48.4 kB]
Get: 134 http://deb.debian.org/debian trixie/main i386 libexpat1-dev i386 2.6.4-1 [165 kB]
Get: 135 http://deb.debian.org/debian trixie/main i386 libfribidi0 i386 1.0.16-1 [27.0 kB]
Get: 136 http://deb.debian.org/debian trixie/main i386 libgpg-error0 i386 1.51-3 [87.3 kB]
Get: 137 http://deb.debian.org/debian trixie/main i386 libgcrypt20 i386 1.11.0-7 [799 kB]
Get: 138 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14.2.0-16 [735 kB]
Get: 139 http://deb.debian.org/debian trixie/main i386 libgraphite2-3 i386 1.3.14-2+b1 [77.8 kB]
Get: 140 http://deb.debian.org/debian trixie/main i386 libharfbuzz0b i386 10.2.0-1 [504 kB]
Get: 141 http://deb.debian.org/debian trixie/main i386 libsz2 i386 1.1.3-1+b1 [8128 B]
Get: 142 http://deb.debian.org/debian trixie/main i386 libhdf5-310 i386 1.14.5+repack-3 [1327 kB]
Get: 143 http://deb.debian.org/debian trixie/main i386 libhdf5-hl-310 i386 1.14.5+repack-3 [81.6 kB]
Get: 144 http://deb.debian.org/debian trixie/main i386 libimagequant0 i386 2.18.0-1+b2 [36.0 kB]
Get: 145 http://deb.debian.org/debian trixie/main i386 libjbig0 i386 2.1-6.1+b2 [32.2 kB]
Get: 146 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-3+b1 [171 kB]
Get: 147 http://deb.debian.org/debian trixie/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 148 http://deb.debian.org/debian trixie/main i386 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get: 149 http://deb.debian.org/debian trixie/main i386 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB]
Get: 150 http://deb.debian.org/debian trixie/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 151 http://deb.debian.org/debian trixie/main i386 libjs-sphinxdoc all 8.1.3-4 [30.4 kB]
Get: 152 http://deb.debian.org/debian trixie/main i386 libjson-perl all 4.10000-1 [87.5 kB]
Get: 153 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.1-2 [2198 kB]
Get: 154 http://deb.debian.org/debian trixie/main i386 liblbfgsb0 i386 3.0+dfsg.4-1+b2 [29.5 kB]
Get: 155 http://deb.debian.org/debian trixie/main i386 liblcms2-2 i386 2.16-2 [171 kB]
Get: 156 http://deb.debian.org/debian trixie/main i386 liblerc4 i386 4.0.0+ds-5 [191 kB]
Get: 157 http://deb.debian.org/debian trixie/main i386 liblua5.4-0 i386 5.4.7-1+b2 [170 kB]
Get: 158 http://deb.debian.org/debian trixie/main i386 liblzo2-2 i386 2.10-3+b1 [59.5 kB]
Get: 159 http://deb.debian.org/debian trixie/main i386 libnetcdf19t64 i386 1:4.9.2-7+b1 [529 kB]
Get: 160 http://deb.debian.org/debian trixie/main i386 libnorm1t64 i386 1.5.9+dfsg-3.1+b2 [239 kB]
Get: 161 http://deb.debian.org/debian trixie/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 162 http://deb.debian.org/debian trixie/main i386 libtirpc3t64 i386 1.3.4+ds-1.3+b1 [90.5 kB]
Get: 163 http://deb.debian.org/debian trixie/main i386 libnsl2 i386 1.3.0-3+b3 [42.7 kB]
Get: 164 http://deb.debian.org/debian trixie/main i386 libnuma1 i386 2.0.18-1+b1 [23.9 kB]
Get: 165 http://deb.debian.org/debian trixie/main i386 libopenjp2-7 i386 2.5.3-1 [215 kB]
Get: 166 http://deb.debian.org/debian trixie/main i386 libpgm-5.3-0t64 i386 5.3.128~dfsg-2.1+b1 [169 kB]
Get: 167 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Get: 168 http://deb.debian.org/debian trixie/main i386 libpython3.13-dev i386 3.13.2-1 [5181 kB]
Get: 169 http://deb.debian.org/debian trixie/main i386 libpython3-dev i386 3.13.1-2 [10.2 kB]
Get: 170 http://deb.debian.org/debian trixie/main i386 libpython3.12-stdlib i386 3.12.9-1 [1972 kB]
Get: 171 http://deb.debian.org/debian trixie/main i386 libpython3.12t64 i386 3.12.9-1 [2172 kB]
Get: 172 http://deb.debian.org/debian trixie/main i386 libpython3.12-dev i386 3.12.9-1 [5283 kB]
Get: 173 http://deb.debian.org/debian trixie/main i386 libpython3-all-dev i386 3.13.1-2 [1072 B]
Get: 174 http://deb.debian.org/debian trixie/main i386 libqhull-r8.0 i386 2020.2-6+b2 [259 kB]
Get: 175 http://deb.debian.org/debian trixie/main i386 libraqm0 i386 0.10.2-1 [14.6 kB]
Get: 176 http://deb.debian.org/debian trixie/main i386 libsharpyuv0 i386 1.5.0-0.1 [115 kB]
Get: 177 http://deb.debian.org/debian trixie/main i386 libsodium23 i386 1.0.18-1+b2 [186 kB]
Get: 178 http://deb.debian.org/debian trixie/main i386 libwebp7 i386 1.5.0-0.1 [329 kB]
Get: 179 http://deb.debian.org/debian trixie/main i386 libtiff6 i386 4.5.1+git230720-5 [339 kB]
Get: 180 http://deb.debian.org/debian trixie/main i386 libwebpdemux2 i386 1.5.0-0.1 [114 kB]
Get: 181 http://deb.debian.org/debian trixie/main i386 libwebpmux3 i386 1.5.0-0.1 [127 kB]
Get: 182 http://deb.debian.org/debian trixie/main i386 libxslt1.1 i386 1.1.35-1.1+b1 [243 kB]
Get: 183 http://deb.debian.org/debian trixie/main i386 libyaml-0-2 i386 0.2.5-2 [55.8 kB]
Get: 184 http://deb.debian.org/debian trixie/main i386 libzmq5 i386 4.3.5-1+b3 [308 kB]
Get: 185 http://deb.debian.org/debian trixie/main i386 pandoc-data all 3.1.11.1-3 [459 kB]
Get: 186 http://deb.debian.org/debian trixie/main i386 pandoc i386 3.1.11.1+ds-2 [37.3 MB]
Get: 187 http://deb.debian.org/debian trixie/main i386 python-babel-localedata all 2.17.0-1 [6050 kB]
Get: 188 http://deb.debian.org/debian trixie/main i386 python-matplotlib-data all 3.8.3-3 [2731 kB]
Get: 189 http://deb.debian.org/debian trixie/main i386 python-tables-data all 3.10.2-2 [47.3 kB]
Get: 190 http://deb.debian.org/debian trixie/main i386 python-tinycss2-common all 1.4.0-1 [44.8 kB]
Get: 191 http://deb.debian.org/debian trixie/main i386 python3-alabaster all 0.7.16-0.1 [27.9 kB]
Get: 192 http://deb.debian.org/debian trixie/main i386 python3.12 i386 3.12.9-1 [681 kB]
Get: 193 http://deb.debian.org/debian trixie/main i386 python3-all i386 3.13.1-2 [1052 B]
Get: 194 http://deb.debian.org/debian trixie/main i386 python3.13-dev i386 3.13.2-1 [505 kB]
Get: 195 http://deb.debian.org/debian trixie/main i386 python3-dev i386 3.13.1-2 [26.1 kB]
Get: 196 http://deb.debian.org/debian trixie/main i386 python3.12-dev i386 3.12.9-1 [505 kB]
Get: 197 http://deb.debian.org/debian trixie/main i386 python3-all-dev i386 3.13.1-2 [1076 B]
Get: 198 http://deb.debian.org/debian trixie/main i386 python3-asttokens all 3.0.0-1 [20.1 kB]
Get: 199 http://deb.debian.org/debian trixie/main i386 python3-attr all 25.1.0-1 [68.7 kB]
Get: 200 http://deb.debian.org/debian trixie/main i386 python3-babel all 2.17.0-1 [117 kB]
Get: 201 http://deb.debian.org/debian trixie/main i386 python3-webencodings all 0.5.1-5 [11.1 kB]
Get: 202 http://deb.debian.org/debian trixie/main i386 python3-html5lib all 1.2-1 [92.2 kB]
Get: 203 http://deb.debian.org/debian trixie/main i386 python3-bleach all 6.2.0-1 [51.2 kB]
Get: 204 http://deb.debian.org/debian trixie/main i386 python3-brotli i386 1.1.0-2+b6 [319 kB]
Get: 205 http://deb.debian.org/debian trixie/main i386 python3-soupsieve all 2.6-1 [38.3 kB]
Get: 206 http://deb.debian.org/debian trixie/main i386 python3-bs4 all 4.13.3-1 [166 kB]
Get: 207 http://deb.debian.org/debian trixie/main i386 python3-certifi all 2025.1.31+ds-1 [9652 B]
Get: 208 http://deb.debian.org/debian trixie/main i386 python3-cffi-backend i386 1.17.1-2+b1 [95.5 kB]
Get: 209 http://deb.debian.org/debian trixie/main i386 python3-numpy i386 1:1.26.4+ds-13 [4751 kB]
Get: 210 http://deb.debian.org/debian trixie/main i386 python3-cftime i386 1.6.4-1+b3 [305 kB]
Get: 211 http://deb.debian.org/debian trixie/main i386 python3-chardet all 5.2.0+dfsg-2 [108 kB]
Get: 212 http://deb.debian.org/debian trixie/main i386 python3-charset-normalizer i386 3.4.0-1+b1 [139 kB]
Get: 213 http://deb.debian.org/debian trixie/main i386 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB]
Get: 214 http://deb.debian.org/debian trixie/main i386 python3-comm all 0.2.1-1 [8104 B]
