Sat Feb 15 07:21:44 UTC 2025  I: starting to build mdtraj/trixie/arm64 on jenkins on '2025-02-15 07:21'
Sat Feb 15 07:21:44 UTC 2025  I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_1/60357/console.log
Sat Feb 15 07:21:44 UTC 2025  I: Downloading source for trixie/mdtraj=1.10.3-2
--2025-02-15 07:21:44--  http://deb.debian.org/debian/pool/main/m/mdtraj/mdtraj_1.10.3-2.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2677 (2.6K) [text/prs.lines.tag]
Saving to: ‘mdtraj_1.10.3-2.dsc’

     0K ..                                                    100%  482M=0s

2025-02-15 07:21:44 (482 MB/s) - ‘mdtraj_1.10.3-2.dsc’ saved [2677/2677]

Sat Feb 15 07:21:44 UTC 2025  I: mdtraj_1.10.3-2.dsc
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Hash: SHA512

Format: 3.0 (quilt)
Source: mdtraj
Binary: python3-mdtraj, python-mdtraj-doc
Architecture: any-amd64 arm64 i386 all
Version: 1.10.3-2
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Uploaders: Drew Parsons <dparsons@debian.org>
Homepage: https://mdtraj.org/
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/debichem-team/mdtraj
Vcs-Git: https://salsa.debian.org/debichem-team/mdtraj.git
Testsuite: autopkgtest
Testsuite-Triggers: python3-gsd, python3-ipykernel, python3-jupyter-client, python3-matplotlib, python3-nbformat, python3-netcdf4, python3-pandas, python3-pytest, python3-sklearn
Build-Depends: debhelper-compat (= 13), dh-sequence-python3, cython3, python3-setuptools, python3-all-dev, python3-gsd, python3-numpy, python3-scipy, python3-nbsphinx, python3-nbsphinx-link, python3-netcdf4, python3-networkx, python3-pandas, python3-pyparsing, python3-sphinx, python3-tables, python3-versioneer, libjs-mathjax
Build-Depends-Indep: pandoc, python3-msmb-theme, python3-ipykernel, python3-jupyter-client, python3-matplotlib, python3-nbconvert, python3-nbformat, python3-numpydoc, python3-sklearn
Package-List:
 python-mdtraj-doc deb doc optional arch=all
 python3-mdtraj deb python optional arch=any-amd64,arm64,i386
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Files:
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Sat Feb 15 07:21:44 UTC 2025  I: Checking whether the package is not for us
Sat Feb 15 07:21:44 UTC 2025  I: Starting 1st build on remote node codethink03-arm64.debian.net.
Sat Feb 15 07:21:44 UTC 2025  I: Preparing to do remote build '1' on codethink03-arm64.debian.net.
Sat Feb 15 07:54:54 UTC 2025  I: Deleting $TMPDIR on codethink03-arm64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Fri Mar 20 01:44:45 -12 2026
I: pbuilder-time-stamp: 1774014285
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: 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/1325680/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='arm64'
  DEBIAN_FRONTEND='noninteractive'
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
  DISTRIBUTION='trixie'
  HOME='/root'
  HOST_ARCH='arm64'
  IFS=' 	
  '
  INVOCATION_ID='2f3f48f06cd54a95be91cd9697957d7b'
  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='1325680'
  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.7tctVdzV/pbuilderrc_QoFc --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.7tctVdzV/b1 --logfile b1/build.log mdtraj_1.10.3-2.dsc'
  SUDO_GID='109'
  SUDO_UID='104'
  SUDO_USER='jenkins'
  TERM='unknown'
  TZ='/usr/share/zoneinfo/Etc/GMT+12'
  USER='root'
  _='/usr/bin/systemd-run'
  http_proxy='http://192.168.101.4:3128'
I: uname -a
  Linux codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Nov 22  2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/1325680/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: arm64
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 ... 19922 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} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-c5{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap2{a} liblerc4{a} liblua5.4-0{a} liblzo2-2{a} libmagic-mgc{a} libmagic1t64{a} libnetcdf19t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnorm1t64{a} libnsl2{a} libnuma1{a} libopenjp2-7{a} libp11-kit0{a} libpgm-5.3-0t64{a} libpipeline1{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsnappy1v5{a} libsodium23{a} libsource-highlight-common{a} libsource-highlight4t64{a} libssh2-1t64{a} libsz2{a} libtasn1-6{a} libtcl8.6{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} libzmq5{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} pandoc{a} pandoc-data{a} po-debconf{a} procps{a} python-babel-localedata{a} python-matplotlib-data{a} python-tables-data{a} python-tinycss2-common{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-asttokens{a} python3-attr{a} python3-autocommand{a} python3-babel{a} python3-bleach{a} python3-brotli{a} python3-bs4{a} python3-certifi{a} python3-cffi-backend{a} python3-cftime{a} python3-chardet{a} python3-charset-normalizer{a} python3-comm{a} python3-contourpy{a} python3-coverage{a} python3-cpuinfo{a} python3-cycler{a} python3-dateutil{a} python3-debugpy{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-executing{a} python3-fastjsonschema{a} python3-fonttools{a} python3-fs{a} python3-gsd{a} python3-html5lib{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-ipykernel{a} python3-ipython{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jedi{a} python3-jinja2{a} python3-joblib{a} python3-jsonschema{a} python3-jsonschema-specifications{a} python3-jupyter-client{a} python3-jupyter-core{a} python3-jupyterlab-pygments{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-markupsafe{a} python3-matplotlib{a} python3-matplotlib-inline{a} python3-minimal{a} python3-mistune{a} python3-more-itertools{a} python3-mpmath{a} python3-msmb-theme{a} python3-nbclient{a} python3-nbconvert{a} python3-nbformat{a} python3-nbsphinx{a} python3-nbsphinx-link{a} python3-nest-asyncio{a} python3-netcdf4{a} python3-networkx{a} python3-numexpr{a} python3-numpy{a} python3-numpydoc{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pandocfilters{a} python3-parso{a} python3-pexpect{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-platformdirs{a} python3-prompt-toolkit{a} python3-psutil{a} python3-ptyprocess{a} python3-pure-eval{a} python3-pygments{a} python3-pyparsing{a} python3-pytz{a} python3-referencing{a} python3-requests{a} python3-roman{a} python3-rpds-py{a} python3-scipy{a} python3-setuptools{a} python3-sklearn{a} python3-sklearn-lib{a} python3-snowballstemmer{a} python3-soupsieve{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-sphinxcontrib.jquery{a} python3-stack-data{a} python3-sympy{a} python3-tables{a} python3-tables-lib{a} python3-tabulate{a} python3-threadpoolctl{a} python3-tinycss2{a} python3-tk{a} python3-tornado{a} python3-traitlets{a} python3-typeguard{a} python3-typeshed{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-urllib3{a} python3-versioneer{a} python3-wcwidth{a} python3-webencodings{a} python3-zipp{a} python3-zmq{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} python3.12-tk{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} python3.13-tk{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} tk8.6-blt2.5{a} tzdata{a} ucf{a} unicode-data{a} x11-common{a} xml-core{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  curl isympy-common javascript-common krb5-locales libarchive-cpio-perl libc6-dbg libglib2.0-data libgpg-error-l10n libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-bottleneck python3-cssselect python3-fqdn python3-gdal python3-isoduration python3-json-pointer python3-odf python3-olefile python3-openpyxl python3-pooch python3-pydot python3-pygraphviz python3-pytest python3-rfc3339-validator python3-rfc3986-validator python3-rfc3987 python3-sphinxcontrib.bibtex python3-uritemplate python3-webcolors python3-yaml shared-mime-info wget xdg-user-dirs 
0 packages upgraded, 306 newly installed, 0 to remove and 0 not upgraded.
Need to get 220 MB of archives. After unpacking 1203 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main arm64 fonts-lato all 2.015-1 [2780 kB]
Get: 2 http://deb.debian.org/debian trixie/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B]
Get: 3 http://deb.debian.org/debian trixie/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B]
Get: 4 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-7 [62.4 kB]
Get: 5 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-7 [868 kB]
Get: 6 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB]
Get: 7 http://deb.debian.org/debian trixie/main arm64 ucf all 3.0049 [42.5 kB]
Get: 8 http://deb.debian.org/debian trixie/main arm64 libdebuginfod-common all 0.192-4 [23.7 kB]
Get: 9 http://deb.debian.org/debian trixie/main arm64 libpython3.13-minimal arm64 3.13.2-1 [853 kB]
Get: 10 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB]
Get: 11 http://deb.debian.org/debian trixie/main arm64 python3.13-minimal arm64 3.13.2-1 [1997 kB]
Get: 12 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.13.1-2 [27.0 kB]
Get: 13 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB]
Get: 14 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB]
Get: 15 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024b-6 [257 kB]
Get: 16 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB]
Get: 17 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB]
Get: 18 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB]
Get: 19 http://deb.debian.org/debian trixie/main arm64 libpython3.13-stdlib arm64 3.13.2-1 [1914 kB]
Get: 20 http://deb.debian.org/debian trixie/main arm64 python3.13 arm64 3.13.2-1 [745 kB]
Get: 21 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.13.1-2 [9952 B]
Get: 22 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.13.1-2 [28.0 kB]
Get: 23 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.9-1 [810 kB]
Get: 24 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.9-1 [1941 kB]
Get: 25 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB]
Get: 26 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.4.0-2 [1385 kB]
Get: 27 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20241223 [164 kB]
Get: 28 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB]
Get: 29 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB]
Get: 30 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB]
Get: 31 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB]
Get: 32 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB]
Get: 33 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB]
Get: 34 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-3 [92.0 kB]
Get: 35 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB]
Get: 36 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB]
Get: 37 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB]
Get: 38 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB]
Get: 39 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 40 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-3 [862 kB]
Get: 41 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB]
Get: 42 http://deb.debian.org/debian trixie/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [984 kB]
Get: 43 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB]
Get: 44 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.46-4 [276 kB]
Get: 45 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB]
Get: 46 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 47 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 48 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-2 [317 kB]
Get: 49 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-2 [386 kB]
Get: 50 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB]
Get: 51 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB]
Get: 52 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB]
Get: 53 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.10-2 [337 kB]
Get: 54 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB]
Get: 55 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b4 [27.2 kB]
Get: 56 http://deb.debian.org/debian trixie/main arm64 libxft2 arm64 2.3.6-1+b4 [51.6 kB]
Get: 57 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB]
Get: 58 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+24 [217 kB]
Get: 59 http://deb.debian.org/debian trixie/main arm64 libxss1 arm64 1:1.2.3-1+b3 [17.1 kB]
Get: 60 http://deb.debian.org/debian trixie/main arm64 libtk8.6 arm64 8.6.16-1 [741 kB]
Get: 61 http://deb.debian.org/debian trixie/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7+b1 [538 kB]
Get: 62 http://deb.debian.org/debian trixie/main arm64 blt arm64 2.5.3+dfsg-7+b1 [6344 B]
Get: 63 http://deb.debian.org/debian trixie/main arm64 cython3 arm64 3.0.11+dfsg-2 [2726 kB]
Get: 64 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 65 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-3 [539 kB]
Get: 66 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 67 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 68 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 69 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 70 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get: 71 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get: 72 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB]
Get: 73 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB]
Get: 74 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB]
Get: 75 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB]
Get: 76 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 77 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 78 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB]
Get: 79 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 80 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 81 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 82 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB]
Get: 83 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 84 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get: 85 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 86 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 75.6.0-1 [222 kB]
Get: 87 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 88 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 89 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 75.6.0-1 [720 kB]
Get: 90 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20250108 [113 kB]
Get: 91 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB]
Get: 92 http://deb.debian.org/debian trixie/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB]
Get: 93 http://deb.debian.org/debian trixie/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB]
Get: 94 http://deb.debian.org/debian trixie/main arm64 fonts-lyx all 2.4.3-1 [190 kB]
Get: 95 http://deb.debian.org/debian trixie/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB]
Get: 96 http://deb.debian.org/debian trixie/main arm64 libdw1t64 arm64 0.192-4 [237 kB]
Get: 97 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.83.3-2 [1421 kB]
Get: 98 http://deb.debian.org/debian trixie/main arm64 libbabeltrace1 arm64 1.5.11-4+b1 [164 kB]
Get: 99 http://deb.debian.org/debian trixie/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB]
Get: 100 http://deb.debian.org/debian trixie/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB]
Get: 101 http://deb.debian.org/debian trixie/main arm64 libtasn1-6 arm64 4.19.0-3+b3 [46.9 kB]
Get: 102 http://deb.debian.org/debian trixie/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB]
Get: 103 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-4 [32.2 kB]
Get: 104 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB]
Get: 105 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-4 [81.5 kB]
Get: 106 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B]
Get: 107 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-4 [308 kB]
Get: 108 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-4 [127 kB]
Get: 109 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8+b1 [20.3 kB]
Get: 110 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8+b1 [55.7 kB]
Get: 111 http://deb.debian.org/debian trixie/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB]
Get: 112 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB]
Get: 113 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.6.0-2 [60.5 kB]
Get: 114 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.9.1-1 [109 kB]
Get: 115 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.9.1-1 [17.3 kB]
Get: 116 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB]
Get: 117 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB]
Get: 118 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB]
Get: 119 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.12.0+git20250209.89ed161+ds-1 [336 kB]
Get: 120 http://deb.debian.org/debian trixie/main arm64 libjson-c5 arm64 0.18+ds-1 [45.2 kB]
Get: 121 http://deb.debian.org/debian trixie/main arm64 libdebuginfod1t64 arm64 0.192-4 [31.3 kB]
Get: 122 http://deb.debian.org/debian trixie/main arm64 libpython3.13 arm64 3.13.2-1 [1970 kB]
Get: 123 http://deb.debian.org/debian trixie/main arm64 libsource-highlight-common all 3.1.9-4.3 [77.5 kB]
Get: 124 http://deb.debian.org/debian trixie/main arm64 libsource-highlight4t64 arm64 3.1.9-4.3+b1 [294 kB]
Get: 125 http://deb.debian.org/debian trixie/main arm64 gdb arm64 16.2-1 [6734 kB]
Get: 126 http://deb.debian.org/debian trixie/main arm64 libaec0 arm64 1.1.3-1+b1 [22.5 kB]
Get: 127 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.1-2 [104 kB]
