I: pbuilder: network access will be disabled during build
I: Current time: Sun Mar  9 00:39:26 -12 2025
I: pbuilder-time-stamp: 1741523966
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: 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/3264135/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='amd64'
  DEBIAN_FRONTEND='noninteractive'
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 '
  DISTRIBUTION='unstable'
  HOME='/root'
  HOST_ARCH='amd64'
  IFS=' 	
  '
  INVOCATION_ID='57d09cdc33c44f7abf821a9887ae150b'
  LANG='C'
  LANGUAGE='en_US:en'
  LC_ALL='C'
  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='3264135'
  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.uE2gtBhR/pbuilderrc_P9Sd --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.uE2gtBhR/b1 --logfile b1/build.log mdtraj_1.10.3-2.dsc'
  SUDO_GID='111'
  SUDO_UID='106'
  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 ionos11-amd64 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 Mar  4 11:20 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/3264135/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: amd64
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 ... 19783 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} libnetcdf22{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnorm1t64{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} libpython3.13{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} 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-numpy-dev{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} python3.13{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 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-numba 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, 297 newly installed, 0 to remove and 0 not upgraded.
Need to get 223 MB of archives. After unpacking 1042 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 fonts-lato all 2.015-1 [2780 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B]
Get: 3 http://deb.debian.org/debian unstable/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B]
Get: 4 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-7 [878 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0050 [42.7 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 libdebuginfod-common all 0.192-4 [23.7 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.2-2 [27.1 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB]
Get: 14 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-2 [259 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.2-1 [745 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.1 kB]
Get: 22 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.2-2 [28.1 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-4 [139 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-2 [160 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.3+ds-4 [5085 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.4.1-1 [1427 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20241223 [164 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 33 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 35 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 36 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 37 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
Get: 38 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 39 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 40 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-7 [294 kB]
Get: 41 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 42 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 43 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB]
Get: 44 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 45 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB]
Get: 46 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB]
Get: 47 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.47-1 [282 kB]
Get: 48 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB]
Get: 49 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 50 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 51 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB]
Get: 52 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB]
Get: 53 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB]
Get: 54 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB]
Get: 55 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB]
Get: 56 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB]
Get: 57 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB]
Get: 58 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB]
Get: 59 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB]
Get: 60 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB]
Get: 61 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+24 [217 kB]
Get: 62 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB]
Get: 63 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB]
Get: 64 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [591 kB]
Get: 65 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-8 [5984 B]
Get: 66 http://deb.debian.org/debian unstable/main amd64 cython3 amd64 3.0.11+dfsg-2+b1 [2504 kB]
Get: 67 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 68 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB]
Get: 69 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 70 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 71 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 72 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 73 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 74 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 75 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 76 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 77 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB]
Get: 78 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 79 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 80 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 81 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Get: 82 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250308 [115 kB]
Get: 83 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB]
Get: 84 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB]
Get: 85 http://deb.debian.org/debian unstable/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB]
Get: 86 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.3-1 [190 kB]
Get: 87 http://deb.debian.org/debian unstable/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB]
Get: 88 http://deb.debian.org/debian unstable/main amd64 libdw1t64 amd64 0.192-4 [255 kB]
Get: 89 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.83.5-1 [1513 kB]
Get: 90 http://deb.debian.org/debian unstable/main amd64 libbabeltrace1 amd64 1.5.11-4+b2 [176 kB]
Get: 91 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB]
Get: 92 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get: 93 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB]
Get: 94 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB]
Get: 95 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB]
Get: 96 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
Get: 97 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB]
Get: 98 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get: 99 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB]
Get: 100 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB]
Get: 101 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB]
Get: 102 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB]
Get: 103 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB]
Get: 104 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get: 105 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB]
Get: 106 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB]
Get: 107 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB]
Get: 108 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get: 109 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get: 110 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get: 111 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.12.1-3 [365 kB]
Get: 112 http://deb.debian.org/debian unstable/main amd64 libjson-c5 amd64 0.18+ds-1 [46.0 kB]
Get: 113 http://deb.debian.org/debian unstable/main amd64 libdebuginfod1t64 amd64 0.192-4 [32.4 kB]
Get: 114 http://deb.debian.org/debian unstable/main amd64 libipt2 amd64 2.1.2-1 [47.8 kB]
Get: 115 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.2-1 [2151 kB]
Get: 116 http://deb.debian.org/debian unstable/main amd64 libsource-highlight-common all 3.1.9-4.3 [77.5 kB]
Get: 117 http://deb.debian.org/debian unstable/main amd64 libsource-highlight4t64 amd64 3.1.9-4.3+b1 [335 kB]
Get: 118 http://deb.debian.org/debian unstable/main amd64 gdb amd64 16.2-2 [3992 kB]
Get: 119 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB]
Get: 120 http://deb.debian.org/debian unstable/main amd64 libsnappy1v5 amd64 1.2.1-1+b1 [29.6 kB]
Get: 121 http://deb.debian.org/debian unstable/main amd64 libblosc1 amd64 1.21.5+ds-1+b2 [49.5 kB]
Get: 122 http://deb.debian.org/debian unstable/main amd64 libblosc2-4 amd64 2.17.0+ds-1 [193 kB]
Get: 123 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.12.1-3 [369 kB]
Get: 124 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB]
Get: 125 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB]
Get: 126 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB]