Get: 215 http://deb.debian.org/debian trixie/main i386 python3-contourpy i386 1.3.1-1 [271 kB]
Get: 216 http://deb.debian.org/debian trixie/main i386 python3-coverage i386 7.6.0+dfsg1-2+b1 [177 kB]
Get: 217 http://deb.debian.org/debian trixie/main i386 python3-cpuinfo all 9.0.0+git20221119-3 [23.5 kB]
Get: 218 http://deb.debian.org/debian trixie/main i386 python3-cycler all 0.12.1-1 [9496 B]
Get: 219 http://deb.debian.org/debian trixie/main i386 python3-dateutil all 2.9.0-3 [79.3 kB]
Get: 220 http://deb.debian.org/debian trixie/main i386 python3-debugpy i386 1.8.8+ds-2 [1066 kB]
Get: 221 http://deb.debian.org/debian trixie/main i386 python3-decorator all 5.1.1-5 [15.1 kB]
Get: 222 http://deb.debian.org/debian trixie/main i386 python3-defusedxml all 0.7.1-3 [43.4 kB]
Get: 223 http://deb.debian.org/debian trixie/main i386 python3-roman all 5.0-1 [10.6 kB]
Get: 224 http://deb.debian.org/debian trixie/main i386 python3-docutils all 0.21.2+dfsg-2 [403 kB]
Get: 225 http://deb.debian.org/debian trixie/main i386 python3-executing all 2.2.0-0.1 [24.5 kB]
Get: 226 http://deb.debian.org/debian trixie/main i386 python3-fastjsonschema all 2.21.1-1 [22.4 kB]
Get: 227 http://deb.debian.org/debian trixie/main i386 python3-pytz all 2025.1-3 [150 kB]
Get: 228 http://deb.debian.org/debian trixie/main i386 python3-tz all 2025.1-3 [4004 B]
Get: 229 http://deb.debian.org/debian trixie/main i386 python3-platformdirs all 4.3.6-1 [16.6 kB]
Get: 230 http://deb.debian.org/debian trixie/main i386 python3-fs all 2.4.16-6 [95.1 kB]
Get: 231 http://deb.debian.org/debian trixie/main i386 python3-lxml i386 5.3.0-1+b1 [1586 kB]
Get: 232 http://deb.debian.org/debian trixie/main i386 python3-lz4 i386 4.4.0+dfsg-1 [25.5 kB]
Get: 233 http://deb.debian.org/debian trixie/main i386 python3-scipy i386 1.14.1-4 [20.1 MB]
Get: 234 http://deb.debian.org/debian trixie/main i386 python3-mpmath all 1.3.0-1 [419 kB]
Get: 235 http://deb.debian.org/debian trixie/main i386 python3-sympy all 1.13.3-1 [4147 kB]
Get: 236 http://deb.debian.org/debian trixie/main i386 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB]
Get: 237 http://deb.debian.org/debian trixie/main i386 unicode-data all 15.1.0-1 [8547 kB]
Get: 238 http://deb.debian.org/debian trixie/main i386 python3-fonttools i386 4.55.3-2 [1591 kB]
Get: 239 http://deb.debian.org/debian trixie/main i386 python3-gsd i386 3.4.2-2 [238 kB]
Get: 240 http://deb.debian.org/debian trixie/main i386 python3-idna all 3.10-1 [42.0 kB]
Get: 241 http://deb.debian.org/debian trixie/main i386 python3-imagesize all 1.4.1-1 [6688 B]
Get: 242 http://deb.debian.org/debian trixie/main i386 python3-parso all 0.8.4-1 [67.8 kB]
Get: 243 http://deb.debian.org/debian trixie/main i386 python3-typeshed all 0.0~git20241223.ea91db2-1 [1530 kB]
Get: 244 http://deb.debian.org/debian trixie/main i386 python3-jedi all 0.19.1+ds1-1 [691 kB]
Get: 245 http://deb.debian.org/debian trixie/main i386 python3-matplotlib-inline all 0.1.6-2 [8652 B]
Get: 246 http://deb.debian.org/debian trixie/main i386 python3-wcwidth all 0.2.13+dfsg1-1 [24.9 kB]
Get: 247 http://deb.debian.org/debian trixie/main i386 python3-prompt-toolkit all 3.0.50-1 [278 kB]
Get: 248 http://deb.debian.org/debian trixie/main i386 python3-pygments all 2.18.0+dfsg-2 [836 kB]
Get: 249 http://deb.debian.org/debian trixie/main i386 python3-pure-eval all 0.2.3-1 [11.2 kB]
Get: 250 http://deb.debian.org/debian trixie/main i386 python3-stack-data all 0.6.3-1 [21.6 kB]
Get: 251 http://deb.debian.org/debian trixie/main i386 python3-ptyprocess all 0.7.0-6 [14.5 kB]
Get: 252 http://deb.debian.org/debian trixie/main i386 python3-pexpect all 4.9-3 [55.6 kB]
Get: 253 http://deb.debian.org/debian trixie/main i386 python3-ipython all 8.30.0-2 [568 kB]
Get: 254 http://deb.debian.org/debian trixie/main i386 python3-jupyter-core all 5.7.2-5 [35.3 kB]
Get: 255 http://deb.debian.org/debian trixie/main i386 python3-psutil i386 5.9.8-2 [226 kB]
Get: 256 http://deb.debian.org/debian trixie/main i386 python3-tornado i386 6.4.2-1 [349 kB]
Get: 257 http://deb.debian.org/debian trixie/main i386 python3-zmq i386 26.2.1-1 [210 kB]
Get: 258 http://deb.debian.org/debian trixie/main i386 python3-jupyter-client all 8.6.3-2 [92.4 kB]
Get: 259 http://deb.debian.org/debian trixie/main i386 python3-nest-asyncio all 1.5.4-1 [6248 B]
Get: 260 http://deb.debian.org/debian trixie/main i386 python3-packaging all 24.2-1 [55.3 kB]
Get: 261 http://deb.debian.org/debian trixie/main i386 python3-ipykernel all 6.29.5-2 [102 kB]
Get: 262 http://deb.debian.org/debian trixie/main i386 python3-markupsafe i386 2.1.5-1+b2 [13.9 kB]
Get: 263 http://deb.debian.org/debian trixie/main i386 python3-jinja2 all 3.1.5-2 [107 kB]
Get: 264 http://deb.debian.org/debian trixie/main i386 python3-joblib all 1.3.2-6 [216 kB]
Get: 265 http://deb.debian.org/debian trixie/main i386 python3-rpds-py i386 0.21.0-2 [313 kB]
Get: 266 http://deb.debian.org/debian trixie/main i386 python3-referencing all 0.35.1-2 [23.5 kB]
Get: 267 http://deb.debian.org/debian trixie/main i386 python3-jsonschema-specifications all 2023.12.1-2 [9020 B]
Get: 268 http://deb.debian.org/debian trixie/main i386 python3-jsonschema all 4.19.2-6 [71.4 kB]
Get: 269 http://deb.debian.org/debian trixie/main i386 python3-jupyterlab-pygments all 0.2.2-3 [6096 B]
Get: 270 http://deb.debian.org/debian trixie/main i386 python3-kiwisolver i386 1.4.7-3 [83.3 kB]
Get: 271 http://deb.debian.org/debian trixie/main i386 python3-pil i386 11.1.0-5 [535 kB]
Get: 272 http://deb.debian.org/debian trixie/main i386 python3.12-tk i386 3.12.9-1 [114 kB]
Get: 273 http://deb.debian.org/debian trixie/main i386 python3.13-tk i386 3.13.2-1 [104 kB]
Get: 274 http://deb.debian.org/debian trixie/main i386 python3-tk i386 3.13.1-1 [9464 B]
Get: 275 http://deb.debian.org/debian trixie/main i386 python3-pil.imagetk i386 11.1.0-5 [81.8 kB]
Get: 276 http://deb.debian.org/debian trixie/main i386 python3-pyparsing all 3.1.2-1 [146 kB]
Get: 277 http://deb.debian.org/debian trixie/main i386 python3-matplotlib i386 3.8.3-3+b3 [5658 kB]
Get: 278 http://deb.debian.org/debian trixie/main i386 python3-mistune all 3.0.2-2 [33.2 kB]
Get: 279 http://deb.debian.org/debian trixie/main i386 sphinx-common all 8.1.3-4 [616 kB]
Get: 280 http://deb.debian.org/debian trixie/main i386 python3-urllib3 all 2.3.0-1 [114 kB]
Get: 281 http://deb.debian.org/debian trixie/main i386 python3-requests all 2.32.3+dfsg-1 [71.9 kB]
Get: 282 http://deb.debian.org/debian trixie/main i386 python3-snowballstemmer all 2.2.0-4 [58.0 kB]
Get: 283 http://deb.debian.org/debian trixie/main i386 python3-sphinx all 8.1.3-4 [468 kB]
Get: 284 http://deb.debian.org/debian trixie/main i386 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1023 kB]
Get: 285 http://deb.debian.org/debian trixie/main i386 python3-sphinxcontrib.jquery all 4.1-5 [7348 B]
Get: 286 http://deb.debian.org/debian trixie/main i386 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [29.7 kB]
Get: 287 http://deb.debian.org/debian trixie/main i386 python3-msmb-theme all 1.2.0-4 [33.8 kB]
Get: 288 http://deb.debian.org/debian trixie/main i386 python3-nbformat all 5.9.1-1 [45.1 kB]
Get: 289 http://deb.debian.org/debian trixie/main i386 python3-nbclient all 0.8.0-2 [62.2 kB]
Get: 290 http://deb.debian.org/debian trixie/main i386 python3-tinycss2 all 1.4.0-1 [24.9 kB]
Get: 291 http://deb.debian.org/debian trixie/main i386 python3-pandocfilters all 1.5.1-1 [23.7 kB]
Get: 292 http://deb.debian.org/debian trixie/main i386 python3-nbconvert all 7.16.6-1 [160 kB]
Get: 293 http://deb.debian.org/debian trixie/main i386 python3-nbsphinx all 0.9.5+ds-1 [39.9 kB]