Get: 128 http://deb.debian.org/debian trixie/main arm64 libsnappy1v5 arm64 1.2.1-1+b1 [28.7 kB]
Get: 129 http://deb.debian.org/debian trixie/main arm64 libblosc1 arm64 1.21.5+ds-1+b2 [39.2 kB]
Get: 130 http://deb.debian.org/debian trixie/main arm64 libblosc2-4 arm64 2.15.2+ds-6 [165 kB]
Get: 131 http://deb.debian.org/debian trixie/main arm64 libcurl4t64 arm64 8.12.0+git20250209.89ed161+ds-1 [326 kB]
Get: 132 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB]
Get: 133 http://deb.debian.org/debian trixie/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB]
Get: 134 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB]
Get: 135 http://deb.debian.org/debian trixie/main arm64 libgpg-error0 arm64 1.51-3 [78.5 kB]
Get: 136 http://deb.debian.org/debian trixie/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB]
Get: 137 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-16 [361 kB]
Get: 138 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB]
Get: 139 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 10.2.0-1 [443 kB]
Get: 140 http://deb.debian.org/debian trixie/main arm64 libsz2 arm64 1.1.3-1+b1 [8044 B]
Get: 141 http://deb.debian.org/debian trixie/main arm64 libhdf5-310 arm64 1.14.5+repack-3 [1155 kB]
Get: 142 http://deb.debian.org/debian trixie/main arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [66.1 kB]
Get: 143 http://deb.debian.org/debian trixie/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB]
Get: 144 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB]
Get: 145 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB]
Get: 146 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 147 http://deb.debian.org/debian trixie/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get: 148 http://deb.debian.org/debian trixie/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB]
Get: 149 http://deb.debian.org/debian trixie/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 150 http://deb.debian.org/debian trixie/main arm64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB]
Get: 151 http://deb.debian.org/debian trixie/main arm64 libjson-perl all 4.10000-1 [87.5 kB]
Get: 152 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB]
Get: 153 http://deb.debian.org/debian trixie/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b2 [25.6 kB]
Get: 154 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.16-2 [151 kB]
Get: 155 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB]
Get: 156 http://deb.debian.org/debian trixie/main arm64 liblua5.4-0 arm64 5.4.7-1+b2 [134 kB]
Get: 157 http://deb.debian.org/debian trixie/main arm64 liblzo2-2 arm64 2.10-3+b1 [49.6 kB]
Get: 158 http://deb.debian.org/debian trixie/main arm64 libnetcdf19t64 arm64 1:4.9.2-7+b1 [445 kB]
Get: 159 http://deb.debian.org/debian trixie/main arm64 libnorm1t64 arm64 1.5.9+dfsg-3.1+b2 [205 kB]
Get: 160 http://deb.debian.org/debian trixie/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 161 http://deb.debian.org/debian trixie/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB]
Get: 162 http://deb.debian.org/debian trixie/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB]
Get: 163 http://deb.debian.org/debian trixie/main arm64 libnuma1 arm64 2.0.18-1+b1 [21.8 kB]
Get: 164 http://deb.debian.org/debian trixie/main arm64 libopenjp2-7 arm64 2.5.3-1 [189 kB]
Get: 165 http://deb.debian.org/debian trixie/main arm64 libpgm-5.3-0t64 arm64 5.3.128~dfsg-2.1+b1 [152 kB]
Get: 166 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Get: 167 http://deb.debian.org/debian trixie/main arm64 libpython3.13-dev arm64 3.13.2-1 [4678 kB]
Get: 168 http://deb.debian.org/debian trixie/main arm64 libpython3-dev arm64 3.13.1-2 [10.2 kB]
Get: 169 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.9-1 [1909 kB]
Get: 170 http://deb.debian.org/debian trixie/main arm64 libpython3.12t64 arm64 3.12.9-1 [1986 kB]
Get: 171 http://deb.debian.org/debian trixie/main arm64 libpython3.12-dev arm64 3.12.9-1 [4796 kB]
Get: 172 http://deb.debian.org/debian trixie/main arm64 libpython3-all-dev arm64 3.13.1-2 [1072 B]
Get: 173 http://deb.debian.org/debian trixie/main arm64 libqhull-r8.0 arm64 2020.2-6+b2 [229 kB]
Get: 174 http://deb.debian.org/debian trixie/main arm64 libraqm0 arm64 0.10.2-1 [13.6 kB]
Get: 175 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB]
Get: 176 http://deb.debian.org/debian trixie/main arm64 libsodium23 arm64 1.0.18-1+b2 [121 kB]
Get: 177 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB]
Get: 178 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB]
Get: 179 http://deb.debian.org/debian trixie/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [113 kB]
Get: 180 http://deb.debian.org/debian trixie/main arm64 libwebpmux3 arm64 1.5.0-0.1 [125 kB]
Get: 181 http://deb.debian.org/debian trixie/main arm64 libxslt1.1 arm64 1.1.35-1.1+b1 [222 kB]
Get: 182 http://deb.debian.org/debian trixie/main arm64 libyaml-0-2 arm64 0.2.5-2 [49.2 kB]
Get: 183 http://deb.debian.org/debian trixie/main arm64 libzmq5 arm64 4.3.5-1+b3 [253 kB]
Get: 184 http://deb.debian.org/debian trixie/main arm64 pandoc-data all 3.1.11.1-3 [459 kB]
Get: 185 http://deb.debian.org/debian trixie/main arm64 pandoc arm64 3.1.11.1+ds-2 [26.2 MB]
Get: 186 http://deb.debian.org/debian trixie/main arm64 python-babel-localedata all 2.17.0-1 [6050 kB]
Get: 187 http://deb.debian.org/debian trixie/main arm64 python-matplotlib-data all 3.8.3-3 [2731 kB]
Get: 188 http://deb.debian.org/debian trixie/main arm64 python-tables-data all 3.10.2-2 [47.3 kB]
Get: 189 http://deb.debian.org/debian trixie/main arm64 python-tinycss2-common all 1.4.0-1 [44.8 kB]
Get: 190 http://deb.debian.org/debian trixie/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB]
Get: 191 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.9-1 [681 kB]
Get: 192 http://deb.debian.org/debian trixie/main arm64 python3-all arm64 3.13.1-2 [1056 B]
Get: 193 http://deb.debian.org/debian trixie/main arm64 python3.13-dev arm64 3.13.2-1 [505 kB]
Get: 194 http://deb.debian.org/debian trixie/main arm64 python3-dev arm64 3.13.1-2 [26.1 kB]
Get: 195 http://deb.debian.org/debian trixie/main arm64 python3.12-dev arm64 3.12.9-1 [505 kB]
Get: 196 http://deb.debian.org/debian trixie/main arm64 python3-all-dev arm64 3.13.1-2 [1076 B]
Get: 197 http://deb.debian.org/debian trixie/main arm64 python3-asttokens all 3.0.0-1 [20.1 kB]
Get: 198 http://deb.debian.org/debian trixie/main arm64 python3-attr all 25.1.0-1 [68.7 kB]
Get: 199 http://deb.debian.org/debian trixie/main arm64 python3-babel all 2.17.0-1 [117 kB]
Get: 200 http://deb.debian.org/debian trixie/main arm64 python3-webencodings all 0.5.1-5 [11.1 kB]
Get: 201 http://deb.debian.org/debian trixie/main arm64 python3-html5lib all 1.2-1 [92.2 kB]
Get: 202 http://deb.debian.org/debian trixie/main arm64 python3-bleach all 6.2.0-1 [51.2 kB]
Get: 203 http://deb.debian.org/debian trixie/main arm64 python3-brotli arm64 1.1.0-2+b6 [306 kB]
Get: 204 http://deb.debian.org/debian trixie/main arm64 python3-soupsieve all 2.6-1 [38.3 kB]
Get: 205 http://deb.debian.org/debian trixie/main arm64 python3-bs4 all 4.13.3-1 [166 kB]
Get: 206 http://deb.debian.org/debian trixie/main arm64 python3-certifi all 2025.1.31+ds-1 [9652 B]
Get: 207 http://deb.debian.org/debian trixie/main arm64 python3-cffi-backend arm64 1.17.1-2+b1 [94.8 kB]
Get: 208 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.26.4+ds-13 [3815 kB]
Get: 209 http://deb.debian.org/debian trixie/main arm64 python3-cftime arm64 1.6.4-1+b4 [252 kB]
Get: 210 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB]
Get: 211 http://deb.debian.org/debian trixie/main arm64 python3-charset-normalizer arm64 3.4.0-1+b1 [129 kB]
Get: 212 http://deb.debian.org/debian trixie/main arm64 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB]
Get: 213 http://deb.debian.org/debian trixie/main arm64 python3-comm all 0.2.1-1 [8104 B]
Get: 214 http://deb.debian.org/debian trixie/main arm64 python3-contourpy arm64 1.3.1-1 [237 kB]
Get: 215 http://deb.debian.org/debian trixie/main arm64 python3-coverage arm64 7.6.0+dfsg1-2+b1 [177 kB]
Get: 216 http://deb.debian.org/debian trixie/main arm64 python3-cpuinfo all 9.0.0+git20221119-3 [23.5 kB]
Get: 217 http://deb.debian.org/debian trixie/main arm64 python3-cycler all 0.12.1-1 [9496 B]
Get: 218 http://deb.debian.org/debian trixie/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB]
Get: 219 http://deb.debian.org/debian trixie/main arm64 python3-debugpy arm64 1.8.8+ds-2 [980 kB]
Get: 220 http://deb.debian.org/debian trixie/main arm64 python3-decorator all 5.1.1-5 [15.1 kB]
Get: 221 http://deb.debian.org/debian trixie/main arm64 python3-defusedxml all 0.7.1-3 [43.4 kB]
Get: 222 http://deb.debian.org/debian trixie/main arm64 python3-roman all 5.0-1 [10.6 kB]
Get: 223 http://deb.debian.org/debian trixie/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB]
Get: 224 http://deb.debian.org/debian trixie/main arm64 python3-executing all 2.2.0-0.1 [24.5 kB]
Get: 225 http://deb.debian.org/debian trixie/main arm64 python3-fastjsonschema all 2.21.1-1 [22.4 kB]
Get: 226 http://deb.debian.org/debian trixie/main arm64 python3-pytz all 2025.1-3 [150 kB]
Get: 227 http://deb.debian.org/debian trixie/main arm64 python3-tz all 2025.1-3 [4004 B]
Get: 228 http://deb.debian.org/debian trixie/main arm64 python3-platformdirs all 4.3.6-1 [16.6 kB]
Get: 229 http://deb.debian.org/debian trixie/main arm64 python3-fs all 2.4.16-6 [95.1 kB]
Get: 230 http://deb.debian.org/debian trixie/main arm64 python3-lxml arm64 5.3.0-1+b1 [1433 kB]
Get: 231 http://deb.debian.org/debian trixie/main arm64 python3-lz4 arm64 4.4.0+dfsg-1 [25.6 kB]
Get: 232 http://deb.debian.org/debian trixie/main arm64 python3-scipy arm64 1.14.1-4 [18.5 MB]
Get: 233 http://deb.debian.org/debian trixie/main arm64 python3-mpmath all 1.3.0-1 [419 kB]
Get: 234 http://deb.debian.org/debian trixie/main arm64 python3-sympy all 1.13.3-1 [4147 kB]
Get: 235 http://deb.debian.org/debian trixie/main arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB]
Get: 236 http://deb.debian.org/debian trixie/main arm64 unicode-data all 15.1.0-1 [8547 kB]
Get: 237 http://deb.debian.org/debian trixie/main arm64 python3-fonttools arm64 4.55.3-2 [1501 kB]
Get: 238 http://deb.debian.org/debian trixie/main arm64 python3-gsd arm64 3.4.2-2 [218 kB]
Get: 239 http://deb.debian.org/debian trixie/main arm64 python3-idna all 3.10-1 [42.0 kB]
Get: 240 http://deb.debian.org/debian trixie/main arm64 python3-imagesize all 1.4.1-1 [6688 B]
Get: 241 http://deb.debian.org/debian trixie/main arm64 python3-parso all 0.8.4-1 [67.8 kB]
Get: 242 http://deb.debian.org/debian trixie/main arm64 python3-typeshed all 0.0~git20241223.ea91db2-1 [1530 kB]
Get: 243 http://deb.debian.org/debian trixie/main arm64 python3-jedi all 0.19.1+ds1-1 [691 kB]
Get: 244 http://deb.debian.org/debian trixie/main arm64 python3-matplotlib-inline all 0.1.6-2 [8652 B]
Get: 245 http://deb.debian.org/debian trixie/main arm64 python3-wcwidth all 0.2.13+dfsg1-1 [24.9 kB]
Get: 246 http://deb.debian.org/debian trixie/main arm64 python3-prompt-toolkit all 3.0.50-1 [278 kB]
Get: 247 http://deb.debian.org/debian trixie/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB]
Get: 248 http://deb.debian.org/debian trixie/main arm64 python3-pure-eval all 0.2.3-1 [11.2 kB]
Get: 249 http://deb.debian.org/debian trixie/main arm64 python3-stack-data all 0.6.3-1 [21.6 kB]
Get: 250 http://deb.debian.org/debian trixie/main arm64 python3-ptyprocess all 0.7.0-6 [14.5 kB]
Get: 251 http://deb.debian.org/debian trixie/main arm64 python3-pexpect all 4.9-3 [55.6 kB]
Get: 252 http://deb.debian.org/debian trixie/main arm64 python3-ipython all 8.30.0-2 [568 kB]
Get: 253 http://deb.debian.org/debian trixie/main arm64 python3-jupyter-core all 5.7.2-5 [35.3 kB]
Get: 254 http://deb.debian.org/debian trixie/main arm64 python3-psutil arm64 5.9.8-2+b1 [226 kB]
Get: 255 http://deb.debian.org/debian trixie/main arm64 python3-tornado arm64 6.4.2-1 [349 kB]
Get: 256 http://deb.debian.org/debian trixie/main arm64 python3-zmq arm64 26.2.1-1 [193 kB]
Get: 257 http://deb.debian.org/debian trixie/main arm64 python3-jupyter-client all 8.6.3-2 [92.4 kB]
Get: 258 http://deb.debian.org/debian trixie/main arm64 python3-nest-asyncio all 1.5.4-1 [6248 B]
Get: 259 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.2-1 [55.3 kB]
Get: 260 http://deb.debian.org/debian trixie/main arm64 python3-ipykernel all 6.29.5-2 [102 kB]
Get: 261 http://deb.debian.org/debian trixie/main arm64 python3-markupsafe arm64 2.1.5-1+b3 [14.0 kB]
Get: 262 http://deb.debian.org/debian trixie/main arm64 python3-jinja2 all 3.1.5-2 [107 kB]
Get: 263 http://deb.debian.org/debian trixie/main arm64 python3-joblib all 1.3.2-6 [216 kB]
Get: 264 http://deb.debian.org/debian trixie/main arm64 python3-rpds-py arm64 0.21.0-2 [259 kB]
Get: 265 http://deb.debian.org/debian trixie/main arm64 python3-referencing all 0.35.1-2 [23.5 kB]
Get: 266 http://deb.debian.org/debian trixie/main arm64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B]
Get: 267 http://deb.debian.org/debian trixie/main arm64 python3-jsonschema all 4.19.2-6 [71.4 kB]
Get: 268 http://deb.debian.org/debian trixie/main arm64 python3-jupyterlab-pygments all 0.2.2-3 [6096 B]
Get: 269 http://deb.debian.org/debian trixie/main arm64 python3-kiwisolver arm64 1.4.7-3 [71.5 kB]
Get: 270 http://deb.debian.org/debian trixie/main arm64 python3-pil arm64 11.1.0-5 [514 kB]
Get: 271 http://deb.debian.org/debian trixie/main arm64 python3.12-tk arm64 3.12.9-1 [111 kB]
Get: 272 http://deb.debian.org/debian trixie/main arm64 python3.13-tk arm64 3.13.2-1 [102 kB]
Get: 273 http://deb.debian.org/debian trixie/main arm64 python3-tk arm64 3.13.1-1 [9464 B]
Get: 274 http://deb.debian.org/debian trixie/main arm64 python3-pil.imagetk arm64 11.1.0-5 [81.6 kB]
Get: 275 http://deb.debian.org/debian trixie/main arm64 python3-pyparsing all 3.1.2-1 [146 kB]
Get: 276 http://deb.debian.org/debian trixie/main arm64 python3-matplotlib arm64 3.8.3-3+b2 [5583 kB]
Get: 277 http://deb.debian.org/debian trixie/main arm64 python3-mistune all 3.0.2-2 [33.2 kB]
Get: 278 http://deb.debian.org/debian trixie/main arm64 sphinx-common all 8.1.3-4 [616 kB]
Get: 279 http://deb.debian.org/debian trixie/main arm64 python3-urllib3 all 2.3.0-1 [114 kB]
Get: 280 http://deb.debian.org/debian trixie/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB]
Get: 281 http://deb.debian.org/debian trixie/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB]
Get: 282 http://deb.debian.org/debian trixie/main arm64 python3-sphinx all 8.1.3-4 [468 kB]
Get: 283 http://deb.debian.org/debian trixie/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1023 kB]
Get: 284 http://deb.debian.org/debian trixie/main arm64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B]
Get: 285 http://deb.debian.org/debian trixie/main arm64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [29.7 kB]
Get: 286 http://deb.debian.org/debian trixie/main arm64 python3-msmb-theme all 1.2.0-4 [33.8 kB]
Get: 287 http://deb.debian.org/debian trixie/main arm64 python3-nbformat all 5.9.1-1 [45.1 kB]
Get: 288 http://deb.debian.org/debian trixie/main arm64 python3-nbclient all 0.8.0-2 [62.2 kB]
Get: 289 http://deb.debian.org/debian trixie/main arm64 python3-tinycss2 all 1.4.0-1 [24.9 kB]
Get: 290 http://deb.debian.org/debian trixie/main arm64 python3-pandocfilters all 1.5.1-1 [23.7 kB]
Get: 291 http://deb.debian.org/debian trixie/main arm64 python3-nbconvert all 7.16.6-1 [160 kB]
Get: 292 http://deb.debian.org/debian trixie/main arm64 python3-nbsphinx all 0.9.5+ds-1 [39.9 kB]
Get: 293 http://deb.debian.org/debian trixie/main arm64 python3-nbsphinx-link all 1.3.0-4 [6264 B]
Get: 294 http://deb.debian.org/debian trixie/main arm64 python3-netcdf4 arm64 1.7.2-1+b3 [725 kB]
Get: 295 http://deb.debian.org/debian trixie/main arm64 python3-networkx all 3.2.1-5 [13.0 MB]
Get: 296 http://deb.debian.org/debian trixie/main arm64 python3-numexpr arm64 2.10.2-1+b1 [126 kB]
Get: 297 http://deb.debian.org/debian trixie/main arm64 python3-tabulate all 0.9.0-1 [45.9 kB]
Get: 298 http://deb.debian.org/debian trixie/main arm64 python3-numpydoc all 1.8.0-1 [51.4 kB]
Get: 299 http://deb.debian.org/debian trixie/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-8 [6029 kB]
Get: 300 http://deb.debian.org/debian trixie/main arm64 python3-pandas all 2.2.3+dfsg-8 [3097 kB]
Get: 301 http://deb.debian.org/debian trixie/main arm64 python3-threadpoolctl all 3.1.0-1 [21.2 kB]
Get: 302 http://deb.debian.org/debian trixie/main arm64 python3-sklearn-lib arm64 1.4.2+dfsg-7+b1 [5397 kB]
Get: 303 http://deb.debian.org/debian trixie/main arm64 python3-sklearn all 1.4.2+dfsg-7 [2248 kB]
Get: 304 http://deb.debian.org/debian trixie/main arm64 python3-tables-lib arm64 3.10.2-2 [628 kB]
Get: 305 http://deb.debian.org/debian trixie/main arm64 python3-tables all 3.10.2-2 [353 kB]
Get: 306 http://deb.debian.org/debian trixie/main arm64 python3-versioneer all 0.29-1 [43.0 kB]
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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
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invoke-rc.d: could not determine current runlevel
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Current default time zone: 'Etc/UTC'
Local time is now:      Fri Mar 20 13:46:39 UTC 2026.
Universal Time is now:  Fri Mar 20 13:46:39 UTC 2026.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