Get: 127 http://deb.debian.org/debian unstable/main amd64 libgpg-error0 amd64 1.51-3 [82.2 kB]
Get: 128 http://deb.debian.org/debian unstable/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB]
Get: 129 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB]
Get: 130 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB]
Get: 131 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B]
Get: 132 http://deb.debian.org/debian unstable/main amd64 libhdf5-310 amd64 1.14.5+repack-3 [1344 kB]
Get: 133 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [69.3 kB]
Get: 134 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB]
Get: 135 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB]
Get: 136 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB]
Get: 137 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 138 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get: 139 http://deb.debian.org/debian unstable/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB]
Get: 140 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 141 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB]
Get: 142 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB]
Get: 143 http://deb.debian.org/debian unstable/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB]
Get: 144 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB]
Get: 145 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB]
Get: 146 http://deb.debian.org/debian unstable/main amd64 liblua5.4-0 amd64 5.4.7-1+b2 [147 kB]
Get: 147 http://deb.debian.org/debian unstable/main amd64 liblzo2-2 amd64 2.10-3+b1 [55.1 kB]
Get: 148 http://deb.debian.org/debian unstable/main amd64 libnetcdf22 amd64 1:4.9.3-1 [517 kB]
Get: 149 http://deb.debian.org/debian unstable/main amd64 libnorm1t64 amd64 1.5.9+dfsg-3.1+b2 [221 kB]
Get: 150 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB]
Get: 151 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-1 [204 kB]
Get: 152 http://deb.debian.org/debian unstable/main amd64 libpgm-5.3-0t64 amd64 5.3.128~dfsg-2.1+b1 [162 kB]
Get: 153 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get: 154 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.2-1 [5005 kB]
Get: 155 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.2-2 [10.3 kB]
Get: 156 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.13.2-2 [1068 B]
Get: 157 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB]
Get: 158 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB]
Get: 159 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB]
Get: 160 http://deb.debian.org/debian unstable/main amd64 libsodium23 amd64 1.0.18-1+b2 [165 kB]
Get: 161 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB]
Get: 162 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB]
Get: 163 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB]
Get: 164 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB]
Get: 165 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB]
Get: 166 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB]
Get: 167 http://deb.debian.org/debian unstable/main amd64 libzmq5 amd64 4.3.5-1+b3 [283 kB]
Get: 168 http://deb.debian.org/debian unstable/main amd64 pandoc-data all 3.1.11.1-3 [459 kB]
Get: 169 http://deb.debian.org/debian unstable/main amd64 pandoc amd64 3.1.11.1+ds-2 [26.4 MB]
Get: 170 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.17.0-1 [6050 kB]
Get: 171 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.8.3-7 [2735 kB]
Get: 172 http://deb.debian.org/debian unstable/main amd64 python-tables-data all 3.10.2-2 [47.3 kB]
Get: 173 http://deb.debian.org/debian unstable/main amd64 python-tinycss2-common all 1.4.0-1 [44.8 kB]
Get: 174 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB]
Get: 175 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.2-2 [1044 B]
Get: 176 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.2-1 [507 kB]
Get: 177 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.2-2 [26.1 kB]
Get: 178 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.13.2-2 [1064 B]
Get: 179 http://deb.debian.org/debian unstable/main amd64 python3-asttokens all 3.0.0-1 [20.1 kB]
Get: 180 http://deb.debian.org/debian unstable/main amd64 python3-attr all 25.1.0-1 [68.7 kB]
Get: 181 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 182 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.17.0-1 [117 kB]
Get: 183 http://deb.debian.org/debian unstable/main amd64 python3-webencodings all 0.5.1-5 [11.1 kB]
Get: 184 http://deb.debian.org/debian unstable/main amd64 python3-html5lib all 1.2-1 [92.2 kB]
Get: 185 http://deb.debian.org/debian unstable/main amd64 python3-bleach all 6.2.0-1 [51.2 kB]
Get: 186 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b7 [320 kB]
Get: 187 http://deb.debian.org/debian unstable/main amd64 python3-soupsieve all 2.6-1 [38.3 kB]
Get: 188 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 189 http://deb.debian.org/debian unstable/main amd64 python3-bs4 all 4.13.3-1 [166 kB]
Get: 190 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B]
Get: 191 http://deb.debian.org/debian unstable/main amd64 python3-cffi-backend amd64 1.17.1-2+b2 [93.6 kB]
Get: 192 http://deb.debian.org/debian unstable/main amd64 python3-cftime amd64 1.6.4-2 [216 kB]
Get: 193 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB]
Get: 194 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.1-1+b1 [125 kB]
Get: 195 http://deb.debian.org/debian unstable/main amd64 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB]
Get: 196 http://deb.debian.org/debian unstable/main amd64 python3-comm all 0.2.1-1 [8104 B]
Get: 197 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.3.1-1+b1 [216 kB]
Get: 198 http://deb.debian.org/debian unstable/main amd64 python3-coverage amd64 7.6.0+dfsg1-2+b2 [175 kB]
Get: 199 http://deb.debian.org/debian unstable/main amd64 python3-cpuinfo all 9.0.0+git20221119-3 [23.5 kB]
Get: 200 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-1 [9496 B]
Get: 201 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB]
Get: 202 http://deb.debian.org/debian unstable/main amd64 python3-debugpy amd64 1.8.8+ds-2 [1105 kB]
Get: 203 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.1.1-5 [15.1 kB]
Get: 204 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB]
Get: 205 http://deb.debian.org/debian unstable/main amd64 python3-roman all 5.0-1 [10.6 kB]
Get: 206 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB]
Get: 207 http://deb.debian.org/debian unstable/main amd64 python3-executing all 2.2.0-0.1 [24.5 kB]
Get: 208 http://deb.debian.org/debian unstable/main amd64 python3-fastjsonschema all 2.21.1-1 [22.4 kB]
Get: 209 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB]
Get: 210 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-7 [95.2 kB]
Get: 211 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 5.3.1-1+b1 [1288 kB]
Get: 212 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.4.0+dfsg-1+b1 [25.5 kB]
Get: 213 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.14.1-4+b1 [17.1 MB]
Get: 214 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB]
Get: 215 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.13.3-5 [4148 kB]
Get: 216 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB]
Get: 217 http://deb.debian.org/debian unstable/main amd64 unicode-data all 15.1.0-1 [8547 kB]
Get: 218 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.55.3-2+b1 [1448 kB]
Get: 219 http://deb.debian.org/debian unstable/main amd64 python3-gsd amd64 3.4.2-2+b1 [209 kB]
Get: 220 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.10-1 [42.0 kB]
Get: 221 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B]
Get: 222 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 223 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB]
Get: 224 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 225 http://deb.debian.org/debian unstable/main amd64 python3-parso all 0.8.4-1 [67.8 kB]
Get: 226 http://deb.debian.org/debian unstable/main amd64 python3-typeshed all 0.0~git20241223.ea91db2-1 [1530 kB]
Get: 227 http://deb.debian.org/debian unstable/main amd64 python3-jedi all 0.19.1+ds1-1 [691 kB]
Get: 228 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib-inline all 0.1.6-2 [8652 B]
Get: 229 http://deb.debian.org/debian unstable/main amd64 python3-wcwidth all 0.2.13+dfsg1-1 [24.9 kB]
Get: 230 http://deb.debian.org/debian unstable/main amd64 python3-prompt-toolkit all 3.0.50-1 [278 kB]
Get: 231 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB]
Get: 232 http://deb.debian.org/debian unstable/main amd64 python3-pure-eval all 0.2.3-1 [11.2 kB]
Get: 233 http://deb.debian.org/debian unstable/main amd64 python3-stack-data all 0.6.3-1 [21.6 kB]
Get: 234 http://deb.debian.org/debian unstable/main amd64 python3-ptyprocess all 0.7.0-6 [14.5 kB]
Get: 235 http://deb.debian.org/debian unstable/main amd64 python3-pexpect all 4.9-3 [55.6 kB]
Get: 236 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B]
Get: 237 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 238 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.8.0-1 [222 kB]
Get: 239 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 240 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 241 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.8.0-1 [724 kB]
Get: 242 http://deb.debian.org/debian unstable/main amd64 python3-ipython all 8.30.0-2 [568 kB]