Get: 294 http://deb.debian.org/debian trixie/main i386 python3-nbsphinx-link all 1.3.0-4 [6264 B]
Get: 295 http://deb.debian.org/debian trixie/main i386 python3-netcdf4 i386 1.7.2-1+b2 [843 kB]
Get: 296 http://deb.debian.org/debian trixie/main i386 python3-networkx all 3.2.1-5 [13.0 MB]
Get: 297 http://deb.debian.org/debian trixie/main i386 python3-numexpr i386 2.10.2-1+b1 [132 kB]
Get: 298 http://deb.debian.org/debian trixie/main i386 python3-tabulate all 0.9.0-1 [45.9 kB]
Get: 299 http://deb.debian.org/debian trixie/main i386 python3-numpydoc all 1.8.0-1 [51.4 kB]
Get: 300 http://deb.debian.org/debian trixie/main i386 python3-pandas-lib i386 2.2.3+dfsg-8 [6848 kB]
Get: 301 http://deb.debian.org/debian trixie/main i386 python3-pandas all 2.2.3+dfsg-8 [3097 kB]
Get: 302 http://deb.debian.org/debian trixie/main i386 python3-threadpoolctl all 3.1.0-1 [21.2 kB]
Get: 303 http://deb.debian.org/debian trixie/main i386 python3-sklearn-lib i386 1.4.2+dfsg-7+b1 [5794 kB]
Get: 304 http://deb.debian.org/debian trixie/main i386 python3-sklearn all 1.4.2+dfsg-7 [2248 kB]
Get: 305 http://deb.debian.org/debian trixie/main i386 python3-tables-lib i386 3.10.2-2 [774 kB]
Get: 306 http://deb.debian.org/debian trixie/main i386 python3-tables all 3.10.2-2 [353 kB]
Get: 307 http://deb.debian.org/debian trixie/main i386 python3-versioneer all 0.29-1 [43.0 kB]
Fetched 243 MB in 10s (24.5 MB/s)
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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'
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Current default time zone: 'Etc/UTC'
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Setting up python3-pytz (2025.1-3) ...
Setting up python3-tz (2025.1-3) ...
Setting up python3-bs4 (4.13.3-1) ...
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Setting up python3-fs (2.4.16-6) ...
Setting up python3-jupyterlab-pygments (0.2.2-3) ...
Setting up libpython3.12t64:i386 (3.12.9-1) ...
Setting up python3-pil:i386 (11.1.0-5) ...
Setting up python3-inflect (7.3.1-2) ...
Setting up python3-pandas (2.2.3+dfsg-8) ...
Setting up python3-pil.imagetk:i386 (11.1.0-5) ...
Setting up python3-executing (2.2.0-0.1) ...
Setting up python3-jaraco.text (4.0.0-1) ...
Setting up python3-pexpect (4.9-3) ...
Setting up python3-zmq (26.2.1-1) ...
Setting up python3-dev (3.13.1-2) ...
Setting up python3-requests (2.32.3+dfsg-1) ...
Setting up python3-sklearn (1.4.2+dfsg-7) ...
Setting up python3-cftime (1.6.4-1+b3) ...
Setting up python3-numexpr (2.10.2-1+b1) ...
Setting up libhdf5-310:i386 (1.14.5+repack-3) ...
Setting up python3-jupyter-client (8.6.3-2) ...
Setting up python3-stack-data (0.6.3-1) ...
Setting up python3-referencing (0.35.1-2) ...
Setting up python3-pkg-resources (75.6.0-1) ...
Setting up libhdf5-hl-310:i386 (1.14.5+repack-3) ...
Setting up libdebuginfod1t64:i386 (0.192-4) ...
Setting up libnetcdf19t64:i386 (1:4.9.2-7+b1) ...
Setting up python3-setuptools (75.6.0-1) ...
Setting up python3-jedi (0.19.1+ds1-1) ...
Setting up python3-tables-lib (3.10.2-2) ...
Setting up libpython3.12-dev:i386 (3.12.9-1) ...
Setting up python3-tables (3.10.2-2) ...
Setting up python3-networkx (3.2.1-5) ...
Setting up gdb (16.2-1) ...
Setting up libpython3-all-dev:i386 (3.13.1-2) ...
Setting up python3-ipython (8.30.0-2) ...
Setting up python3.12-dev (3.12.9-1) ...
Setting up python3-jsonschema-specifications (2023.12.1-2) ...
Setting up python3-netcdf4 (1.7.2-1+b2) ...
Setting up dh-python (6.20250108) ...
Setting up python3-all-dev (3.13.1-2) ...
Setting up python3-debugpy (1.8.8+ds-2) ...
Setting up python3-jsonschema (4.19.2-6) ...
Setting up python3-ipykernel (6.29.5-2) ...
Setting up python3-nbformat (5.9.1-1) ...
Setting up python3-nbclient (0.8.0-2) ...
Setting up python3-nbconvert (7.16.6-1) ...
Setting up python3-fonttools (4.55.3-2) ...
Setting up python3-ufolib2 (0.17.0+dfsg1-1) ...
Setting up python3-matplotlib (3.8.3-3+b3) ...
Processing triggers for libc-bin (2.40-6) ...
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 (8.1.3-4) ...
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-2) ...
Setting up python3-msmb-theme (1.2.0-4) ...
Processing triggers for ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/mdtraj-1.10.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../mdtraj_1.10.3-2_source.changes
dpkg-buildpackage: info: source package mdtraj
dpkg-buildpackage: info: source version 1.10.3-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Drew Parsons <dparsons@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
dpkg-source: info: using options from mdtraj-1.10.3/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
 debian/rules clean
dh clean --with sphinxdoc --buildsystem=pybuild
   dh_auto_clean -O--buildsystem=pybuild
	pybuild --clean -i python{version} -p "3.12 3.13"
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 14.2.0-16' --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 14.2.0-16) 
/build/reproducible-path/mdtraj-1.10.3/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-1.10.3/.pybuild/cpython3_3.12_mdtraj/build' (and everything under it)
'build/bdist.linux-i686' does not exist -- can't clean it
'build/scripts-3.12' does not exist -- can't clean it
I: pybuild base:311: python3.13 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 14.2.0-16' --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 14.2.0-16) 
/build/reproducible-path/mdtraj-1.10.3/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-1.10.3/.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
	rm -rf .pybuild/
	find . -name \*.pyc -exec rm {} \;
   debian/rules execute_after_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/mdtraj-1.10.3'
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-1.10.3'
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
	rm -f debian/debhelper-build-stamp
	rm -rf debian/.debhelper/
	rm -f -- debian/python3-mdtraj.substvars debian/python-mdtraj-doc.substvars debian/files
	rm -fr -- debian/python3-mdtraj/ debian/tmp/ debian/python-mdtraj-doc/
	find .  \( \( \
		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
		\) -exec rm -f {} + \) -o \
		\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
 debian/rules binary
dh binary --with sphinxdoc --buildsystem=pybuild
   dh_update_autotools_config -O--buildsystem=pybuild
   dh_autoreconf -O--buildsystem=pybuild
   dh_auto_configure -O--buildsystem=pybuild
	pybuild --configure -i python{version} -p "3.12 3.13"
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 14.2.0-16' --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 14.2.0-16) 
/build/reproducible-path/mdtraj-1.10.3/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: python3.13 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 14.2.0-16' --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 14.2.0-16) 
/build/reproducible-path/mdtraj-1.10.3/basesetup.py:483: UserWarning: Unrecognized setuptools command ('config'), proceeding with generating Cython sources and expanding templates
  warnings.warn(
warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'make_whole' to allow an error code to be returned.
performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned.
performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned.
C compiler:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Attempting to autodetect SSE2   support... Compiler supports SSE2
Attempting to autodetect SSE3   support... Compiler supports SSE3
Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1
Attempting to autodetect NEON   support... Did not detect NEON support

[ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx
[ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx
[ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx
[ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx
[ 5/10] Cythonizing mdtraj/geometry/drid.pyx
[ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx
[ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx
[ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx
[ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx
[10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx
running config
   dh_auto_build -O--buildsystem=pybuild
	pybuild --build -i python{version} -p "3.12 3.13"
I: pybuild base:311: /usr/bin/python3.12 setup.py build 
Using built-in specs.
COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-linux-gnu/14/lto-wrapper
Target: i686-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-16' --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 14.2.0-16) 
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-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj
copying mdtraj/io.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj
copying mdtraj/_version.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj
copying mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing
copying mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing
copying mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing
copying mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing
copying mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr
copying mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr
copying mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr
copying mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core
copying mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core
copying mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core
copying mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core
copying mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core
copying mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core
copying mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts
copying mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts
copying mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts
copying mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils
copying mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils
copying mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils
copying mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils
copying mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils
copying mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils
copying mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils
copying mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils
copying mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb
copying mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data
copying mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data
copying mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data
UPDATING /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py
set /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py to '1.10.3'
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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so
I: pybuild base:311: /usr/bin/python3 setup.py build 
Using built-in specs.
COLLECT_GCC=/usr/bin/i686-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/i686-linux-gnu/14/lto-wrapper
Target: i686-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-16' --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 14.2.0-16) 
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-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj
copying mdtraj/io.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj
copying mdtraj/_version.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj
copying mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing
copying mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing
copying mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing
copying mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing
copying mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr
copying mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr
copying mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr
copying mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core
copying mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core
copying mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core
copying mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core
copying mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core
copying mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core
copying mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts
copying mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts
copying mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts
copying mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils
copying mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils
copying mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils
copying mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils
copying mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils
copying mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils
copying mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils
copying mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils
copying mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb
copying mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/data
copying mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/data
copying mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/data
UPDATING /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_version.py
set /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_version.py to '1.10.3'
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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighborlist.cpython-313-i386-linux-gnu.so
   dh_auto_test -O--buildsystem=pybuild
	pybuild --test -i python{version} -p "3.12 3.13"
I: pybuild base:311: cd /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build; python3.12 -m unittest discover -v 