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update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode
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Setting up python3-bs4 (4.13.3-1) ...
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Setting up python3-matplotlib-inline (0.1.6-2) ...
Setting up python3-comm (0.2.1-1) ...
Setting up python3-fs (2.4.16-6) ...
Setting up python3-jupyterlab-pygments (0.2.2-3) ...
Setting up libpython3.12t64:arm64 (3.12.9-1) ...
Setting up python3-pil:arm64 (11.1.0-5) ...
Setting up python3-inflect (7.3.1-2) ...
Setting up python3-pandas (2.2.3+dfsg-8) ...
Setting up python3-pil.imagetk:arm64 (11.1.0-5) ...
Setting up python3-executing (2.2.0-0.1) ...
Setting up python3-jaraco.text (4.0.0-1) ...
Setting up python3-pexpect (4.9-3) ...
Setting up python3-zmq (26.2.1-1) ...
Setting up python3-dev (3.13.1-2) ...
Setting up python3-requests (2.32.3+dfsg-1) ...
Setting up python3-sklearn (1.4.2+dfsg-7) ...
Setting up python3-cftime (1.6.4-1+b4) ...
Setting up python3-numexpr (2.10.2-1+b1) ...
Setting up libhdf5-310:arm64 (1.14.5+repack-3) ...
Setting up python3-jupyter-client (8.6.3-2) ...
Setting up python3-stack-data (0.6.3-1) ...
Setting up python3-referencing (0.35.1-2) ...
Setting up python3-pkg-resources (75.6.0-1) ...
Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3) ...
Setting up libdebuginfod1t64:arm64 (0.192-4) ...
Setting up libnetcdf19t64:arm64 (1:4.9.2-7+b1) ...
Setting up python3-setuptools (75.6.0-1) ...
Setting up python3-jedi (0.19.1+ds1-1) ...
Setting up python3-tables-lib (3.10.2-2) ...
Setting up libpython3.12-dev:arm64 (3.12.9-1) ...
Setting up python3-tables (3.10.2-2) ...
Setting up python3-networkx (3.2.1-5) ...
Setting up gdb (16.2-1) ...
Setting up libpython3-all-dev:arm64 (3.13.1-2) ...
Setting up python3-ipython (8.30.0-2) ...
Setting up python3.12-dev (3.12.9-1) ...
Setting up python3-jsonschema-specifications (2023.12.1-2) ...
Setting up python3-netcdf4 (1.7.2-1+b3) ...
Setting up dh-python (6.20250108) ...
Setting up python3-all-dev (3.13.1-2) ...
Setting up python3-debugpy (1.8.8+ds-2) ...
Setting up python3-jsonschema (4.19.2-6) ...
Setting up python3-ipykernel (6.29.5-2) ...
Setting up python3-nbformat (5.9.1-1) ...
Setting up python3-nbclient (0.8.0-2) ...
Setting up python3-nbconvert (7.16.6-1) ...
Setting up python3-fonttools (4.55.3-2) ...
Setting up python3-ufolib2 (0.17.0+dfsg1-1) ...
Setting up python3-matplotlib (3.8.3-3+b2) ...
Processing triggers for libc-bin (2.40-6) ...
Processing triggers for sgml-base (1.31) ...
Setting up docutils-common (0.21.2+dfsg-2) ...
Processing triggers for sgml-base (1.31) ...
Setting up python3-docutils (0.21.2+dfsg-2) ...
Setting up python3-sphinx (8.1.3-4) ...
Setting up python3-nbsphinx (0.9.5+ds-1) ...
Setting up python3-sphinxcontrib.jquery (4.1-5) ...
Setting up python3-numpydoc (1.8.0-1) ...
Setting up python3-nbsphinx-link (1.3.0-4) ...
Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-2) ...
Setting up python3-msmb-theme (1.2.0-4) ...
Processing triggers for ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/mdtraj-1.10.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../mdtraj_1.10.3-2_source.changes
dpkg-buildpackage: info: source package mdtraj
dpkg-buildpackage: info: source version 1.10.3-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Drew Parsons <dparsons@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
dpkg-source: info: using options from mdtraj-1.10.3/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
 debian/rules clean
dh clean --with sphinxdoc --buildsystem=pybuild
   dh_auto_clean -O--buildsystem=pybuild
	pybuild --clean -i python{version} -p "3.12 3.13"
I: pybuild base:311: python3.12 setup.py clean 
Using built-in specs.
COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/14/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none
OFFLOAD_TARGET_DEFAULT=1
Target: aarch64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-16' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=aarch64-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-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 14.2.0 (Debian 14.2.0-16) 
/build/reproducible-path/mdtraj-1.10.3/basesetup.py:483: UserWarning: Unrecognized setuptools command ('clean'), proceeding with generating Cython sources and expanding templates
  warnings.warn(
warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'make_whole' to allow an error code to be returned.
performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned.
performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned.
C compiler:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Attempting to autodetect SSE2   support... Did not detect SSE2 support
Attempting to autodetect SSE3   support... Did not detect SSE3 support
Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support
Attempting to autodetect NEON   support... Compiler supports NEON

[ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx
[ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx
[ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx
[ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx
[ 5/10] Cythonizing mdtraj/geometry/drid.pyx
[ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx
[ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx
[ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx
[ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx
[10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx
running clean
removing '/build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build' (and everything under it)
'build/bdist.linux-aarch64' does not exist -- can't clean it
'build/scripts-3.12' does not exist -- can't clean it
I: pybuild base:311: python3.13 setup.py clean 
Using built-in specs.
COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/14/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none
OFFLOAD_TARGET_DEFAULT=1
Target: aarch64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-16' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=aarch64-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-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 14.2.0 (Debian 14.2.0-16) 
/build/reproducible-path/mdtraj-1.10.3/basesetup.py:483: UserWarning: Unrecognized setuptools command ('clean'), proceeding with generating Cython sources and expanding templates
  warnings.warn(
warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'make_whole' to allow an error code to be returned.
performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned.
performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned.
C compiler:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Attempting to autodetect SSE2   support... Did not detect SSE2 support
Attempting to autodetect SSE3   support... Did not detect SSE3 support
Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support
Attempting to autodetect NEON   support... Compiler supports NEON

[ 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-aarch64' does not exist -- can't clean it
'build/scripts-3.13' does not exist -- can't clean it
	rm -rf .pybuild/
	find . -name \*.pyc -exec rm {} \;
   debian/rules execute_after_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/mdtraj-1.10.3'
for f in mdtraj/formats/binpos/binpos.c \
  mdtraj/formats/dcd/dcd.c		\
  mdtraj/formats/dtr/dtr.cpp		\
  mdtraj/formats/tng/tng.c		\
  mdtraj/formats/xtc/trr.c		\
  mdtraj/formats/xtc/xtc.c		\
  mdtraj/geometry/drid.cpp		\
  mdtraj/geometry/neighborlist.cpp	\
  mdtraj/geometry/neighbors.cpp		\
  mdtraj/geometry/src/_geometry.cpp	\
  mdtraj/rmsd/_lprmsd.cpp		\
  mdtraj/rmsd/_rmsd.cpp			\
  mdtraj/version.py;                    \
do rm -f $f; done
rm -rf mdtraj/core/lib
rm -rf docs/api/generated
rm -rf __pycache__ .pybuild
find . -name "lib*.a" -delete
make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.10.3'
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
	rm -f debian/debhelper-build-stamp
	rm -rf debian/.debhelper/
	rm -f -- debian/python3-mdtraj.substvars debian/python-mdtraj-doc.substvars debian/files
	rm -fr -- debian/python3-mdtraj/ debian/tmp/ debian/python-mdtraj-doc/
	find .  \( \( \
		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
		\) -exec rm -f {} + \) -o \
		\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
 debian/rules binary
dh binary --with sphinxdoc --buildsystem=pybuild
   dh_update_autotools_config -O--buildsystem=pybuild
   dh_autoreconf -O--buildsystem=pybuild
   dh_auto_configure -O--buildsystem=pybuild
	pybuild --configure -i python{version} -p "3.12 3.13"
I: pybuild base:311: python3.12 setup.py config 
Using built-in specs.
COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/14/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none
OFFLOAD_TARGET_DEFAULT=1
Target: aarch64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-16' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=aarch64-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-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 14.2.0 (Debian 14.2.0-16) 
/build/reproducible-path/mdtraj-1.10.3/basesetup.py:483: UserWarning: Unrecognized setuptools command ('config'), proceeding with generating Cython sources and expanding templates
  warnings.warn(
warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'make_whole' to allow an error code to be returned.
performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned.
performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned.
C compiler:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Attempting to autodetect SSE2   support... Did not detect SSE2 support
Attempting to autodetect SSE3   support... Did not detect SSE3 support
Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support
Attempting to autodetect NEON   support... Compiler supports NEON

[ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx
[ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx
[ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx
[ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx
[ 5/10] Cythonizing mdtraj/geometry/drid.pyx
[ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx
[ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx
[ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx
[ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx
[10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx
running config
I: pybuild base:311: python3.13 setup.py config 
Using built-in specs.
COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/14/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none
OFFLOAD_TARGET_DEFAULT=1
Target: aarch64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-16' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=aarch64-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-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 14.2.0 (Debian 14.2.0-16) 
/build/reproducible-path/mdtraj-1.10.3/basesetup.py:483: UserWarning: Unrecognized setuptools command ('config'), proceeding with generating Cython sources and expanding templates
  warnings.warn(
warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'make_whole' to allow an error code to be returned.
performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned.
performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned.
C compiler:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Attempting to autodetect SSE2   support... Did not detect SSE2 support
Attempting to autodetect SSE3   support... Did not detect SSE3 support
Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support
Attempting to autodetect NEON   support... Compiler supports NEON

[ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx
[ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx
[ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx
[ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx
[ 5/10] Cythonizing mdtraj/geometry/drid.pyx
[ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx
[ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx
[ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx
[ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx
[10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx
running config
   dh_auto_build -O--buildsystem=pybuild
	pybuild --build -i python{version} -p "3.12 3.13"
I: pybuild base:311: /usr/bin/python3.12 setup.py build 
Using built-in specs.
COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/14/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none
OFFLOAD_TARGET_DEFAULT=1
Target: aarch64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-16' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=aarch64-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-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 14.2.0 (Debian 14.2.0-16) 
warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'make_whole' to allow an error code to be returned.
performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned.
performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned.
C compiler:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Attempting to autodetect SSE2   support... Did not detect SSE2 support
Attempting to autodetect SSE3   support... Did not detect SSE3 support
Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support
Attempting to autodetect NEON   support... Compiler supports NEON

[ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx
[ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx
[ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx
[ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx
[ 5/10] Cythonizing mdtraj/geometry/drid.pyx
[ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx
[ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx
[ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx
[ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx
[10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx
running build
running build_py
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj
copying mdtraj/io.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj
copying mdtraj/_version.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj
copying mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils
copying mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils
copying mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils
copying mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils
copying mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils
copying mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils
copying mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils
copying mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils
copying mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing
copying mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing
copying mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing
copying mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing
copying mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts
copying mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts
copying mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts
copying mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr
copying mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr
copying mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr
copying mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
copying mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core
copying mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core
copying mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core
copying mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core
copying mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core
copying mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core
copying mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb
copying mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data
copying mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data
copying mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data
UPDATING /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py
set /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py to '1.10.3'
running build_ext
building 'mdtraj.formats.xtc' extension
creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
  788 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
  785 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1016 |         int errval=1;
      |             ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
 1305 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
 1302 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1509 |         int errval=1;
      |             ^~~~~~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord':
mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable]
   66 |         int i,j,result;
      |               ^
mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable]
   66 |         int i,j,result;
      |             ^
mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes':
mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  119 |     if (NULL == xd)
      |     ^~
mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  122 |         do {
      |         ^~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/xtc.c:1263:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
In function '__Pyx_PyInt_From_int',
    inlined from '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write' at mdtraj/formats/xtc/xtc.c:13728:16,
    inlined from '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write' at mdtraj/formats/xtc/xtc.c:13424:13:
mdtraj/formats/xtc/xtc.c:1165:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized]
 1165 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^
mdtraj/formats/xtc/xtc.c:25481:20: note: in expansion of macro 'PyInt_FromLong'
25481 |             return PyInt_FromLong((long) value);
      |                    ^~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c: In function '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write':
mdtraj/formats/xtc/xtc.c:13444:7: note: '__pyx_v_status' was declared here
13444 |   int __pyx_v_status;
      |       ^~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read':
mdtraj/formats/xtc/xtc.c:11491:10: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11491 |       if (unlikely(__pyx_t_5 != -1)) {
      |          ^
mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here
10279 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11490:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
11490 |       } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1;
      |                 ^
mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here
10279 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11856:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11856 |             } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_5 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here
10277 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11860:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
11860 |             } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_5 = 1;
      |                       ^
mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here
10277 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11864:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
11864 |             } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_5 = 2;
      |                       ^
mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here
10277 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11902:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11902 |             } else if (unlikely(__pyx_t_41 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_5 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:10283:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here
10283 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11826:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11826 |             } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_5 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:10287:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here
10287 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11844:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11844 |             } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_5 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:10291:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here
10291 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11884:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11884 |             } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_5 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here
10295 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11888:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
11888 |             } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_5 = 1;
      |                       ^
mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here
10295 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11892:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
11892 |             } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_5 = 2;
      |                       ^
mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here
10295 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/xtc.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so
building 'mdtraj.formats.trr' extension
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
  788 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
  785 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1016 |         int errval=1;
      |             ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
 1305 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
 1302 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1509 |         int errval=1;
      |             ^~~~~~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/trr.c:1265:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
In function '__Pyx_PyInt_From_int',
    inlined from '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write' at mdtraj/formats/xtc/trr.c:15643:16,
    inlined from '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write' at mdtraj/formats/xtc/trr.c:15083:13:
mdtraj/formats/xtc/trr.c:1167:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized]
 1167 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^
mdtraj/formats/xtc/trr.c:27476:20: note: in expansion of macro 'PyInt_FromLong'
27476 |             return PyInt_FromLong((long) value);
      |                    ^~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c: In function '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write':
mdtraj/formats/xtc/trr.c:15111:7: note: '__pyx_v_status' was declared here
15111 |   int __pyx_v_status;
      |       ^~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read':
mdtraj/formats/xtc/trr.c:12632:12: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
12632 |         if (unlikely(__pyx_t_4 != -1)) {
      |            ^
mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here
10939 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12631:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
12631 |         } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_4 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here
10939 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12580:12: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
12580 |         if (unlikely(__pyx_t_4 != -1)) {
      |            ^
mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here
10955 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12579:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
12579 |         } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_4 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here
10955 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12739:10: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
12739 |       if (unlikely(__pyx_t_4 != -1)) {
      |          ^
mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here
10959 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12738:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
12738 |       } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_4 = 1;
      |                 ^
mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here
10959 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12341:19: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
12341 |         } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_4 = 0;
      |                   ^
mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here
10953 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:2533:90: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized]
 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)
      |                                                                                          ^
mdtraj/formats/xtc/trr.c:12354:42: note: in expansion of macro '__Pyx_BufPtrCContig3d'
12354 |         __pyx_v_frame_vel = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_vel.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_vel.diminfo[0].strides, __pyx_t_30, __pyx_pybuffernd_vel.diminfo[1].strides, __pyx_t_31, __pyx_pybuffernd_vel.diminfo[2].strides))));
      |                                          ^~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here
10953 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12345:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
12345 |         } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_4 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here
10953 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12349:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
12349 |         } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_4 = 2;
      |                   ^
mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here
10953 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12398:19: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
12398 |         } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_4 = 0;
      |                   ^
mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here
10937 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:2533:90: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized]
 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)
      |                                                                                          ^
mdtraj/formats/xtc/trr.c:12411:45: note: in expansion of macro '__Pyx_BufPtrCContig3d'
12411 |         __pyx_v_frame_forces = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_forces.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_forces.diminfo[0].strides, __pyx_t_31, __pyx_pybuffernd_forces.diminfo[1].strides, __pyx_t_30, __pyx_pybuffernd_forces.diminfo[2].strides))));
      |                                             ^~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here
10937 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12402:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
12402 |         } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_4 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here
10937 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12406:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
12406 |         } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_4 = 2;
      |                   ^
mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here
10937 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/trr.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so
building 'mdtraj.formats.dcd' extension
creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd
creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/src
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dcd/dcd.c:1260:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
In function '__Pyx_PyInt_From_int',
    inlined from '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read' at mdtraj/formats/dcd/dcd.c:10190:17:
mdtraj/formats/dcd/dcd.c:1162:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized]
 1162 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^
mdtraj/formats/dcd/dcd.c:18997:20: note: in expansion of macro 'PyInt_FromLong'
18997 |             return PyInt_FromLong((long) value);
      |                    ^~~~~~~~~~~~~~
mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read':
mdtraj/formats/dcd/dcd.c:8994:7: note: '__pyx_v_i' was declared here
 8994 |   int __pyx_v_i;
      |       ^~~~~~~~~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/dcd.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so
building 'mdtraj.formats.dtr' extension
creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr
creating build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/src
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dtr/dtr.cpp:1279:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/dtr/src/dtrplugin.cxx: In member function 'bool desres::molfile::Timekeys::init(const std::string&)':
mdtraj/formats/dtr/src/dtrplugin.cxx: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/aarch64-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/aarch64-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/aarch64-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/aarch64-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 ());
      |                                   ~~~~~~~~~~~~~~~~~
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/dtr.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so
building 'mdtraj._rmsd' extension
creating build/temp.linux-aarch64-cpython-312/mdtraj/rmsd
creating build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_rmsd.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so
building 'mdtraj._lprmsd' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/rmsd/_lprmsd.cpp:1305:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_lprmsd.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/Munkres.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/fancy_index.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so
building 'mdtraj.core.lib.libtheobald' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -O3 -funroll-loops --std=c++11
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o -O3 -funroll-loops --std=c++11
aarch64-linux-gnu-gcc-ar rcs /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/libtheobald.a build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o
building 'mdtraj.geometry._geometry' extension
creating build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/geometry/src/_geometry.cpp:1287:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/_geometry.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dssp.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/geometry.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/sasa.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so
building 'mdtraj.geometry.drid' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/drid.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/drid.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dridkernels.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/moments.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so
building 'mdtraj.geometry.neighbors' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighbors.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighbors.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so
building 'mdtraj.geometry.neighborlist' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighborlist.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighborlist.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so
I: pybuild base:311: /usr/bin/python3 setup.py build 
Using built-in specs.
COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/14/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none
OFFLOAD_TARGET_DEFAULT=1
Target: aarch64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-16' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=aarch64-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-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 14.2.0 (Debian 14.2.0-16) 
warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'make_whole' to allow an error code to be returned.
performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned.
performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned.
C compiler:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Attempting to autodetect SSE2   support... Did not detect SSE2 support
Attempting to autodetect SSE3   support... Did not detect SSE3 support
Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support
Attempting to autodetect NEON   support... Compiler supports NEON

[ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx
[ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx
[ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx
[ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx
[ 5/10] Cythonizing mdtraj/geometry/drid.pyx
[ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx
[ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx
[ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx
[ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx
[10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx
running build
running build_py
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj
copying mdtraj/io.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj
copying mdtraj/_version.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj
copying mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils
copying mdtraj/utils/zipped.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/unitcell.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/rotation.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/contextmanagers.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils
copying mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing
copying mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing
copying mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing
copying mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing
copying mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/testing
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts
copying mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts
copying mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts
copying mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/scripts
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/xtcreporter.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/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters
copying mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr
copying mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr
copying mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr
copying mdtraj/nmr/__init__.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/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/shape.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/rg.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/order.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/hbond.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/distance.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/contact.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/alignment.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry
copying mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry
creating /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/registry.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/prmtop.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/openmmxml.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/mol2.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/lh5.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats
copying mdtraj/formats/gro.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/amberrst.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
creating /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/residue_names.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core
copying mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core
copying mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_math.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/standard_dimensions.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/prefix.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/mymatrix.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
copying mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb
copying mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdb
creating /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/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
copying mdtraj/formats/pdb/data/pdbNames.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-aarch64-cpython-313/mdtraj/formats/xtc/src
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
  788 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
  785 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1016 |         int errval=1;
      |             ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
 1305 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
 1302 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1509 |         int errval=1;
      |             ^~~~~~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord':
mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable]
   66 |         int i,j,result;
      |               ^
mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable]
   66 |         int i,j,result;
      |             ^
mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes':
mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  119 |     if (NULL == xd)
      |     ^~
mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  122 |         do {
      |         ^~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/xtc.c:1263:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
In function '__Pyx_PyInt_From_int',
    inlined from '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write' at mdtraj/formats/xtc/xtc.c:13728:16,
    inlined from '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write' at mdtraj/formats/xtc/xtc.c:13424:13:
mdtraj/formats/xtc/xtc.c:1165:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized]
 1165 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^
mdtraj/formats/xtc/xtc.c:25481:20: note: in expansion of macro 'PyInt_FromLong'
25481 |             return PyInt_FromLong((long) value);
      |                    ^~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c: In function '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write':
mdtraj/formats/xtc/xtc.c:13444:7: note: '__pyx_v_status' was declared here
13444 |   int __pyx_v_status;
      |       ^~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read':
mdtraj/formats/xtc/xtc.c:11491:10: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11491 |       if (unlikely(__pyx_t_5 != -1)) {
      |          ^
mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here
10279 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11490:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
11490 |       } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1;
      |                 ^
mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here
10279 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11856:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11856 |             } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_5 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here
10277 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11860:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
11860 |             } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_5 = 1;
      |                       ^
mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here
10277 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11864:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
11864 |             } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_5 = 2;
      |                       ^
mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here
10277 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11902:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11902 |             } else if (unlikely(__pyx_t_41 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_5 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:10283:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here
10283 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11826:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11826 |             } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_5 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:10287:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here
10287 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11844:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11844 |             } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_5 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:10291:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here
10291 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11884:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11884 |             } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_5 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here
10295 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11888:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
11888 |             } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_5 = 1;
      |                       ^
mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here
10295 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11892:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
11892 |             } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_5 = 2;
      |                       ^
mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here
10295 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/xtc.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so
building 'mdtraj.formats.trr' extension
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
  788 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
  785 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1016 |         int errval=1;
      |             ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
 1305 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
 1302 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1509 |         int errval=1;
      |             ^~~~~~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/trr.c:1265:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
In function '__Pyx_PyInt_From_int',
    inlined from '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write' at mdtraj/formats/xtc/trr.c:15643:16,
    inlined from '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write' at mdtraj/formats/xtc/trr.c:15083:13:
mdtraj/formats/xtc/trr.c:1167:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized]
 1167 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^
mdtraj/formats/xtc/trr.c:27476:20: note: in expansion of macro 'PyInt_FromLong'
27476 |             return PyInt_FromLong((long) value);
      |                    ^~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c: In function '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write':
mdtraj/formats/xtc/trr.c:15111:7: note: '__pyx_v_status' was declared here
15111 |   int __pyx_v_status;
      |       ^~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read':
mdtraj/formats/xtc/trr.c:12632:12: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
12632 |         if (unlikely(__pyx_t_4 != -1)) {
      |            ^
mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here
10939 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12631:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
12631 |         } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_4 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here
10939 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12580:12: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
12580 |         if (unlikely(__pyx_t_4 != -1)) {
      |            ^
mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here
10955 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12579:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
12579 |         } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_4 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here
10955 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12739:10: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
12739 |       if (unlikely(__pyx_t_4 != -1)) {
      |          ^
mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here
10959 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12738:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
12738 |       } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_4 = 1;
      |                 ^
mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here
10959 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12341:19: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
12341 |         } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_4 = 0;
      |                   ^
mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here
10953 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:2533:90: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized]
 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)
      |                                                                                          ^
mdtraj/formats/xtc/trr.c:12354:42: note: in expansion of macro '__Pyx_BufPtrCContig3d'
12354 |         __pyx_v_frame_vel = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_vel.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_vel.diminfo[0].strides, __pyx_t_30, __pyx_pybuffernd_vel.diminfo[1].strides, __pyx_t_31, __pyx_pybuffernd_vel.diminfo[2].strides))));
      |                                          ^~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here
10953 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12345:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
12345 |         } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_4 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here
10953 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12349:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
12349 |         } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_4 = 2;
      |                   ^
mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here
10953 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12398:19: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
12398 |         } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_4 = 0;
      |                   ^
mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here
10937 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:2533:90: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized]
 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)
      |                                                                                          ^
mdtraj/formats/xtc/trr.c:12411:45: note: in expansion of macro '__Pyx_BufPtrCContig3d'
12411 |         __pyx_v_frame_forces = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_forces.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_forces.diminfo[0].strides, __pyx_t_31, __pyx_pybuffernd_forces.diminfo[1].strides, __pyx_t_30, __pyx_pybuffernd_forces.diminfo[2].strides))));
      |                                             ^~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here
10937 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12402:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
12402 |         } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_4 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here
10937 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12406:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
12406 |         } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_4 = 2;
      |                   ^
mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here
10937 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/trr.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so
building 'mdtraj.formats.dcd' extension
creating build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd
creating build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/src
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dcd/dcd.c:1260:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
In function '__Pyx_PyInt_From_int',
    inlined from '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read' at mdtraj/formats/dcd/dcd.c:10190:17:
mdtraj/formats/dcd/dcd.c:1162:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized]
 1162 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^
mdtraj/formats/dcd/dcd.c:18997:20: note: in expansion of macro 'PyInt_FromLong'
18997 |             return PyInt_FromLong((long) value);
      |                    ^~~~~~~~~~~~~~
mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read':
mdtraj/formats/dcd/dcd.c:8994:7: note: '__pyx_v_i' was declared here
 8994 |   int __pyx_v_i;
      |       ^~~~~~~~~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/dcd.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so
building 'mdtraj.formats.dtr' extension
creating build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr
creating build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr/src
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dtr/dtr.cpp:1279:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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 ());
      |                                   ~~~~~~~~~~~~~~~~~
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr/dtr.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so
building 'mdtraj._rmsd' extension
creating build/temp.linux-aarch64-cpython-313/mdtraj/rmsd
creating build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/_rmsd.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so
building 'mdtraj._lprmsd' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/rmsd/_lprmsd.cpp:1305:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/_lprmsd.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/Munkres.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/fancy_index.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so
building 'mdtraj.core.lib.libtheobald' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -O3 -funroll-loops --std=c++11
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o -O3 -funroll-loops --std=c++11
aarch64-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-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o
building 'mdtraj.geometry._geometry' extension
creating build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/geometry/src/_geometry.cpp:1287:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/_geometry.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/dssp.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/geometry.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/sasa.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so
building 'mdtraj.geometry.drid' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/drid.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/geometry/drid.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/dridkernels.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/moments.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so
building 'mdtraj.geometry.neighbors' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/geometry/neighbors.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/neighbors.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so
building 'mdtraj.geometry.neighborlist' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/geometry/neighborlist.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/neighborlist.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so
   dh_auto_test -O--buildsystem=pybuild
	pybuild --test -i python{version} -p "3.12 3.13"
I: pybuild base:311: cd /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build; python3.12 -m unittest discover -v 