Get: 243 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-core all 5.7.2-5 [35.3 kB]
Get: 244 http://deb.debian.org/debian unstable/main amd64 python3-psutil amd64 5.9.8-2 [225 kB]
Get: 245 http://deb.debian.org/debian unstable/main amd64 python3-tornado amd64 6.4.2-1 [349 kB]
Get: 246 http://deb.debian.org/debian unstable/main amd64 python3-zmq amd64 26.2.1-1+b1 [182 kB]
Get: 247 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-client all 8.6.3-2 [92.4 kB]
Get: 248 http://deb.debian.org/debian unstable/main amd64 python3-nest-asyncio all 1.5.4-1 [6248 B]
Get: 249 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB]
Get: 250 http://deb.debian.org/debian unstable/main amd64 python3-ipykernel all 6.29.5-2 [102 kB]
Get: 251 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b3 [14.0 kB]
Get: 252 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.5-2 [107 kB]
Get: 253 http://deb.debian.org/debian unstable/main amd64 python3-joblib all 1.4.2-3 [216 kB]
Get: 254 http://deb.debian.org/debian unstable/main amd64 python3-rpds-py amd64 0.21.0-2+b1 [257 kB]
Get: 255 http://deb.debian.org/debian unstable/main amd64 python3-referencing all 0.35.1-2 [23.5 kB]
Get: 256 http://deb.debian.org/debian unstable/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B]
Get: 257 http://deb.debian.org/debian unstable/main amd64 python3-jsonschema all 4.19.2-6 [71.4 kB]
Get: 258 http://deb.debian.org/debian unstable/main amd64 python3-jupyterlab-pygments all 0.2.2-3 [6096 B]
Get: 259 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.7-3+b1 [62.0 kB]
Get: 260 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 11.1.0-5+b1 [513 kB]
Get: 261 http://deb.debian.org/debian unstable/main amd64 python3.13-tk amd64 3.13.2-1 [103 kB]
Get: 262 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.13.2-1 [9516 B]
Get: 263 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 11.1.0-5+b1 [81.6 kB]
Get: 264 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB]
Get: 265 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.8.3-7+b1 [23.0 MB]
Get: 266 http://deb.debian.org/debian unstable/main amd64 python3-mistune all 3.0.2-2 [33.2 kB]
Get: 267 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 8.1.3-5 [617 kB]
Get: 268 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.3.0-1 [114 kB]
Get: 269 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.3+dfsg-4 [72.1 kB]
Get: 270 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB]
Get: 271 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 8.1.3-5 [468 kB]
Get: 272 http://deb.debian.org/debian unstable/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1023 kB]
Get: 273 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B]
Get: 274 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [29.7 kB]
Get: 275 http://deb.debian.org/debian unstable/main amd64 python3-msmb-theme all 1.2.0-4 [33.8 kB]
Get: 276 http://deb.debian.org/debian unstable/main amd64 python3-nbformat all 5.9.1-1 [45.1 kB]
Get: 277 http://deb.debian.org/debian unstable/main amd64 python3-nbclient all 0.8.0-2 [62.2 kB]
Get: 278 http://deb.debian.org/debian unstable/main amd64 python3-tinycss2 all 1.4.0-1 [24.9 kB]
Get: 279 http://deb.debian.org/debian unstable/main amd64 python3-pandocfilters all 1.5.1-1 [23.7 kB]
Get: 280 http://deb.debian.org/debian unstable/main amd64 python3-nbconvert all 7.16.6-1 [160 kB]
Get: 281 http://deb.debian.org/debian unstable/main amd64 python3-nbsphinx all 0.9.5+ds-1 [39.9 kB]
Get: 282 http://deb.debian.org/debian unstable/main amd64 python3-nbsphinx-link all 1.3.0-4 [6264 B]
Get: 283 http://deb.debian.org/debian unstable/main amd64 python3-netcdf4 amd64 1.7.2-1+b4 [622 kB]
Get: 284 http://deb.debian.org/debian unstable/main amd64 python3-networkx all 3.2.1-5 [13.0 MB]
Get: 285 http://deb.debian.org/debian unstable/main amd64 python3-numexpr amd64 2.10.2-1+b2 [129 kB]
Get: 286 http://deb.debian.org/debian unstable/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB]
Get: 287 http://deb.debian.org/debian unstable/main amd64 python3-numpydoc all 1.8.0-1 [51.4 kB]
Get: 288 http://deb.debian.org/debian unstable/main amd64 python3-pytz all 2025.1-3 [150 kB]
Get: 289 http://deb.debian.org/debian unstable/main amd64 python3-tz all 2025.1-3 [4004 B]
Get: 290 http://deb.debian.org/debian unstable/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-8+b1 [4517 kB]
Get: 291 http://deb.debian.org/debian unstable/main amd64 python3-pandas all 2.2.3+dfsg-8 [3097 kB]
Get: 292 http://deb.debian.org/debian unstable/main amd64 python3-threadpoolctl all 3.1.0-1 [21.2 kB]
Get: 293 http://deb.debian.org/debian unstable/main amd64 python3-sklearn-lib amd64 1.4.2+dfsg-7+b3 [3879 kB]
Get: 294 http://deb.debian.org/debian unstable/main amd64 python3-sklearn all 1.4.2+dfsg-7 [2248 kB]
Get: 295 http://deb.debian.org/debian unstable/main amd64 python3-tables-lib amd64 3.10.2-2+b1 [503 kB]
Get: 296 http://deb.debian.org/debian unstable/main amd64 python3-tables all 3.10.2-2 [353 kB]
Get: 297 http://deb.debian.org/debian unstable/main amd64 python3-versioneer all 0.29-1 [43.0 kB]
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Reading package lists...
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 -> 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 amd64
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 3.13
I: pybuild base:311: python3.13 setup.py clean 
Using built-in specs.
COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-linux-gnu/14/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-17' --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=x86_64-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-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 14.2.0 (Debian 14.2.0-17) 
/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-x86_64' 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 3.13
I: pybuild base:311: python3.13 setup.py config 
Using built-in specs.
COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-linux-gnu/14/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-17' --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=x86_64-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-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 14.2.0 (Debian 14.2.0-17) 
/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 3.13
I: pybuild base:311: /usr/bin/python3 setup.py build 
Using built-in specs.
COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-linux-gnu/14/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-17' --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=x86_64-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-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 14.2.0 (Debian 14.2.0-17) 
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/__init__.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/io.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/core
copying mdtraj/core/__init__.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
copying mdtraj/core/topology.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/element.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
creating /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/hbond.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/thermodynamic_properties.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
copying mdtraj/geometry/shape.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/rg.py -> /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/internal.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/angle.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/contact.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
creating /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
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
creating /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/__init__.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/lh5.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/psf.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/lammpstrj.py -> /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/prmtop.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
copying mdtraj/formats/mol2.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/hoomdxml.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/amberrst.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/gsd.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/reporters
copying mdtraj/reporters/__init__.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
copying mdtraj/reporters/dcdreporter.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/hdf5reporter.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/scalar_couplings.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
creating /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/delay_import.py -> /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/validation.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/unitcell.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/rotation.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/testing
copying mdtraj/testing/__init__.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/testing.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/formats/pdb
copying mdtraj/formats/pdb/__init__.py -> /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
creating /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/unit.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