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Ran 0 tests in 0.000s

NO TESTS RAN
I: pybuild base:311: cd /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build; python3.13 -m unittest discover -v 

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Ran 0 tests in 0.000s

NO TESTS RAN
	rm -fr -- /tmp/dh-xdg-rundir-eOQFqG2v
   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-1.10.3/debian/tmp
	pybuild --install -i python{version} -p "3.12 3.13" --dest-dir=/build/reproducible-path/mdtraj-1.10.3/debian/tmp
I: pybuild base:311: /usr/bin/python3.12 setup.py install --root /build/reproducible-path/mdtraj-1.10.3/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 14.2.0-16' --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 14.2.0-16) 
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-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py
set /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py to '1.10.3'
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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so
running install_lib
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/io.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/docscrape.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/testing.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/docstrings.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/netcdfreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/dcdreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/hdf5reporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/basereporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/xtcreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/scalar_couplings.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/shift_wrappers.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbstructure.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbfile.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/arc.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/pdbx.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/psf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/mol2.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/lh5.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/mdcrd.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/hoomdxml.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/lammpstrj.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/netcdf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/registry.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/amberrst.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/prmtop.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/gro.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/gsd.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/hdf5.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/xyzfile.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/openmmxml.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__pycache__/_version.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/center.h -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/libtheobald.a -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/theobald_rmsd.h -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/trajectory.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/selection.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/topology.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/residue_names.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/element.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__pycache__
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/angle.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/rg.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/dssp.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/thermodynamic_properties.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/order.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/distance.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/sasa.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/dihedral.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/shape.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/contact.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/rdf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/hbond.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_definitions.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/mymatrix.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/baseunit.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/prefix.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/standard_dimensions.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/quantity.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_operators.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/basedimension.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/validation.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/zipped.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/unitcell.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/delay_import.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/rotation.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/contextmanagers.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/singleton.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/io.py to io.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/testing.py to testing.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/docscrape.py to docscrape.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/docstrings.py to docstrings.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/_version.py to _version.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/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-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/scalar_couplings.py to scalar_couplings.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/hdf5.py to hdf5.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdbx.py to pdbx.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/mol2.py to mol2.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/registry.py to registry.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/gro.py to gro.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/prmtop.py to prmtop.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/psf.py to psf.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/netcdf.py to netcdf.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/gsd.py to gsd.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/amberrst.py to amberrst.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/lh5.py to lh5.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/arc.py to arc.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/topology.py to topology.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/element.py to element.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/selection.py to selection.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/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-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/trajectory.py to trajectory.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/mdconvert.py to mdconvert.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/sasa.py to sasa.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/rdf.py to rdf.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/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-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/rg.py to rg.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/distance.py to distance.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/hbond.py to hbond.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/contact.py to contact.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/shape.py to shape.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/internal.py to internal.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/order.py to order.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/alignment.py to alignment.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/angle.py to angle.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/dssp.py to dssp.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/singleton.py to singleton.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/rotation.py to rotation.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unitcell.py to unitcell.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/zipped.py to zipped.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/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-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/validation.py to validation.cpython-312.pyc
running install_egg_info
running egg_info
creating mdtraj.egg-info
writing mdtraj.egg-info/PKG-INFO
writing dependency_links to mdtraj.egg-info/dependency_links.txt
writing entry points to mdtraj.egg-info/entry_points.txt
writing requirements to mdtraj.egg-info/requires.txt
writing top-level names to mdtraj.egg-info/top_level.txt
writing manifest file 'mdtraj.egg-info/SOURCES.txt'
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
reading manifest file 'mdtraj.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
no previously-included directories found matching '__pycache__'
no previously-included directories found matching '*.pyc'
adding license file 'LICENSE'
writing manifest file 'mdtraj.egg-info/SOURCES.txt'
Copying mdtraj.egg-info to /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj-1.10.3.egg-info
Skipping SOURCES.txt
running install_scripts
Installing mdconvert-mdtraj script to /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/bin
Installing mdinspect script to /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/bin
I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/mdtraj-1.10.3/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 14.2.0-16' --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 14.2.0-16) 
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-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_version.py
set /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_version.py to '1.10.3'
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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3=. -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-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighborlist.cpython-313-i386-linux-gnu.so
running install_lib
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/io.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_rmsd.cpython-313-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/__pycache__/docscrape.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/__pycache__/testing.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/__pycache__/docstrings.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__pycache__/basereporter.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__pycache__/xtcreporter.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__pycache__/dcdreporter.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__pycache__/netcdfreporter.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__pycache__/hdf5reporter.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_version.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/__pycache__/shift_wrappers.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/__pycache__/scalar_couplings.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_lprmsd.cpython-313-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/data
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/data
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/data
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbstructure.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbfile.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/trr.cpython-313-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dtr.cpython-313-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dcd.cpython-313-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/pdbx.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/amberrst.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/netcdf.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/gro.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/mdcrd.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/hdf5.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/registry.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/openmmxml.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/psf.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/gsd.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/arc.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/hoomdxml.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/xyzfile.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/lh5.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/mol2.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/lammpstrj.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/prmtop.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/xtc.cpython-313-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/__pycache__/_version.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/__pycache__
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/lib
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/lib/center.h -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/lib
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/lib/libtheobald.a -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/lib
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/lib/theobald_rmsd.h -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/lib
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__pycache__/residue_names.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__pycache__/selection.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__pycache__/element.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__pycache__/trajectory.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__pycache__/topology.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts/__pycache__
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighbors.cpython-313-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/drid.cpython-313-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighborlist.cpython-313-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/dihedral.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/thermodynamic_properties.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/distance.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/sasa.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/dssp.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/angle.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/contact.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/rdf.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/hbond.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/shape.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/rg.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/order.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/_geometry.cpython-313-i386-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/unit.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/mymatrix.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_definitions.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/prefix.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_operators.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/basedimension.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/quantity.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/baseunit.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/standard_dimensions.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/contextmanagers.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/singleton.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/rotation.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/validation.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/zipped.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/unitcell.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/delay_import.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/io.py to io.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/testing.py to testing.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/docscrape.py to docscrape.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/__init__.py to __init__.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/docstrings.py to docstrings.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__init__.py to __init__.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/_version.py to _version.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/__init__.py to __init__.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/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-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/scalar_couplings.py to scalar_couplings.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/__init__.py to __init__.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/hdf5.py to hdf5.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx.py to pdbx.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/mol2.py to mol2.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/registry.py to registry.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/gro.py to gro.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/prmtop.py to prmtop.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__init__.py to __init__.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/psf.py to psf.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/netcdf.py to netcdf.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/gsd.py to gsd.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/amberrst.py to amberrst.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/lh5.py to lh5.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/arc.py to arc.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/topology.py to topology.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/element.py to element.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__init__.py to __init__.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/selection.py to selection.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/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-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/trajectory.py to trajectory.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts/mdconvert.py to mdconvert.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts/__init__.py to __init__.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/sasa.py to sasa.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/rdf.py to rdf.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/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-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/rg.py to rg.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/distance.py to distance.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/hbond.py to hbond.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/__init__.py to __init__.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/contact.py to contact.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/shape.py to shape.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/internal.py to internal.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/order.py to order.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/alignment.py to alignment.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/angle.py to angle.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/dssp.py to dssp.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/singleton.py to singleton.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/rotation.py to rotation.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unitcell.py to unitcell.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__init__.py to __init__.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/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-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/zipped.py to zipped.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/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-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/validation.py to validation.cpython-313.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-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj-1.10.3.egg-info
Skipping SOURCES.txt
running install_scripts
Installing mdconvert-mdtraj script to /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/bin
Installing mdinspect script to /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/bin
   debian/rules execute_after_dh_auto_install-indep
make[1]: Entering directory '/build/reproducible-path/mdtraj-1.10.3'
cp -a /build/reproducible-path/mdtraj-1.10.3/examples /build/reproducible-path/mdtraj-1.10.3/examples.orig
mkdir -p /build/reproducible-path/mdtraj-1.10.3/build/html/examples/iterload
ln -s /build/reproducible-path/mdtraj-1.10.3/examples/data /build/reproducible-path/mdtraj-1.10.3/build/html/examples/iterload/data
sed "s|http://www.rcsb.org/pdb/files|/build/reproducible-path/mdtraj-1.10.3/debian/external|g" -i /build/reproducible-path/mdtraj-1.10.3/examples/*.ipynb
PYTHONPATH=/build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build \
    MPLCONFIGDIR=/build/reproducible-path/mdtraj-1.10.3/build/matplotlib \
	make -C docs BUILDDIR=/build/reproducible-path/mdtraj-1.10.3/build  html
make[2]: Entering directory '/build/reproducible-path/mdtraj-1.10.3/docs'
sphinx-build -b html -d /build/reproducible-path/mdtraj-1.10.3/build/doctrees   . /build/reproducible-path/mdtraj-1.10.3/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-1.10.3/docs/api/generated/mdtraj.Topology.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.Trajectory.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.Trajectory.superpose.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.acylindricity.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.asphericity.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.baker_hubbard.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.chemical_shifts_ppm.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.chemical_shifts_shiftx2.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.chemical_shifts_spartaplus.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.compute_J3_HN_C.rst, ..., /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.utils.check_random_state.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.utils.ensure_type.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.utils.ilen.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.utils.import_.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.utils.in_units_of.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.utils.rotation_matrix_from_quaternion.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.utils.timing.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.utils.uniform_quaternion.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.wernet_nilsson.rst
Writing evaluated template result to /build/reproducible-path/mdtraj-1.10.3/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
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/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-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/topology.py.
  while not self._is_at_section() and not self._doc.eof():
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/build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.asphericity:9: WARNING: Explicit markup ends without a blank line; unexpected unindent. [docutils]
/build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:33: ERROR: Unexpected indentation. [docutils]
docstring of mdtraj.formats.dtr.load_dtr:7: ERROR: Unexpected indentation. [docutils]
/build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:9: WARNING: Explicit markup ends without a blank line; unexpected unindent. [docutils]
/build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:11: ERROR: Unexpected indentation. [docutils]
/build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_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-1.10.3/.pybuild/cpython3_3.13_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-1.10.3/.pybuild/cpython3_3.13_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-1.10.3/.pybuild/cpython3_3.13_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-1.10.3/docs/examples/atom-selection.rst:4: ERROR: Unknown directive type "notebook".