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

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

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

NO TESTS RAN
	rm -fr -- /tmp/dh-xdg-rundir-VWYGIy3z
   create-stamp debian/debhelper-build-stamp
   dh_testroot -O--buildsystem=pybuild
   dh_prep -O--buildsystem=pybuild
	rm -f -- debian/python3-mdtraj.substvars debian/python-mdtraj-doc.substvars
	rm -fr -- debian/.debhelper/generated/python3-mdtraj/ debian/python3-mdtraj/ debian/tmp/ debian/.debhelper/generated/python-mdtraj-doc/ debian/python-mdtraj-doc/
   dh_installdirs -O--buildsystem=pybuild
	install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples/data
   dh_auto_install -O--buildsystem=pybuild
	install -m0755 -d /build/reproducible-path/mdtraj-1.10.3/debian/tmp
	pybuild --install -i python{version} -p "3.12 3.13" --dest-dir=/build/reproducible-path/mdtraj-1.10.3/debian/tmp
I: pybuild base:311: /usr/bin/python3.12 setup.py install --root /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj 
Using built-in specs.
COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/14/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none
OFFLOAD_TARGET_DEFAULT=1
Target: aarch64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-16' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=aarch64-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-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 14.2.0 (Debian 14.2.0-16) 
warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'make_whole' to allow an error code to be returned.
performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned.
performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned.
C compiler:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Attempting to autodetect SSE2   support... Did not detect SSE2 support
Attempting to autodetect SSE3   support... Did not detect SSE3 support
Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support
Attempting to autodetect NEON   support... Compiler supports NEON

[ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx
[ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx
[ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx
[ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx
[ 5/10] Cythonizing mdtraj/geometry/drid.pyx
[ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx
[ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx
[ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx
[ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx
[10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx
running install
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  self.initialize_options()
running build
running build_py
UPDATING /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py
set /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py to '1.10.3'
running build_ext
building 'mdtraj.formats.xtc' extension
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
  788 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
  785 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1016 |         int errval=1;
      |             ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
 1305 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
 1302 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1509 |         int errval=1;
      |             ^~~~~~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord':
mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable]
   66 |         int i,j,result;
      |               ^
mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable]
   66 |         int i,j,result;
      |             ^
mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes':
mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  119 |     if (NULL == xd)
      |     ^~
mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  122 |         do {
      |         ^~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/xtc.c:1263:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
In function '__Pyx_PyInt_From_int',
    inlined from '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write' at mdtraj/formats/xtc/xtc.c:13728:16,
    inlined from '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write' at mdtraj/formats/xtc/xtc.c:13424:13:
mdtraj/formats/xtc/xtc.c:1165:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized]
 1165 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^
mdtraj/formats/xtc/xtc.c:25481:20: note: in expansion of macro 'PyInt_FromLong'
25481 |             return PyInt_FromLong((long) value);
      |                    ^~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c: In function '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write':
mdtraj/formats/xtc/xtc.c:13444:7: note: '__pyx_v_status' was declared here
13444 |   int __pyx_v_status;
      |       ^~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read':
mdtraj/formats/xtc/xtc.c:11491:10: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11491 |       if (unlikely(__pyx_t_5 != -1)) {
      |          ^
mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here
10279 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11490:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
11490 |       } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1;
      |                 ^
mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here
10279 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11856:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11856 |             } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_5 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here
10277 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11860:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
11860 |             } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_5 = 1;
      |                       ^
mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here
10277 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11864:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
11864 |             } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_5 = 2;
      |                       ^
mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here
10277 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11902:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11902 |             } else if (unlikely(__pyx_t_41 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_5 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:10283:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here
10283 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11826:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11826 |             } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_5 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:10287:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here
10287 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11844:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11844 |             } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_5 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:10291:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here
10291 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11884:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11884 |             } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_5 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here
10295 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11888:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
11888 |             } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_5 = 1;
      |                       ^
mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here
10295 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11892:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
11892 |             } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_5 = 2;
      |                       ^
mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here
10295 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/xtc.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so
building 'mdtraj.formats.trr' extension
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
  788 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
  785 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1016 |         int errval=1;
      |             ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
 1305 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
 1302 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1509 |         int errval=1;
      |             ^~~~~~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/trr.c:1265:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
In function '__Pyx_PyInt_From_int',
    inlined from '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write' at mdtraj/formats/xtc/trr.c:15643:16,
    inlined from '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write' at mdtraj/formats/xtc/trr.c:15083:13:
mdtraj/formats/xtc/trr.c:1167:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized]
 1167 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^
mdtraj/formats/xtc/trr.c:27476:20: note: in expansion of macro 'PyInt_FromLong'
27476 |             return PyInt_FromLong((long) value);
      |                    ^~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c: In function '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write':
mdtraj/formats/xtc/trr.c:15111:7: note: '__pyx_v_status' was declared here
15111 |   int __pyx_v_status;
      |       ^~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read':
mdtraj/formats/xtc/trr.c:12632:12: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
12632 |         if (unlikely(__pyx_t_4 != -1)) {
      |            ^
mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here
10939 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12631:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
12631 |         } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_4 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here
10939 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12580:12: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
12580 |         if (unlikely(__pyx_t_4 != -1)) {
      |            ^
mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here
10955 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12579:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
12579 |         } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_4 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here
10955 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12739:10: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
12739 |       if (unlikely(__pyx_t_4 != -1)) {
      |          ^
mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here
10959 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12738:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
12738 |       } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_4 = 1;
      |                 ^
mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here
10959 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12341:19: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
12341 |         } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_4 = 0;
      |                   ^
mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here
10953 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:2533:90: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized]
 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)
      |                                                                                          ^
mdtraj/formats/xtc/trr.c:12354:42: note: in expansion of macro '__Pyx_BufPtrCContig3d'
12354 |         __pyx_v_frame_vel = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_vel.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_vel.diminfo[0].strides, __pyx_t_30, __pyx_pybuffernd_vel.diminfo[1].strides, __pyx_t_31, __pyx_pybuffernd_vel.diminfo[2].strides))));
      |                                          ^~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here
10953 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12345:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
12345 |         } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_4 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here
10953 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12349:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
12349 |         } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_4 = 2;
      |                   ^
mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here
10953 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12398:19: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
12398 |         } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_4 = 0;
      |                   ^
mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here
10937 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:2533:90: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized]
 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)
      |                                                                                          ^
mdtraj/formats/xtc/trr.c:12411:45: note: in expansion of macro '__Pyx_BufPtrCContig3d'
12411 |         __pyx_v_frame_forces = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_forces.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_forces.diminfo[0].strides, __pyx_t_31, __pyx_pybuffernd_forces.diminfo[1].strides, __pyx_t_30, __pyx_pybuffernd_forces.diminfo[2].strides))));
      |                                             ^~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here
10937 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12402:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
12402 |         } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_4 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here
10937 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12406:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
12406 |         } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_4 = 2;
      |                   ^
mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here
10937 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/xtc/trr.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so
building 'mdtraj.formats.dcd' extension
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dcd/dcd.c:1260:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
In function '__Pyx_PyInt_From_int',
    inlined from '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read' at mdtraj/formats/dcd/dcd.c:10190:17:
mdtraj/formats/dcd/dcd.c:1162:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized]
 1162 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^
mdtraj/formats/dcd/dcd.c:18997:20: note: in expansion of macro 'PyInt_FromLong'
18997 |             return PyInt_FromLong((long) value);
      |                    ^~~~~~~~~~~~~~
mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read':
mdtraj/formats/dcd/dcd.c:8994:7: note: '__pyx_v_i' was declared here
 8994 |   int __pyx_v_i;
      |       ^~~~~~~~~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/dcd.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so
building 'mdtraj.formats.dtr' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dtr/dtr.cpp:1279:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/dtr/src/dtrplugin.cxx: In member function 'bool desres::molfile::Timekeys::init(const std::string&)':
mdtraj/formats/dtr/src/dtrplugin.cxx: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/aarch64-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/aarch64-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/aarch64-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/aarch64-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 ());
      |                                   ~~~~~~~~~~~~~~~~~
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/dtr.o build/temp.linux-aarch64-cpython-312/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so
building 'mdtraj._rmsd' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_rmsd.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so
building 'mdtraj._lprmsd' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/rmsd/_lprmsd.cpp:1305:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/_lprmsd.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/Munkres.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/fancy_index.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-312/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so
building 'mdtraj.geometry._geometry' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/geometry/src/_geometry.cpp:1287:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/_geometry.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dssp.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/geometry.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/sasa.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so
building 'mdtraj.geometry.drid' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/drid.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/drid.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/dridkernels.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/moments.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so
building 'mdtraj.geometry.neighbors' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighbors.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighbors.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so
building 'mdtraj.geometry.neighborlist' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/mdtraj/geometry/neighborlist.o build/temp.linux-aarch64-cpython-312/mdtraj/geometry/src/neighborlist.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so
running install_lib
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__pycache__/_version.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__pycache__
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/trajectory.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/selection.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/residue_names.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/topology.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/element.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__pycache__
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/center.h -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/theobald_rmsd.h -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/lib/libtheobald.a -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/lib
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/element.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/selection.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/topology.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/openmmxml.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/psf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/prmtop.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/mol2.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/hoomdxml.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/gsd.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/xyzfile.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/pdbx.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/netcdf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/mdcrd.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/lh5.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/lammpstrj.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/hdf5.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/gro.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/arc.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/registry.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/amberrst.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__pycache__
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbstructure.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/pdbfile.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__pycache__
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data/pdbNames.xml -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/data/residues.xml -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/data
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/pdbfile.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdb/pdbstructure.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/amberrst.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/arc.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gro.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/gsd.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/hdf5.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/hoomdxml.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lammpstrj.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/lh5.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/mdcrd.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/mol2.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/netcdf.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/openmmxml.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/prmtop.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/psf.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/registry.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/formats/xyzfile.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/thermodynamic_properties.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/shape.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/sasa.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/rg.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/rdf.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/order.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/hbond.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/dssp.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/dihedral.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/contact.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/distance.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/angle.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/alignment.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/contact.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/dihedral.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/distance.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/dssp.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/hbond.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/internal.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/order.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/rdf.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/rg.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/sasa.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/shape.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/geometry/thermodynamic_properties.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/shift_wrappers.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/scalar_couplings.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/scalar_couplings.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/nmr/shift_wrappers.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/xtcreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/netcdfreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/hdf5reporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/basereporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/dcdreporter.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/basereporter.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/dcdreporter.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/netcdfreporter.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/reporters/xtcreporter.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/mdconvert.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/scripts/mdinspect.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/testing.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/docscrape.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/docstrings.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docscrape.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/docstrings.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/testing/testing.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/singleton.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/zipped.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/unitcell.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/validation.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/rotation.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/delay_import.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/contextmanagers.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__pycache__
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/quantity.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_operators.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/basedimension.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/standard_dimensions.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/mymatrix.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/prefix.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/baseunit.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_definitions.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/constants.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/prefix.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/quantity.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/standard_dimensions.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_definitions.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_math.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit_operators.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/basedimension.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/doctests.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unit/unit.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/contextmanagers.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/delay_import.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/singleton.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/unitcell.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/validation.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/utils/zipped.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/_version.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.12_mdtraj/build/mdtraj/io.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/element.py to element.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/residue_names.py to residue_names.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/selection.py to selection.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/topology.py to topology.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/core/trajectory.py to trajectory.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/pdbfile.py to pdbfile.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdb/pdbstructure.py to pdbstructure.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/amberrst.py to amberrst.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/arc.py to arc.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/gro.py to gro.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/gsd.py to gsd.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/hdf5.py to hdf5.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/hoomdxml.py to hoomdxml.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/lammpstrj.py to lammpstrj.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/lh5.py to lh5.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/mdcrd.py to mdcrd.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/mol2.py to mol2.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/netcdf.py to netcdf.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/openmmxml.py to openmmxml.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/pdbx.py to pdbx.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/prmtop.py to prmtop.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/psf.py to psf.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/registry.py to registry.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/formats/xyzfile.py to xyzfile.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/alignment.py to alignment.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/angle.py to angle.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/contact.py to contact.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/dihedral.py to dihedral.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/distance.py to distance.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/dssp.py to dssp.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/hbond.py to hbond.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/internal.py to internal.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/order.py to order.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/rdf.py to rdf.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/rg.py to rg.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/sasa.py to sasa.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/shape.py to shape.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/geometry/thermodynamic_properties.py to thermodynamic_properties.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/scalar_couplings.py to scalar_couplings.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/nmr/shift_wrappers.py to shift_wrappers.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/basereporter.py to basereporter.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/dcdreporter.py to dcdreporter.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/hdf5reporter.py to hdf5reporter.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/netcdfreporter.py to netcdfreporter.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/reporters/xtcreporter.py to xtcreporter.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/mdconvert.py to mdconvert.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/scripts/mdinspect.py to mdinspect.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/docscrape.py to docscrape.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/docstrings.py to docstrings.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/testing/testing.py to testing.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/mymatrix.py to mymatrix.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/constants.py to constants.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/prefix.py to prefix.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/quantity.py to quantity.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/standard_dimensions.py to standard_dimensions.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/unit_definitions.py to unit_definitions.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/unit_math.py to unit_math.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/unit_operators.py to unit_operators.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/basedimension.py to basedimension.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/baseunit.py to baseunit.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/doctests.py to doctests.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unit/unit.py to unit.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/contextmanagers.py to contextmanagers.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/delay_import.py to delay_import.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/rotation.py to rotation.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/singleton.py to singleton.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/unitcell.py to unitcell.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/validation.py to validation.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/utils/zipped.py to zipped.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/_version.py to _version.cpython-312.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj/io.py to io.cpython-312.pyc
running install_egg_info
running egg_info
creating mdtraj.egg-info
writing mdtraj.egg-info/PKG-INFO
writing dependency_links to mdtraj.egg-info/dependency_links.txt
writing entry points to mdtraj.egg-info/entry_points.txt
writing requirements to mdtraj.egg-info/requires.txt
writing top-level names to mdtraj.egg-info/top_level.txt
writing manifest file 'mdtraj.egg-info/SOURCES.txt'
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
reading manifest file 'mdtraj.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
no previously-included directories found matching '__pycache__'
no previously-included directories found matching '*.pyc'
adding license file 'LICENSE'
writing manifest file 'mdtraj.egg-info/SOURCES.txt'
Copying mdtraj.egg-info to /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.12/dist-packages/mdtraj-1.10.3.egg-info
Skipping SOURCES.txt
running install_scripts
Installing mdconvert-mdtraj script to /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/bin
Installing mdinspect script to /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/bin
I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj 
Using built-in specs.
COLLECT_GCC=/usr/bin/aarch64-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/14/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none
OFFLOAD_TARGET_DEFAULT=1
Target: aarch64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-16' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=aarch64-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-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=4
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 14.2.0 (Debian 14.2.0-16) 
warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
performance hint: mdtraj/geometry/src/image_molecules.pxi:15:5: Exception check on 'make_whole' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'make_whole' to allow an error code to be returned.
performance hint: mdtraj/geometry/src/image_molecules.pxi:36:5: Exception check on 'anchor_dists' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned.
performance hint: mdtraj/geometry/src/image_molecules.pxi:68:5: Exception check on 'wrap_mols' will always require the GIL to be acquired.
Possible solutions:
	1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned.
C compiler:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Attempting to autodetect SSE2   support... Did not detect SSE2 support
Attempting to autodetect SSE3   support... Did not detect SSE3 support
Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support
Attempting to autodetect NEON   support... Compiler supports NEON

[ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx
[ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx
[ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx
[ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx
[ 5/10] Cythonizing mdtraj/geometry/drid.pyx
[ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx
[ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx
[ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx
[ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx
[10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx
running install
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  self.initialize_options()
running build
running build_py
UPDATING /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_version.py
set /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_version.py to '1.10.3'
running build_ext
building 'mdtraj.formats.xtc' extension
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
  788 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
  785 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1016 |         int errval=1;
      |             ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
 1305 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
 1302 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1509 |         int errval=1;
      |             ^~~~~~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'xtc_coord':
mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable 'j' [-Wunused-variable]
   66 |         int i,j,result;
      |               ^
mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable 'i' [-Wunused-variable]
   66 |         int i,j,result;
      |             ^
mdtraj/formats/xtc/src/xdrfile_xtc.c: In function 'read_xtc_nframes':
mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  119 |     if (NULL == xd)
      |     ^~
mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  122 |         do {
      |         ^~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/xtc.c:1263:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
In function '__Pyx_PyInt_From_int',
    inlined from '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write' at mdtraj/formats/xtc/xtc.c:13728:16,
    inlined from '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write' at mdtraj/formats/xtc/xtc.c:13424:13:
mdtraj/formats/xtc/xtc.c:1165:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized]
 1165 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^
mdtraj/formats/xtc/xtc.c:25481:20: note: in expansion of macro 'PyInt_FromLong'
25481 |             return PyInt_FromLong((long) value);
      |                    ^~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c: In function '__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write':
mdtraj/formats/xtc/xtc.c:13444:7: note: '__pyx_v_status' was declared here
13444 |   int __pyx_v_status;
      |       ^~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c: In function '__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read':
mdtraj/formats/xtc/xtc.c:11491:10: warning: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11491 |       if (unlikely(__pyx_t_5 != -1)) {
      |          ^
mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[0].shape' was declared here
10279 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11490:17: warning: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
11490 |       } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1;
      |                 ^
mdtraj/formats/xtc/xtc.c:10279:21: note: '__pyx_pybuffernd_framebuffer.diminfo[1].shape' was declared here
10279 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11856:23: warning: '__pyx_pybuffernd_box_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11856 |             } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_5 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[0].shape' was declared here
10277 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11860:23: warning: '__pyx_pybuffernd_box_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
11860 |             } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_5 = 1;
      |                       ^
mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[1].shape' was declared here
10277 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11864:23: warning: '__pyx_pybuffernd_box_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
11864 |             } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_5 = 2;
      |                       ^
mdtraj/formats/xtc/xtc.c:10277:21: note: '__pyx_pybuffernd_box_stride.diminfo[2].shape' was declared here
10277 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11902:23: warning: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11902 |             } else if (unlikely(__pyx_t_41 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_5 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:10283:21: note: '__pyx_pybuffernd_prec_stride.diminfo[0].shape' was declared here
10283 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11826:23: warning: '__pyx_pybuffernd_step_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11826 |             } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_5 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:10287:21: note: '__pyx_pybuffernd_step_stride.diminfo[0].shape' was declared here
10287 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11844:23: warning: '__pyx_pybuffernd_time_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11844 |             } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_5 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:10291:21: note: '__pyx_pybuffernd_time_stride.diminfo[0].shape' was declared here
10291 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11884:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
11884 |             } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_5 = 0;
      |                       ^
mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[0].shape' was declared here
10295 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11888:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
11888 |             } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_5 = 1;
      |                       ^
mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[1].shape' was declared here
10295 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/xtc.c:11892:23: warning: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
11892 |             } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_5 = 2;
      |                       ^
mdtraj/formats/xtc/xtc.c:10295:21: note: '__pyx_pybuffernd_xyz_stride.diminfo[2].shape' was declared here
10295 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/xtc.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so
building 'mdtraj.formats.trr' extension
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
  788 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
  785 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_float':
mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1016 |         int errval=1;
      |             ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_decompress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable 'larger' set but not used [-Wunused-but-set-variable]
 1305 |         int smallnum, smaller, larger, i, is_smaller, run;
      |                                ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable 'minidx' set but not used [-Wunused-but-set-variable]
 1302 |         int smallidx, minidx, maxidx;
      |                       ^~~~~~
mdtraj/formats/xtc/src/xdrfile.c: In function 'xdrfile_compress_coord_double':
mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable 'errval' set but not used [-Wunused-but-set-variable]
 1509 |         int errval=1;
      |             ^~~~~~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/trr.c:1265:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
In function '__Pyx_PyInt_From_int',
    inlined from '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write' at mdtraj/formats/xtc/trr.c:15643:16,
    inlined from '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write' at mdtraj/formats/xtc/trr.c:15083:13:
mdtraj/formats/xtc/trr.c:1167:40: warning: '__pyx_v_status' may be used uninitialized [-Wmaybe-uninitialized]
 1167 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^
mdtraj/formats/xtc/trr.c:27476:20: note: in expansion of macro 'PyInt_FromLong'
27476 |             return PyInt_FromLong((long) value);
      |                    ^~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c: In function '__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write':
mdtraj/formats/xtc/trr.c:15111:7: note: '__pyx_v_status' was declared here
15111 |   int __pyx_v_status;
      |       ^~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c: In function '__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read':
mdtraj/formats/xtc/trr.c:12632:12: warning: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
12632 |         if (unlikely(__pyx_t_4 != -1)) {
      |            ^
mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[0].shape' was declared here
10939 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12631:19: warning: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
12631 |         } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_4 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:10939:21: note: '__pyx_pybuffernd_forces_buffer.diminfo[1].shape' was declared here
10939 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12580:12: warning: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
12580 |         if (unlikely(__pyx_t_4 != -1)) {
      |            ^
mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[0].shape' was declared here
10955 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12579:19: warning: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
12579 |         } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_4 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:10955:21: note: '__pyx_pybuffernd_vel_buffer.diminfo[1].shape' was declared here
10955 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12739:10: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
12739 |       if (unlikely(__pyx_t_4 != -1)) {
      |          ^
mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[0].shape' was declared here
10959 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12738:17: warning: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
12738 |       } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_4 = 1;
      |                 ^
mdtraj/formats/xtc/trr.c:10959:21: note: '__pyx_pybuffernd_xyz_buffer.diminfo[1].shape' was declared here
10959 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12341:19: warning: '__pyx_pybuffernd_vel.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
12341 |         } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_4 = 0;
      |                   ^
mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].shape' was declared here
10953 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:2533:90: warning: '__pyx_pybuffernd_vel.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized]
 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)
      |                                                                                          ^
mdtraj/formats/xtc/trr.c:12354:42: note: in expansion of macro '__Pyx_BufPtrCContig3d'
12354 |         __pyx_v_frame_vel = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_vel.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_vel.diminfo[0].strides, __pyx_t_30, __pyx_pybuffernd_vel.diminfo[1].strides, __pyx_t_31, __pyx_pybuffernd_vel.diminfo[2].strides))));
      |                                          ^~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[0].strides' was declared here
10953 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12345:19: warning: '__pyx_pybuffernd_vel.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
12345 |         } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_4 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[1].shape' was declared here
10953 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12349:19: warning: '__pyx_pybuffernd_vel.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
12349 |         } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_4 = 2;
      |                   ^
mdtraj/formats/xtc/trr.c:10953:21: note: '__pyx_pybuffernd_vel.diminfo[2].shape' was declared here
10953 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_vel;
      |                     ^~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12398:19: warning: '__pyx_pybuffernd_forces.diminfo[0].shape' may be used uninitialized [-Wmaybe-uninitialized]
12398 |         } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_4 = 0;
      |                   ^
mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].shape' was declared here
10937 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:2533:90: warning: '__pyx_pybuffernd_forces.diminfo[0].strides' may be used uninitialized [-Wmaybe-uninitialized]
 2533 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2)
      |                                                                                          ^
mdtraj/formats/xtc/trr.c:12411:45: note: in expansion of macro '__Pyx_BufPtrCContig3d'
12411 |         __pyx_v_frame_forces = ((rvec *)(&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_forces.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_forces.diminfo[0].strides, __pyx_t_31, __pyx_pybuffernd_forces.diminfo[1].strides, __pyx_t_30, __pyx_pybuffernd_forces.diminfo[2].strides))));
      |                                             ^~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[0].strides' was declared here
10937 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12402:19: warning: '__pyx_pybuffernd_forces.diminfo[1].shape' may be used uninitialized [-Wmaybe-uninitialized]
12402 |         } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_4 = 1;
      |                   ^
mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[1].shape' was declared here
10937 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/xtc/trr.c:12406:19: warning: '__pyx_pybuffernd_forces.diminfo[2].shape' may be used uninitialized [-Wmaybe-uninitialized]
12406 |         } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_4 = 2;
      |                   ^
mdtraj/formats/xtc/trr.c:10937:21: note: '__pyx_pybuffernd_forces.diminfo[2].shape' was declared here
10937 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_forces;
      |                     ^~~~~~~~~~~~~~~~~~~~~~~
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/xtc/trr.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so
building 'mdtraj.formats.dcd' extension
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dcd/dcd.c:1260:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
In function '__Pyx_PyInt_From_int',
    inlined from '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read' at mdtraj/formats/dcd/dcd.c:10190:17:
mdtraj/formats/dcd/dcd.c:1162:40: warning: '__pyx_v_i' may be used uninitialized [-Wmaybe-uninitialized]
 1162 |   #define PyInt_FromLong               PyLong_FromLong
      |                                        ^
mdtraj/formats/dcd/dcd.c:18997:20: note: in expansion of macro 'PyInt_FromLong'
18997 |             return PyInt_FromLong((long) value);
      |                    ^~~~~~~~~~~~~~
mdtraj/formats/dcd/dcd.c: In function '__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read':
mdtraj/formats/dcd/dcd.c:8994:7: note: '__pyx_v_i' was declared here
 8994 |   int __pyx_v_i;
      |       ^~~~~~~~~
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mdtraj-1.10.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/dcd.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so
building 'mdtraj.formats.dtr' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dtr/dtr.cpp:1279:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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 ());
      |                                   ~~~~~~~~~~~~~~~~~
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr/dtr.o build/temp.linux-aarch64-cpython-313/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so
building 'mdtraj._rmsd' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/_rmsd.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so
building 'mdtraj._lprmsd' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/rmsd/_lprmsd.cpp:1305:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/_lprmsd.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/Munkres.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/center.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/fancy_index.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/rotation.o build/temp.linux-aarch64-cpython-313/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so
building 'mdtraj.geometry._geometry' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/geometry/src/_geometry.cpp:1287:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/_geometry.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/dssp.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/geometry.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/sasa.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so
building 'mdtraj.geometry.drid' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/drid.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/geometry/drid.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/dridkernels.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/moments.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so
building 'mdtraj.geometry.neighbors' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/geometry/neighbors.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/neighbors.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so
building 'mdtraj.geometry.neighborlist' extension
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/geometry/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare
aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/mdtraj/geometry/neighborlist.o build/temp.linux-aarch64-cpython-313/mdtraj/geometry/src/neighborlist.o -L/usr/lib/aarch64-linux-gnu -lgomp -o /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighborlist.cpython-313-aarch64-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/_lprmsd.cpython-313-aarch64-linux-gnu.so -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/_rmsd.cpython-313-aarch64-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__/_version.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/__pycache__
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core
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__/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__/selection.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/__pycache__/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__/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__/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__
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/__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/element.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/residue_names.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/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/topology.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/trajectory.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/dtr.cpython-313-aarch64-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/dcd.cpython-313-aarch64-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/trr.cpython-313-aarch64-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/xtc.cpython-313-aarch64-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__/openmmxml.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/psf.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/gro.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/__pycache__/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__/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__/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__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__pycache__
creating /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/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
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/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/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/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/gsd.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/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/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/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/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/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/mol2.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/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/openmmxml.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/formats/pdbx.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
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/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/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/xyzfile.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/neighborlist.cpython-313-aarch64-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/neighbors.cpython-313-aarch64-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/drid.cpython-313-aarch64-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-aarch64-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/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/__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/__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/alignment.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/angle.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/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/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/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/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/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/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/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/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/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/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/shape.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/thermodynamic_properties.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/nmr
creating /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/__pycache__/shift_wrappers.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/__pycache__/scalar_couplings.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/nmr/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/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/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__/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__/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__/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__/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__/__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/__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/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/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/hdf5reporter.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/reporters/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/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/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/__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
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/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__/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__/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__/__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/__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
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/testing/testing.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/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__/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__/zipped.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/unitcell.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/__pycache__/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__/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__/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__/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__/__init__.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__pycache__
creating /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__/quantity.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/unit_operators.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/basedimension.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/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__/mymatrix.cpython-313.pyc -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__pycache__
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/__pycache__/unit.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__/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__/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__/__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/__init__.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/mymatrix.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/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/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/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/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/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/basedimension.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/baseunit.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/unit/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.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/__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/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/delay_import.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/rotation.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/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/unitcell.py -> /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils
copying /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/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/__init__.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/_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
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/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/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/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/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/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/__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/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/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/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/gsd.py to gsd.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/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/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/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/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/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/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/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/openmmxml.py to openmmxml.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx.py to pdbx.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/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/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/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/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/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/alignment.py to alignment.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/angle.py to angle.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/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/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/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/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/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/internal.py to internal.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/order.py to order.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/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/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/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/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/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/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/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/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/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/hdf5reporter.py to hdf5reporter.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/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/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/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/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/docstrings.py to docstrings.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/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/utils/unit/__init__.py to __init__.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/mymatrix.py to mymatrix.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/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/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/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/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/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/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/baseunit.py to baseunit.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/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.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/__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/contextmanagers.py to contextmanagers.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/delay_import.py to delay_import.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/rotation.py to rotation.cpython-313.pyc
byte-compiling /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/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/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/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/__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/_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
running install_egg_info
running egg_info
writing mdtraj.egg-info/PKG-INFO
writing dependency_links to mdtraj.egg-info/dependency_links.txt
writing entry points to mdtraj.egg-info/entry_points.txt
writing requirements to mdtraj.egg-info/requires.txt
writing top-level names to mdtraj.egg-info/top_level.txt
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
dependency /usr/lib/python3/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
reading manifest file 'mdtraj.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
no previously-included directories found matching '__pycache__'
no previously-included directories found matching '*.pyc'
adding license file 'LICENSE'
writing manifest file 'mdtraj.egg-info/SOURCES.txt'
Copying mdtraj.egg-info to /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj-1.10.3.egg-info
Skipping SOURCES.txt
running install_scripts
Installing mdconvert-mdtraj script to /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/bin
Installing mdinspect script to /build/reproducible-path/mdtraj-1.10.3/debian/python3-mdtraj/usr/bin
   debian/rules execute_after_dh_auto_install-indep
make[1]: Entering directory '/build/reproducible-path/mdtraj-1.10.3'
cp -a /build/reproducible-path/mdtraj-1.10.3/examples /build/reproducible-path/mdtraj-1.10.3/examples.orig
mkdir -p /build/reproducible-path/mdtraj-1.10.3/build/html/examples/iterload
ln -s /build/reproducible-path/mdtraj-1.10.3/examples/data /build/reproducible-path/mdtraj-1.10.3/build/html/examples/iterload/data
sed "s|http://www.rcsb.org/pdb/files|/build/reproducible-path/mdtraj-1.10.3/debian/external|g" -i /build/reproducible-path/mdtraj-1.10.3/examples/*.ipynb
PYTHONPATH=/build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build \
    MPLCONFIGDIR=/build/reproducible-path/mdtraj-1.10.3/build/matplotlib \
	make -C docs BUILDDIR=/build/reproducible-path/mdtraj-1.10.3/build  html
make[2]: Entering directory '/build/reproducible-path/mdtraj-1.10.3/docs'
sphinx-build -b html -d /build/reproducible-path/mdtraj-1.10.3/build/doctrees   . /build/reproducible-path/mdtraj-1.10.3/build/html
Running Sphinx v8.1.3
WARNING: Calling get_html_theme_path is deprecated. If you are calling it to define html_theme_path, you are safe to remove that code.
loading translations [en]... done
Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`.
[autosummary] generating autosummary for: analysis.rst, api/reporters.rst, api/trajectory_files.rst, api/utils.rst, atom_selection.rst, building_docs.rst, examples/atom-selection.rst, examples/centroids.rst, examples/clustering.rst, examples/hbonds.rst, ..., notebook-examples/iterload.nblink, notebook-examples/native-contact.nblink, notebook-examples/openmm.nblink, notebook-examples/pca.nblink, notebook-examples/ramachandran-plot.nblink, notebook-examples/rmsd-benchmark.nblink, notebook-examples/rmsd-drift.nblink, notebook-examples/solvent-accessible-surface-area.nblink, notebook-examples/two-pass-clustering.nblink, whatsnew.rst
[autosummary] generating autosummary for: /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.Topology.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.Trajectory.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.Trajectory.superpose.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.acylindricity.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.asphericity.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.baker_hubbard.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.chemical_shifts_ppm.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.chemical_shifts_shiftx2.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.chemical_shifts_spartaplus.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.compute_J3_HN_C.rst, ..., /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.utils.check_random_state.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.utils.ensure_type.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.utils.ilen.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.utils.import_.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.utils.in_units_of.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.utils.rotation_matrix_from_quaternion.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.utils.timing.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.utils.uniform_quaternion.rst, /build/reproducible-path/mdtraj-1.10.3/docs/api/generated/mdtraj.wernet_nilsson.rst
Writing evaluated template result to /build/reproducible-path/mdtraj-1.10.3/build/html/_static/nbsphinx-code-cells.css
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 44 source files that are out of date
updating environment: [new config] 140 added, 0 changed, 0 removed
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/usr/lib/python3/dist-packages/numpydoc/docscrape.py:203: UserWarning: potentially wrong underline length... 
Returns 
---------- in 
Get the indices of biologically-relevant groups by name.
... in the docstring of select_atom_indices in /build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/core/topology.py.
  while not self._is_at_section() and not self._doc.eof():
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/build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.asphericity:9: WARNING: Explicit markup ends without a blank line; unexpected unindent. [docutils]
/build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/contact.py:docstring of mdtraj.geometry.contact.compute_contacts:33: ERROR: Unexpected indentation. [docutils]
docstring of mdtraj.formats.dtr.load_dtr:7: ERROR: Unexpected indentation. [docutils]
/build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:9: WARNING: Explicit markup ends without a blank line; unexpected unindent. [docutils]
/build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:11: ERROR: Unexpected indentation. [docutils]
/build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:12: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:14: WARNING: Definition list ends without a blank line; unexpected unindent. [docutils]
/build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/geometry/shape.py:docstring of mdtraj.geometry.shape.relative_shape_anisotropy:15: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/build/reproducible-path/mdtraj-1.10.3/.pybuild/cpython3_3.13_mdtraj/build/mdtraj/utils/rotation.py:docstring of mdtraj.utils.rotation.uniform_quaternion:39: ERROR: Error in "rubric" directive:
no content permitted.