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/quantity.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/basedimension.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_definitions.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/prefix.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
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-x86_64-cpython-313/mdtraj/formats/xtc/src
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/xtc.c:1263:
/usr/lib/x86_64-linux-gnu/python3-numpy/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 " \
      |  ^~~~~~~
x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/xtc.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/xtc.cpython-313-x86_64-linux-gnu.so
building 'mdtraj.formats.trr' extension
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/trr.c:1265:
/usr/lib/x86_64-linux-gnu/python3-numpy/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 " \
      |  ^~~~~~~
x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/trr.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/trr.cpython-313-x86_64-linux-gnu.so
building 'mdtraj.formats.dcd' extension
creating build/temp.linux-x86_64-cpython-313/mdtraj/formats/dcd
creating build/temp.linux-x86_64-cpython-313/mdtraj/formats/dcd/src
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dcd/dcd.c:1260:
/usr/lib/x86_64-linux-gnu/python3-numpy/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 " \
      |  ^~~~~~~
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/formats/dcd/dcd.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dcd.cpython-313-x86_64-linux-gnu.so
building 'mdtraj.formats.dtr' extension
creating build/temp.linux-x86_64-cpython-313/mdtraj/formats/dtr
creating build/temp.linux-x86_64-cpython-313/mdtraj/formats/dtr/src
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dtr/dtr.cpp:1279:
/usr/lib/x86_64-linux-gnu/python3-numpy/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 " \
      |  ^~~~~~~
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-x86_64-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:487:27: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=]
  487 |             printf("size %d framesize %d\n\n",
      |                          ~^
      |                           |
      |                           int
      |                          %ld
  488 |                     keys[i].size(), m_framesize);
      |                     ~~~~~~~~~~~~~~
      |                                 |
      |                                 uint64_t {aka 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 unsigned int'} [-Wformat=]
  487 |             printf("size %d framesize %d\n\n",
      |                                       ~^
      |                                        |
      |                                        int
      |                                       %ld
  488 |                     keys[i].size(), m_framesize);
      |                                     ~~~~~~~~~~~
      |                                     |
      |                                     uint64_t {aka 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/x86_64-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/x86_64-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/x86_64-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/x86_64-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 ());
      |                                   ~~~~~~~~~~~~~~~~~
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/formats/dtr/dtr.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dtr.cpython-313-x86_64-linux-gnu.so
building 'mdtraj._rmsd' extension
creating build/temp.linux-x86_64-cpython-313/mdtraj/rmsd
creating build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/_rmsd.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/center.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/rotation.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_rmsd.cpython-313-x86_64-linux-gnu.so
building 'mdtraj._lprmsd' extension
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-x86_64-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/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5,
                 from mdtraj/rmsd/_lprmsd.cpp:1307:
/usr/lib/x86_64-linux-gnu/python3-numpy/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 " \
      |  ^~~~~~~
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/_lprmsd.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/Munkres.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/center.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/fancy_index.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/rotation.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_lprmsd.cpython-313-x86_64-linux-gnu.so
building 'mdtraj.core.lib.libtheobald' extension
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -msse2 -mssse3 -O3 -funroll-loops --std=c++11
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/center.o -msse2 -mssse3 -O3 -funroll-loops --std=c++11
x86_64-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-x86_64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/center.o
building 'mdtraj.geometry._geometry' extension
creating build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-x86_64-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/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5,
                 from mdtraj/geometry/src/_geometry.cpp:1289:
/usr/lib/x86_64-linux-gnu/python3-numpy/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 " \
      |  ^~~~~~~
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/_geometry.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/dssp.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/geometry.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/sasa.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/_geometry.cpython-313-x86_64-linux-gnu.so
building 'mdtraj.geometry.drid' extension
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/drid.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/drid.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/geometry/drid.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/dridkernels.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/moments.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/drid.cpython-313-x86_64-linux-gnu.so
building 'mdtraj.geometry.neighbors' extension
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/geometry/neighbors.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/neighbors.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighbors.cpython-313-x86_64-linux-gnu.so
building 'mdtraj.geometry.neighborlist' extension
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/geometry/neighborlist.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/neighborlist.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighborlist.cpython-313-x86_64-linux-gnu.so
   dh_auto_test -O--buildsystem=pybuild
	pybuild --test -i python{version} -p 3.13
I: pybuild base:311: cd /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build; python3.13 -m unittest discover -v 

----------------------------------------------------------------------
Ran 0 tests in 0.000s

NO TESTS RAN
	rm -fr -- /tmp/dh-xdg-rundir-1YnmtW8a
   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 3.13 --dest-dir=/build/reproducible-path/mdtraj-1.10.3/debian/tmp
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/x86_64-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-linux-gnu/14/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-17' --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=x86_64-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-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 14.2.0 (Debian 14.2.0-17) 
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:79: 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
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/xtc.c:1263:
/usr/lib/x86_64-linux-gnu/python3-numpy/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 " \
      |  ^~~~~~~
x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/xtc.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/xtc.cpython-313-x86_64-linux-gnu.so
building 'mdtraj.formats.trr' extension
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/trr.c:1265:
/usr/lib/x86_64-linux-gnu/python3-numpy/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 " \
      |  ^~~~~~~
x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/xtc/trr.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/trr.cpython-313-x86_64-linux-gnu.so
building 'mdtraj.formats.dcd' extension
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dcd/dcd.c:1260:
/usr/lib/x86_64-linux-gnu/python3-numpy/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 " \
      |  ^~~~~~~
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/formats/dcd/dcd.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dcd.cpython-313-x86_64-linux-gnu.so
building 'mdtraj.formats.dtr' extension
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dtr/dtr.cpp:1279:
/usr/lib/x86_64-linux-gnu/python3-numpy/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 " \
      |  ^~~~~~~
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-x86_64-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:487:27: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=]
  487 |             printf("size %d framesize %d\n\n",