.. notebook:: examples/atom-selection.ipynb
   :skip_exceptions: [docutils]
/build/reproducible-path/mdtraj-1.10.3/docs/examples/centroids.rst:4: ERROR: Unknown directive type "notebook".

.. notebook:: examples/centroids.ipynb
   :skip_exceptions: [docutils]
/build/reproducible-path/mdtraj-1.10.3/docs/examples/clustering.rst:4: ERROR: Unknown directive type "notebook".

.. notebook:: examples/clustering.ipynb
   :skip_exceptions: [docutils]
/build/reproducible-path/mdtraj-1.10.3/docs/examples/hbonds.rst:4: ERROR: Unknown directive type "notebook".

.. notebook:: examples/hbonds.ipynb
   :skip_exceptions: [docutils]
/build/reproducible-path/mdtraj-1.10.3/docs/examples/iterload.rst:4: ERROR: Unknown directive type "notebook".

.. notebook:: examples/iterload.ipynb
   :skip_exceptions: [docutils]
/build/reproducible-path/mdtraj-1.10.3/docs/examples/native-contact.rst:4: ERROR: Unknown directive type "notebook".

.. notebook:: examples/native-contact.ipynb
   :skip_exceptions: [docutils]
/build/reproducible-path/mdtraj-1.10.3/docs/examples/nmr.rst:4: ERROR: Unknown directive type "notebook".

.. notebook:: examples/nmr.ipynb
   :skip_exceptions: [docutils]
/build/reproducible-path/mdtraj-1.10.3/docs/examples/openmm.rst:4: ERROR: Unknown directive type "notebook".

.. notebook:: examples/simulation-with-openmm.ipynb
   :skip_exceptions: [docutils]
/build/reproducible-path/mdtraj-1.10.3/docs/examples/pca.rst:4: ERROR: Unknown directive type "notebook".

.. notebook:: examples/principal-components.ipynb
   :skip_exceptions: [docutils]
/build/reproducible-path/mdtraj-1.10.3/docs/examples/ramachandran-plot.rst:4: ERROR: Unknown directive type "notebook".

.. notebook:: examples/ramachandran-plot.ipynb
   :skip_exceptions: [docutils]
/build/reproducible-path/mdtraj-1.10.3/docs/examples/rmsd-benchmark.rst:4: ERROR: Unknown directive type "notebook".

.. notebook:: examples/rmsd-benchmark.ipynb
   :skip_exceptions: [docutils]
/build/reproducible-path/mdtraj-1.10.3/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-1.10.3/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-1.10.3/docs/index.rst:26: WARNING: toctree contains reference to nonexisting document '.. examples/index' [toc.not_readable]
/build/reproducible-path/mdtraj-1.10.3/docs/installation.rst:1: WARNING: malformed hyperlink target. [docutils]
/build/reproducible-path/mdtraj-1.10.3/docs/mdconvert.rst:2: WARNING: Title underline too short.

``mdconvert`` (``mdconvert-mdtraj``)
============= [docutils]
/build/reproducible-path/mdtraj-1.10.3/docs/whatsnew.rst:31: WARNING: Title underline too short.

v1.10.2 (December 11, 2024)
-------------------------- [docutils]
/build/reproducible-path/mdtraj-1.10.3/docs/whatsnew.rst:31: WARNING: Title underline too short.

v1.10.2 (December 11, 2024)
-------------------------- [docutils]
/build/reproducible-path/mdtraj-1.10.3/docs/whatsnew.rst:96: WARNING: Title underline too short.

v1.9.9 (July 22, 2023)
--------------------- [docutils]
/build/reproducible-path/mdtraj-1.10.3/docs/whatsnew.rst:96: WARNING: Title underline too short.

v1.9.9 (July 22, 2023)
--------------------- [docutils]
/build/reproducible-path/mdtraj-1.10.3/docs/whatsnew.rst:151: WARNING: Title underline too short.

v1.9.7 (November 12, 2021)
----------------------- [docutils]
/build/reproducible-path/mdtraj-1.10.3/docs/whatsnew.rst:151: WARNING: Title underline too short.

v1.9.7 (November 12, 2021)
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	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.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf
	ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.woff2
	ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.ttf
	ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.ttf
	ln -sf ../../../../../sphinx_rtd_theme/static/js/theme.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/theme.js
	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 ../../../../javascript/sphinxdoc/1.0/language_data.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/language_data.js
	ln -sf ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/searchtools.js
	ln -sf ../../../../javascript/sphinxdoc/1.0/doctools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js
	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-1.10.3'
   dh_sphinxdoc -O--buildsystem=pybuild -Npython-mdtraj-doc
dh_sphinxdoc: warning: Sphinx documentation not found
   dh_installchangelogs -O--buildsystem=pybuild
	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
	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
   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/mdinspect.1
	man-recode --to-code UTF-8 --suffix .dh-new 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
	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
   dh_python3 -O--buildsystem=pybuild
D: dh_python3 dh_python3:180: version: 6.20250108
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=3.13)
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-1.10.3.egg-info/requires.txt'}, 'egg-info': {'debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.10.3.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 netCDF4 (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 numpy<3,>=1.25.0 (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-scipy', 'python3 (>= 3.12~)', 'python3 (<< 3.14)', 'python3:any', 'python3-packaging', 'python3-numpy', 'python3-pyparsing', 'python3-netcdf4'}; 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-1.10.3'
dh_numpy3
	mv debian/python3-mdtraj.substvars.new debian/python3-mdtraj.substvars
	mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars
# setup.py builds the static lib libtheobald.a for each python version
# but dh_python3 can't tell the difference between the different builds,
# since py3.11 compiles libtheobald.o with -fwrapv, where py3.12 uses -fno-strict-overflow
# So clean up manually (assume the binary difference is not an issue)
rm -f debian/python3-mdtraj/usr/lib/python3.*/dist-packages/mdtraj/core/lib/libtheobald.a
for d in debian/python3-mdtraj/usr/lib/python3.*/dist-packages/mdtraj/core/lib; do if [-d $d]; then rmdir -p --ignore-fail-on-non-empty $d; fi; done
/bin/sh: 1: [-d: not found
make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.10.3'
   dh_installsystemduser -O--buildsystem=pybuild
   dh_perl -O--buildsystem=pybuild
   dh_link -O--buildsystem=pybuild
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/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/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-Italic.ttf
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.ttf
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.ttf
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.ttf
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/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/RobotoSlab-Bold.woff2
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Bold.woff2
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.woff2
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.woff2
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.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-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-Regular.ttf
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.ttf
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.woff2
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.woff2
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-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/RobotoSlab-Regular.woff2
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Regular.woff2
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/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.woff
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.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/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/doctools.js
	ln -s ../../../../javascript/sphinxdoc/1.0/doctools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/sphinx_highlight.js
	ln -s ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/sphinx_highlight.js
   dh_strip_nondeterminism -O--buildsystem=pybuild
	Using 1739273589 as canonical time
	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/_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_clustering_11_0.png using File::StripNondeterminism::handlers::png
	Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_solvent-accessible-surface-area_8_0.png using File::StripNondeterminism::handlers::png
	Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_pca_12_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_hbonds_9_1.png using File::StripNondeterminism::handlers::png
	Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_ramachandran-plot_7_1.png using File::StripNondeterminism::handlers::png
	Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_native-contact_6_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/_static/minus.png using File::StripNondeterminism::handlers::png
	Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/file.png using File::StripNondeterminism::handlers::png
	Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/plus.png using File::StripNondeterminism::handlers::png
   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
	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/python3-mdtraj/changelog.Debian usr/share/man/man1/mdconvert-mdtraj.1 usr/share/man/man1/mdinspect.1
	gzip -9nf usr/share/doc/python-mdtraj-doc/changelog.Debian usr/share/doc/python-mdtraj-doc/html/_static/example-trajectoryview-data.json usr/share/doc/python-mdtraj-doc/html/_static/mdtraj_logo.xcf 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-1.10.3'
	cd '/build/reproducible-path/mdtraj-1.10.3'
   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/f9
	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/f9/7ff05caca8d84b531f09b2b2763f1b1354d492.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/f9/7ff05caca8d84b531f09b2b2763f1b1354d492.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/f9/7ff05caca8d84b531f09b2b2763f1b1354d492.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/e9
	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/e9/50bc0a856ba9f6398f2e1eb9500412f73a4335.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e9/50bc0a856ba9f6398f2e1eb9500412f73a4335.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/e9/50bc0a856ba9f6398f2e1eb9500412f73a4335.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/05
	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/05/b712224701634d119807749ef0d8fb6387e228.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/05/b712224701634d119807749ef0d8fb6387e228.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/05/b712224701634d119807749ef0d8fb6387e228.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/ba
	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/ba/f2539622a66450ec9f18b8fb3d708d1e4b73f0.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/ba/f2539622a66450ec9f18b8fb3d708d1e4b73f0.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/ba/f2539622a66450ec9f18b8fb3d708d1e4b73f0.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/5e
	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/5e/784a56608b8ee092b86c84e5dd6a4f7f38b2a2.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/5e/784a56608b8ee092b86c84e5dd6a4f7f38b2a2.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/5e/784a56608b8ee092b86c84e5dd6a4f7f38b2a2.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/87
	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/87/f5f74cf657eed79c10d628f4845f382cec6eb8.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/87/f5f74cf657eed79c10d628f4845f382cec6eb8.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/87/f5f74cf657eed79c10d628f4845f382cec6eb8.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/97
	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/97/6cc3067799d3ac85fb08fc4c8348138d6cc91e.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/97/6cc3067799d3ac85fb08fc4c8348138d6cc91e.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/97/6cc3067799d3ac85fb08fc4c8348138d6cc91e.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/ce
	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/ce/df60fcca8df1e4a17bae753ed9c63da610560f.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/ce/df60fcca8df1e4a17bae753ed9c63da610560f.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/ce/df60fcca8df1e4a17bae753ed9c63da610560f.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/fd
	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/fd/0b359460af9654a81e0b059030dd8c7ed9fa3b.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/fd/0b359460af9654a81e0b059030dd8c7ed9fa3b.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/fd/0b359460af9654a81e0b059030dd8c7ed9fa3b.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/04
	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/04/6916a6c781ed7734d0ca589058474797dccb79.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/04/6916a6c781ed7734d0ca589058474797dccb79.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/04/6916a6c781ed7734d0ca589058474797dccb79.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/04
	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/04/d37fcb4ad4b42f53120522164099ca4e1fe8a3.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/04/d37fcb4ad4b42f53120522164099ca4e1fe8a3.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/04/d37fcb4ad4b42f53120522164099ca4e1fe8a3.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/trr.cpython-312-i386-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/11/c213173359e5836079897797dee0e415bdee9a.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/11/c213173359e5836079897797dee0e415bdee9a.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/11/c213173359e5836079897797dee0e415bdee9a.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/38
	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/38/b80a50964deb78a078645564f6a1d67b35e692.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/38/b80a50964deb78a078645564f6a1d67b35e692.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/38/b80a50964deb78a078645564f6a1d67b35e692.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/47
	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/47/e8b8ca1f02d22b1c1cce2ec20e372339b249a4.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/47/e8b8ca1f02d22b1c1cce2ec20e372339b249a4.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/47/e8b8ca1f02d22b1c1cce2ec20e372339b249a4.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/1f
	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/1f/d728f8c4ec4403705cddc68d9b3486f5233f22.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/1f/d728f8c4ec4403705cddc68d9b3486f5233f22.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/1f/d728f8c4ec4403705cddc68d9b3486f5233f22.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/de
	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/de/4e18412503c491fe0890bf17f99c9c1ddcc8f7.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/de/4e18412503c491fe0890bf17f99c9c1ddcc8f7.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/de/4e18412503c491fe0890bf17f99c9c1ddcc8f7.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-i386-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/cc
	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/cc/2d8c609f0fa92cc62b4aa261b95564c23f816b.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/cc/2d8c609f0fa92cc62b4aa261b95564c23f816b.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/cc/2d8c609f0fa92cc62b4aa261b95564c23f816b.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/5e
	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/5e/829edca89825b0c4e00b3438d3f10343ba658d.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/5e/829edca89825b0c4e00b3438d3f10343ba658d.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/5e/829edca89825b0c4e00b3438d3f10343ba658d.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/65
	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/65/e6909b54333045a7b247a17fa08ec0beb98827.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/65/e6909b54333045a7b247a17fa08ec0beb98827.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/65/e6909b54333045a7b247a17fa08ec0beb98827.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/ef
	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/ef/9b00d0da7b0cb1e10888b64d88b933fd9074a4.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/ef/9b00d0da7b0cb1e10888b64d88b933fd9074a4.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/ef/9b00d0da7b0cb1e10888b64d88b933fd9074a4.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.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-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/formats/dcd.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/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/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/trr.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-i386-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/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/drid.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/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/_geometry.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=046916a6c781ed7734d0ca589058474797dccb79 04d37fcb4ad4b42f53120522164099ca4e1fe8a3 05b712224701634d119807749ef0d8fb6387e228 11c213173359e5836079897797dee0e415bdee9a 1fd728f8c4ec4403705cddc68d9b3486f5233f22 38b80a50964deb78a078645564f6a1d67b35e692 47e8b8ca1f02d22b1c1cce2ec20e372339b249a4 5e784a56608b8ee092b86c84e5dd6a4f7f38b2a2 5e829edca89825b0c4e00b3438d3f10343ba658d 65e6909b54333045a7b247a17fa08ec0beb98827 87f5f74cf657eed79c10d628f4845f382cec6eb8 976cc3067799d3ac85fb08fc4c8348138d6cc91e baf2539622a66450ec9f18b8fb3d708d1e4b73f0 cc2d8c609f0fa92cc62b4aa261b95564c23f816b cedf60fcca8df1e4a17bae753ed9c63da610560f de4e18412503c491fe0890bf17f99c9c1ddcc8f7 e950bc0a856ba9f6398f2e1eb9500412f73a4335 ef9b00d0da7b0cb1e10888b64d88b933fd9074a4 f97ff05caca8d84b531f09b2b2763f1b1354d492 fd0b359460af9654a81e0b059030dd8c7ed9fa3b" -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
	cd debian/python3-mdtraj >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	install -m0755 -d debian/python-mdtraj-doc/DEBIAN
	cd debian/python-mdtraj-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/python-mdtraj-doc/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
   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_1.10.3-2_i386.deb'.
dpkg-deb: building package 'python-mdtraj-doc' in '../python-mdtraj-doc_1.10.3-2_all.deb'.
dpkg-deb: building package 'python3-mdtraj-dbgsym' in '../python3-mdtraj-dbgsym_1.10.3-2_i386.deb'.
 dpkg-genbuildinfo --build=binary -O../mdtraj_1.10.3-2_i386.buildinfo
 dpkg-genchanges --build=binary -O../mdtraj_1.10.3-2_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-source: info: using options from mdtraj-1.10.3/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env 
I: removing directory /srv/workspace/pbuilder/20968 and its subdirectories
I: Current time: Sat Feb 15 21:48:08 -12 2025
I: pbuilder-time-stamp: 1739699288
Sun Feb 16 09:48:10 UTC 2025  I: 1st build successful. Starting 2nd build on remote node ionos16-i386.debian.net.
Sun Feb 16 09:48:10 UTC 2025  I: Preparing to do remote build '2' on ionos16-i386.debian.net.
Sun Feb 16 10:09:02 UTC 2025  I: Deleting $TMPDIR on ionos16-i386.debian.net.
Sun Feb 16 10:09:03 UTC 2025  I: mdtraj_1.10.3-2_i386.changes:
Format: 1.8
Date: Tue, 11 Feb 2025 12:33:09 +0100
Source: mdtraj
Binary: python-mdtraj-doc python3-mdtraj python3-mdtraj-dbgsym
Architecture: all i386
Version: 1.10.3-2
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Changed-By: Drew Parsons <dparsons@debian.org>
Description:
 python-mdtraj-doc - Read, write and analyze MD trajectories in Python (documentation)
 python3-mdtraj - Read, write and analyze MD trajectories in Python
Changes:
 mdtraj (1.10.3-2) unstable; urgency=medium
 .
   * move pandoc to Build-Depends-Indep (for doc build)
Checksums-Sha1:
 d0d674eff6fbad39b833b82c5aa3b6c2eab701e9 14134 mdtraj_1.10.3-2_i386.buildinfo
 ed65d84f60dfae27ac67689f4fd6d1bc35c1376f 1869916 python-mdtraj-doc_1.10.3-2_all.deb
 8ce49b1db7de8f023cf82829fe8c448442ea5a81 10875416 python3-mdtraj-dbgsym_1.10.3-2_i386.deb
 0a2d73439b9fa5998df9ce9a0654ad222c777da3 1404200 python3-mdtraj_1.10.3-2_i386.deb
Checksums-Sha256:
 8c8556228d62dfe5c0392ab0adb813846d7d8fe98137fc18622c7284682b65a4 14134 mdtraj_1.10.3-2_i386.buildinfo
 a8bcc3f62836e43fb2dbf0c61972519460f72806f752dfce8f0aaca2d39fd86e 1869916 python-mdtraj-doc_1.10.3-2_all.deb
 012c06efc4e9b61515716fcf368b61a5370c6ffad852ae603f59ebb911a374e6 10875416 python3-mdtraj-dbgsym_1.10.3-2_i386.deb
 1ef3ebf20c35c7728e25db6b68f7bc103acddef6ce6ac6f4fffd7d9016d9eff9 1404200 python3-mdtraj_1.10.3-2_i386.deb
Files:
 8d0f83d8dce9cedfaed0716bbf409533 14134 python optional mdtraj_1.10.3-2_i386.buildinfo
 3938d0dd0ed50484408b899c0013b0aa 1869916 doc optional python-mdtraj-doc_1.10.3-2_all.deb
 d4cb5dbbe4e9f8d893d19c0c84a177cc 10875416 debug optional python3-mdtraj-dbgsym_1.10.3-2_i386.deb
 c3ee0374c8029cfb93cc6ed3ec124e97 1404200 python optional python3-mdtraj_1.10.3-2_i386.deb
Sun Feb 16 10:09:04 UTC 2025  I: diffoscope 288 will be used to compare the two builds:
Running as unit: rb-diffoscope-i386_12-40004.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.LUHbQ27q/mdtraj_1.10.3-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.LUHbQ27q/mdtraj_1.10.3-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.LUHbQ27q/mdtraj_1.10.3-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.LUHbQ27q/b1/mdtraj_1.10.3-2_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.LUHbQ27q/b2/mdtraj_1.10.3-2_i386.changes