      |                          ~^
      |                           |
      |                           int
      |                          %ld
  488 |                     keys[i].size(), m_framesize);
      |                     ~~~~~~~~~~~~~~
      |                                 |
      |                                 uint64_t {aka 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 unsigned int'} [-Wformat=]
  487 |             printf("size %d framesize %d\n\n",
      |                                       ~^
      |                                        |
      |                                        int
      |                                       %ld
  488 |                     keys[i].size(), m_framesize);
      |                                     ~~~~~~~~~~~
      |                                     |
      |                                     uint64_t {aka 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/x86_64-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/x86_64-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/x86_64-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/x86_64-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 ());
      |                                   ~~~~~~~~~~~~~~~~~
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/formats/dtr/dtr.o build/temp.linux-x86_64-cpython-313/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dtr.cpython-313-x86_64-linux-gnu.so
building 'mdtraj._rmsd' extension
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/_rmsd.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/center.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/rotation.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_rmsd.cpython-313-x86_64-linux-gnu.so
building 'mdtraj._lprmsd' extension
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-x86_64-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/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5,
                 from mdtraj/rmsd/_lprmsd.cpp:1307:
/usr/lib/x86_64-linux-gnu/python3-numpy/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 " \
      |  ^~~~~~~
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/_lprmsd.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/Munkres.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/center.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/fancy_index.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/rotation.o build/temp.linux-x86_64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_lprmsd.cpython-313-x86_64-linux-gnu.so
building 'mdtraj.geometry._geometry' extension
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-x86_64-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/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5,
                 from mdtraj/geometry/src/_geometry.cpp:1289:
/usr/lib/x86_64-linux-gnu/python3-numpy/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 " \
      |  ^~~~~~~
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/_geometry.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/dssp.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/geometry.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/sasa.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/_geometry.cpython-313-x86_64-linux-gnu.so
building 'mdtraj.geometry.drid' extension
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/drid.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/drid.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/geometry/drid.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/dridkernels.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/moments.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/drid.cpython-313-x86_64-linux-gnu.so
building 'mdtraj.geometry.neighbors' extension
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/neighbors.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/geometry/neighbors.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/neighbors.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighbors.cpython-313-x86_64-linux-gnu.so
building 'mdtraj.geometry.neighborlist' extension
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/neighborlist.o -fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-x86_64-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
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/mdtraj/geometry/neighborlist.o build/temp.linux-x86_64-cpython-313/mdtraj/geometry/src/neighborlist.o -L/usr/lib/x86_64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighborlist.cpython-313-x86_64-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/__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/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/trajectory.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/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/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/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/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/element.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__/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__/__init__.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__/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/residue_names.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/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/drid.cpython-313-x86_64-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/neighborlist.cpython-313-x86_64-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/_geometry.cpython-313-x86_64-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/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/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/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/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/shape.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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/__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/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/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/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/internal.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/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/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/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/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/neighbors.cpython-313-x86_64-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/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
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
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__
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
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/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/__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/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/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/trr.cpython-313-x86_64-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/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/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/xtc.cpython-313-x86_64-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-x86_64-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/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/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/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/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/xyzfile.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-x86_64-linux-gnu.so -> /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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/__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/__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__/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__/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/mol2.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/__init__.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/pdbfile.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/pdbstructure.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__
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/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/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/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/amberrst.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
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/_version.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/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-x86_64-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/__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__
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__
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/__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/xtcreporter.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__/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__/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__/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__/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__/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__/__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/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/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