## close_archive (total time: 0.000s)
       0.000s     22 calls    diffoscope.comparators.xz.XzContainer
       0.000s     10 calls    diffoscope.comparators.deb.DebContainer
       0.000s     14 calls    diffoscope.comparators.tar.TarContainer
       0.000s      8 calls    diffoscope.comparators.deb.DebTarContainer

## command (total time: 69.273s)
      28.367s   2006 calls    readelf
      26.796s    234 calls    diff
      11.334s    440 calls    objdump
       1.303s      4 calls    objcopy
       1.248s     22 calls    xz
       0.188s     44 calls    strings
       0.017s      3 calls    cmp
       0.017s      3 calls    cmp (external)
       0.002s     20 calls    cmp (internal)

## compare_files (cumulative) (total time: 217.728s)
      40.570s      1 call     abc.DotChangesFile
      40.503s      2 calls    abc.DebFile
      40.372s      4 calls    abc.XzFile
      39.672s      2 calls    abc.DebDataTarFile
      39.220s      4 calls    abc.ElfFile
      16.260s     20 calls    diffoscope.comparators.elf.ElfCodeSection
       0.961s     66 calls    diffoscope.comparators.elf.ElfSection
       0.083s      2 calls    abc.TarFile
       0.036s      4 calls    diffoscope.comparators.elf.ElfStringSection
       0.020s      2 calls    diffoscope.comparators.elf.MonkeyPatchedElfSection
       0.015s      1 call     abc.TextFile
       0.013s      2 calls    abc.Md5sumsFile

## container_extract (total time: 1.630s)
       1.250s     22 calls    diffoscope.comparators.xz.XzContainer
       0.254s    284 calls    diffoscope.comparators.deb.DebTarContainer
       0.115s     26 calls    diffoscope.comparators.deb.DebContainer
       0.011s     22 calls    diffoscope.comparators.tar.TarContainer

## diff (total time: 0.358s)
       0.358s    119 calls    linediff

## has_same_content_as (total time: 0.022s)
       0.013s      2 calls    abc.DebDataTarFile
       0.005s      3 calls    abc.DebFile
       0.001s      6 calls    abc.TextFile
       0.001s      4 calls    abc.ElfFile
       0.000s      4 calls    abc.Md5sumsFile
       0.000s     66 calls    diffoscope.comparators.elf.ElfSection
       0.000s      2 calls    abc.TarFile
       0.000s      4 calls    abc.XzFile
       0.000s      1 call     diffoscope.comparators.utils.libarchive.LibarchiveSymlink
       0.000s      1 call     abc.DotChangesFile
       0.000s      1 call     diffoscope.comparators.binary.FilesystemFile
       0.000s     20 calls    diffoscope.comparators.elf.ElfCodeSection
       0.000s      4 calls    diffoscope.comparators.elf.ElfStringSection
       0.000s      2 calls    diffoscope.comparators.elf.MonkeyPatchedElfSection

## main (total time: 42.151s)
      42.150s      2 calls    outputs
       0.001s      1 call     cleanup

## open_archive (total time: 0.000s)
       0.000s     22 calls    diffoscope.comparators.xz.XzContainer
       0.000s      8 calls    diffoscope.comparators.deb.DebTarContainer
       0.000s     14 calls    diffoscope.comparators.tar.TarContainer
       0.000s     10 calls    diffoscope.comparators.deb.DebContainer

## output (total time: 1.115s)
       0.831s      1 call     html
       0.166s      1 call     text
       0.118s      1 call     json

## recognizes (total time: 1.409s)
       0.767s    920 calls    diffoscope.comparators.utils.archive.ArchiveMember
       0.401s   2206 calls    diffoscope.comparators.utils.libarchive.LibarchiveMember
       0.142s     12 calls    diffoscope.comparators.binary.FilesystemFile
       0.100s    324 calls    diffoscope.comparators.debian.DebControlMember

## specialize (total time: 0.659s)
       0.659s    119 calls    specialize
Finished with result: success
Main processes terminated with: code=exited/status=1
Service runtime: 42.461s
CPU time consumed: 54.915s
Sun Feb 16 10:09:47 UTC 2025  W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate.
Sun Feb 16 10:09:47 UTC 2025  E: mdtraj failed to build reproducibly in trixie on i386.
Sun Feb 16 10:09:53 UTC 2025  I: Submitting .buildinfo files to external archives:
Sun Feb 16 10:09:53 UTC 2025  I: Submitting 16K	b1/mdtraj_1.10.3-2_i386.buildinfo.asc
Sun Feb 16 10:09:54 UTC 2025  I: Submitting 16K	b2/mdtraj_1.10.3-2_i386.buildinfo.asc
Sun Feb 16 10:09:54 UTC 2025  I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sun Feb 16 10:09:54 UTC 2025  I: Done submitting .buildinfo files.
Sun Feb 16 10:09:54 UTC 2025  I: Removing signed mdtraj_1.10.3-2_i386.buildinfo.asc files:
removed './b1/mdtraj_1.10.3-2_i386.buildinfo.asc'
removed './b2/mdtraj_1.10.3-2_i386.buildinfo.asc'