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
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/scalar_couplings.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
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__
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/__init__.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/delay_import.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/__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/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/constants.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/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/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/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/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/basedimension.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__/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__/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__/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__/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__/__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/__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__/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__/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/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_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/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/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/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/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/validation.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/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/unitcell.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__/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__/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__/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__/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__/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/__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__/__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__/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/contextmanagers.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
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/__init__.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
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__/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/__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/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/docstrings.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/_lprmsd.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj
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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/__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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/_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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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_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/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/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/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/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/validation.py to validation.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/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/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/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/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/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/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/docstrings.py to docstrings.cpython-313.pyc
running install_egg_info
running egg_info
creating mdtraj.egg-info
writing mdtraj.egg-info/PKG-INFO
writing dependency_links to mdtraj.egg-info/dependency_links.txt
writing entry points to mdtraj.egg-info/entry_points.txt
writing requirements to mdtraj.egg-info/requires.txt
writing top-level names to mdtraj.egg-info/top_level.txt
writing manifest file 'mdtraj.egg-info/SOURCES.txt'
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/x86_64-linux-gnu/python3-numpy/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
reading sources... [  1%] analysis
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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)
----------------------- [docutils]
looking for now-outdated files... none found
pickling environment... WARNING: cannot cache unpickable configuration value: 'nbsphinx_custom_formats' (because it contains a function, class, or module object) [config.cache]
done
checking consistency... /build/reproducible-path/mdtraj-1.10.3/docs/building_docs.rst: WARNING: document isn't included in any toctree
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	ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.woff2
	ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff2
	ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.eot debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.eot
	ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.woff2
	ln -sf ../../../../../sphinx_rtd_theme/static/css/badge_only.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css
	ln -sf ../../../../../sphinx_rtd_theme/static/css/theme.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css
	ln -sf ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/searchtools.js
	ln -sf ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/sphinx_highlight.js
	ln -sf ../../../../javascript/sphinxdoc/1.0/doctools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js
	ln -sf ../../../../javascript/sphinxdoc/1.0/language_data.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/language_data.js
	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/python3-mdtraj/usr/share/doc/python3-mdtraj
	install -p -m0644 debian/.debhelper/generated/python3-mdtraj/dh_installchangelogs.dch.trimmed debian/python3-mdtraj/usr/share/doc/python3-mdtraj/changelog.Debian
	install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc
	install -p -m0644 debian/.debhelper/generated/python-mdtraj-doc/dh_installchangelogs.dch.trimmed debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/changelog.Debian
   dh_installexamples -O--buildsystem=pybuild
dh_installexamples: warning: Cannot auto-detect main package for python-mdtraj-doc.  If the default is wrong, please use --doc-main-package
	install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/1vii_3frames.pdb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/ala2.h5 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/atom-selection.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/centroids.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/clustering.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/data debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/hbonds.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/iterload.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/native-contact.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/nmr.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/principal-components.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/ramachandran-plot.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/rmsd-benchmark.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/rmsd-drift.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/simulation-with-openmm.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/solvent-accessible-surface-area.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/test_examples.py debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/two-pass-clustering.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
   dh_installman -O--buildsystem=pybuild
	install -m0755 -d debian/python3-mdtraj/usr/share/man/man1/
	install -p -m0644 ./debian/mdconvert-mdtraj.1 debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1
	install -m0755 -d debian/python3-mdtraj/usr/share/man/man1/
	install -p -m0644 ./debian/mdinspect.1 debian/python3-mdtraj/usr/share/man/man1/mdinspect.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/python3-mdtraj/usr/share/man/man1/mdinspect.1
	mv debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1.dh-new debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1
	chmod 0644 -- debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1
	mv debian/python3-mdtraj/usr/share/man/man1/mdinspect.1.dh-new debian/python3-mdtraj/usr/share/man/man1/mdinspect.1
	chmod 0644 -- debian/python3-mdtraj/usr/share/man/man1/mdinspect.1
   dh_python3 -O--buildsystem=pybuild
D: dh_python3 dh_python3:180: version: 6.20250308
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: 3.13 (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/python3.13/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('3.13')}, '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-netcdf4', 'python3-numpy', 'python3-packaging', 'python3-scipy', 'python3 (>= 3.13~)', 'python3:any', 'python3 (<< 3.14)', 'python3-pyparsing'}; 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
Possible precedence issue with control flow operator (return) at /usr/bin/dh_numpy3 line 57.
	mv debian/python3-mdtraj.substvars.new debian/python3-mdtraj.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/theme.css
	ln -s ../../../../../sphinx_rtd_theme/static/css/theme.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css
	ln -s ../../../../../sphinx_rtd_theme/static/css/badge_only.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/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/fontawesome-webfont.eot
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.eot debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.eot
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/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-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/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-Italic.ttf
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.ttf
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-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.woff
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.ttf
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.ttf
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.ttf
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.ttf
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Bold.woff2
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Bold.woff2
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Regular.woff2
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Regular.woff2
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.svg
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.svg debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.svg
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/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/searchtools.js
	ln -s ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/searchtools.js
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/sphinx_highlight.js
	ln -s ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/sphinx_highlight.js
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js
	ln -s ../../../../javascript/sphinxdoc/1.0/doctools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/language_data.js
	ln -s ../../../../javascript/sphinxdoc/1.0/language_data.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/language_data.js
   dh_strip_nondeterminism -O--buildsystem=pybuild
	Using 1739273589 as canonical time
	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/_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_clustering_11_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/plus.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/minus.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_pca_12_0.png using File::StripNondeterminism::handlers::png
	Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_pca_9_0.png using File::StripNondeterminism::handlers::png
	Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_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_ramachandran-plot_7_1.png using File::StripNondeterminism::handlers::png
	Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_hbonds_9_1.png using File::StripNondeterminism::handlers::png
   dh_compress -O--buildsystem=pybuild
	cd debian/python3-mdtraj
	cd debian/python-mdtraj-doc
	chmod a-x usr/share/doc/python3-mdtraj/changelog.Debian usr/share/man/man1/mdconvert-mdtraj.1 usr/share/man/man1/mdinspect.1
	gzip -9nf usr/share/doc/python3-mdtraj/changelog.Debian usr/share/man/man1/mdconvert-mdtraj.1 usr/share/man/man1/mdinspect.1
	cd '/build/reproducible-path/mdtraj-1.10.3'
	chmod a-x usr/share/doc/python-mdtraj-doc/changelog.Debian usr/share/doc/python-mdtraj-doc/html/_static/example-trajectoryview-data.json usr/share/doc/python-mdtraj-doc/html/_static/mdtraj_logo.xcf usr/share/doc/python-mdtraj-doc/html/notebook-examples/atom-selection.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/clustering.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/hbonds.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/iterload.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/native-contact.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/openmm.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/pca.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/ramachandran-plot.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/rmsd-benchmark.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/rmsd-drift.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/solvent-accessible-surface-area.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/two-pass-clustering.ipynb
	gzip -9nf usr/share/doc/python-mdtraj-doc/changelog.Debian usr/share/doc/python-mdtraj-doc/html/_static/example-trajectoryview-data.json usr/share/doc/python-mdtraj-doc/html/_static/mdtraj_logo.xcf usr/share/doc/python-mdtraj-doc/html/notebook-examples/atom-selection.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/clustering.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/hbonds.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/iterload.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/native-contact.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/openmm.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/pca.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/ramachandran-plot.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/rmsd-benchmark.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/rmsd-drift.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/solvent-accessible-surface-area.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/two-pass-clustering.ipynb
	cd '/build/reproducible-path/mdtraj-1.10.3'
   dh_fixperms -O--buildsystem=pybuild
	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 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/python3-mdtraj/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-mdtraj/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/python-mdtraj-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/python-mdtraj-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/python3-mdtraj/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/python3-mdtraj/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/python-mdtraj-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/python3-mdtraj -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/python-mdtraj-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/python3-mdtraj/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
	find debian/python3-mdtraj/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
   dh_missing -O--buildsystem=pybuild
   dh_dwz -a -O--buildsystem=pybuild
	install -m0755 -d debian/python3-mdtraj/usr/lib/debug/.dwz/x86_64-linux-gnu
	dwz -mdebian/python3-mdtraj/usr/lib/debug/.dwz/x86_64-linux-gnu/python3-mdtraj.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/python3-mdtraj.debug -- debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-x86_64-linux-gnu.so
	objcopy --compress-debug-sections debian/python3-mdtraj/usr/lib/debug/.dwz/x86_64-linux-gnu/python3-mdtraj.debug
	chmod 0644 -- debian/python3-mdtraj/usr/lib/debug/.dwz/x86_64-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/92
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/92/f70a6f952a1404811b9e99af8b9a482fd2427f.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/92/f70a6f952a1404811b9e99af8b9a482fd2427f.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-x86_64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/92/f70a6f952a1404811b9e99af8b9a482fd2427f.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-x86_64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/41
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/41/ea8adcf322e5f8b31e3179a8cbf28c2aa0188e.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/41/ea8adcf322e5f8b31e3179a8cbf28c2aa0188e.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-x86_64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/41/ea8adcf322e5f8b31e3179a8cbf28c2aa0188e.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-x86_64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/2f
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/2f/1bb04f49f645748228d668180714c2064e1c99.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/2f/1bb04f49f645748228d668180714c2064e1c99.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-x86_64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/2f/1bb04f49f645748228d668180714c2064e1c99.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-x86_64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e5
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e5/8288958c987b5be458456614f059f67fe7aa9e.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e5/8288958c987b5be458456614f059f67fe7aa9e.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-x86_64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e5/8288958c987b5be458456614f059f67fe7aa9e.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-x86_64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/34
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/34/c4c4bcae9c694d5d105ba96cb655212222f071.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/34/c4c4bcae9c694d5d105ba96cb655212222f071.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-x86_64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/34/c4c4bcae9c694d5d105ba96cb655212222f071.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-x86_64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/43
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/43/cc263baf6e390a309004ccad7c72fed49773c1.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/43/cc263baf6e390a309004ccad7c72fed49773c1.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-x86_64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/43/cc263baf6e390a309004ccad7c72fed49773c1.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-x86_64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/45
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/45/3752c83dad5a66cba3a40e1206aee0f6cf1b94.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/45/3752c83dad5a66cba3a40e1206aee0f6cf1b94.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-x86_64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/45/3752c83dad5a66cba3a40e1206aee0f6cf1b94.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-x86_64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/0e
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/0e/154b46f6ae1bcdaa101f5bc99d9a3e031042ef.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/0e/154b46f6ae1bcdaa101f5bc99d9a3e031042ef.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-x86_64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/0e/154b46f6ae1bcdaa101f5bc99d9a3e031042ef.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-x86_64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/0c
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/0c/7811c9587a1c6ca0cc89ec4fcb723ea334e407.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/0c/7811c9587a1c6ca0cc89ec4fcb723ea334e407.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-x86_64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/0c/7811c9587a1c6ca0cc89ec4fcb723ea334e407.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-x86_64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4a
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-x86_64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4a/7ca48ba1a7775a8dbf81606f1e9e92d035c134.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4a/7ca48ba1a7775a8dbf81606f1e9e92d035c134.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-x86_64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4a/7ca48ba1a7775a8dbf81606f1e9e92d035c134.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-x86_64-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/x86_64-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-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-x86_64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-x86_64-linux-gnu.so
   dh_installdeb -O--buildsystem=pybuild
	install -m0755 -d debian/python3-mdtraj/DEBIAN
	printf '#!/bin/sh\nset -e\n' > debian/python3-mdtraj/DEBIAN/postinst
	cat debian/python3-mdtraj.postinst.debhelper >> debian/python3-mdtraj/DEBIAN/postinst
	chmod 0755 -- debian/python3-mdtraj/DEBIAN/postinst
	printf '#!/bin/sh\nset -e\n' > debian/python3-mdtraj/DEBIAN/prerm
	cat debian/python3-mdtraj.prerm.debhelper >> debian/python3-mdtraj/DEBIAN/prerm
	chmod 0755 -- debian/python3-mdtraj/DEBIAN/prerm
	install -m0755 -d debian/python-mdtraj-doc/DEBIAN
   dh_gencontrol -O--buildsystem=pybuild
	install -m0755 -d debian/python-mdtraj-doc/DEBIAN
	echo misc:Depends= >> debian/python-mdtraj-doc.substvars
	echo misc:Pre-Depends= >> debian/python-mdtraj-doc.substvars
	dpkg-gencontrol -ppython-mdtraj-doc -ldebian/changelog -Tdebian/python-mdtraj-doc.substvars -cdebian/control -Pdebian/python-mdtraj-doc
	install -m0755 -d debian/python3-mdtraj/DEBIAN
	echo misc:Depends= >> debian/python3-mdtraj.substvars
	echo misc:Pre-Depends= >> debian/python3-mdtraj.substvars
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN
	dpkg-gencontrol -ppython3-mdtraj -ldebian/changelog -Tdebian/python3-mdtraj.substvars -cdebian/control -Pdebian/.debhelper/python3-mdtraj/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=python3-mdtraj-dbgsym "-DDepends=python3-mdtraj (= \${binary:Version})" "-DDescription=debug symbols for python3-mdtraj" "-DBuild-Ids=0c7811c9587a1c6ca0cc89ec4fcb723ea334e407 0e154b46f6ae1bcdaa101f5bc99d9a3e031042ef 2f1bb04f49f645748228d668180714c2064e1c99 34c4c4bcae9c694d5d105ba96cb655212222f071 41ea8adcf322e5f8b31e3179a8cbf28c2aa0188e 43cc263baf6e390a309004ccad7c72fed49773c1 453752c83dad5a66cba3a40e1206aee0f6cf1b94 4a7ca48ba1a7775a8dbf81606f1e9e92d035c134 92f70a6f952a1404811b9e99af8b9a482fd2427f e58288958c987b5be458456614f059f67fe7aa9e" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
	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 ${sphinxdoc:Built-Using} unused, but is defined
	chmod 0644 -- debian/python-mdtraj-doc/DEBIAN/control
	chmod 0644 -- debian/python3-mdtraj/DEBIAN/control
   dh_md5sums -O--buildsystem=pybuild
	install -m0755 -d debian/python3-mdtraj/DEBIAN
	install -m0755 -d debian/python-mdtraj-doc/DEBIAN
	cd debian/python-mdtraj-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	cd debian/python3-mdtraj >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/python3-mdtraj/DEBIAN/md5sums
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN
	cd debian/.debhelper/python3-mdtraj/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/python-mdtraj-doc/DEBIAN/md5sums
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN/md5sums
   dh_builddeb -O--buildsystem=pybuild
	dpkg-deb --root-owner-group --build debian/python-mdtraj-doc ..
dpkg-deb: building package 'python-mdtraj-doc' in '../python-mdtraj-doc_1.10.3-2_all.deb'.
	dpkg-deb --root-owner-group --build debian/.debhelper/python3-mdtraj/dbgsym-root ..
	dpkg-deb --root-owner-group --build debian/python3-mdtraj ..
dpkg-deb: building package 'python3-mdtraj-dbgsym' in '../python3-mdtraj-dbgsym_1.10.3-2_amd64.deb'.
dpkg-deb: building package 'python3-mdtraj' in '../python3-mdtraj_1.10.3-2_amd64.deb'.
 dpkg-genbuildinfo --build=binary -O../mdtraj_1.10.3-2_amd64.buildinfo
 dpkg-genchanges --build=binary -O../mdtraj_1.10.3-2_amd64.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/3264135 and its subdirectories
I: Current time: Sun Mar  9 01:04:30 -12 2025
I: pbuilder-time-stamp: 1741525470