.. rubric:: References

 .. [R17e8d31e726c-1] K. Shoemake. Uniform random rotations. In D. Kirk, editor, Graphics
    Gems III, pages 124-132. Academic, New York, 1992.
 .. [R17e8d31e726c-2] http://planning.cs.uiuc.edu/node198.html [docutils]
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	install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples/data
	cp --reflink=auto -a ./debian/external/2EQQ.pdb ./debian/external/2MI7.pdb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples/data/
	install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doi-10.1016_j.bpj.2015.08.015-blue.svg
	cp --reflink=auto -a ./debian/external/doi-10.1016_j.bpj.2015.08.015-blue.svg debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doi-10.1016_j.bpj.2015.08.015-blue.svg/
   dh_installdocs -O--buildsystem=pybuild
dh_installdocs: warning: Cannot auto-detect main package for python-mdtraj-doc.  If the default is wrong, please use --doc-main-package
	install -m0755 -d debian/python3-mdtraj/usr/share/doc/python3-mdtraj
	install -p -m0644 debian/copyright debian/python3-mdtraj/usr/share/doc/python3-mdtraj/copyright
	install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc
	cd './build/html/..' && find 'html' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/mdtraj-1.10.3/debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc
	cp --reflink=auto -a ./README.md debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc
	chmod -R u\+rw,go=rX debian/python-mdtraj-doc/usr/share/doc
	install -p -m0644 debian/copyright debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/copyright
	install -m0755 -d debian/python-mdtraj-doc/usr/share/doc-base/
	install -p -m0644 debian/python-mdtraj-doc.doc-base debian/python-mdtraj-doc/usr/share/doc-base/python-mdtraj-doc.mdtraj
   debian/rules override_dh_sphinxdoc-indep
make[1]: Entering directory '/build/reproducible-path/mdtraj-1.10.3'
dh_sphinxdoc -i
	ln -sf ../../../../../sphinx_rtd_theme/static/js/theme.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/js/theme.js
	ln -sf ../../../../../sphinx_rtd_theme/static/fonts/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.woff debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff
	ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.ttf
	ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.svg debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.svg
	ln -sf ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.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.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.ttf
	ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Italic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.ttf
	ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf
	ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.ttf
	ln -sf ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Regular.woff2
	ln -sf ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Bold.woff2
	ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.woff2
	ln -sf ../../../../../sphinx_rtd_theme/static/fonts/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/Lato-BoldItalic.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.woff2
	ln -sf ../../../../../sphinx_rtd_theme/static/fonts/Lato-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.woff2
	ln -sf ../../../../../sphinx_rtd_theme/static/css/theme.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css
	ln -sf ../../../../../sphinx_rtd_theme/static/css/badge_only.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css
	ln -sf ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/sphinx_highlight.js
	ln -sf ../../../../javascript/sphinxdoc/1.0/language_data.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/language_data.js
	ln -sf ../../../../javascript/sphinxdoc/1.0/doctools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js
	ln -sf ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/searchtools.js
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/.buildinfo
	mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars
	mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars
	mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars
	mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars
	mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars
	mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars
sed "s|src=\"https://img.shields.io/badge/DOI-10.1016%2Fj.bpj.2015.08.015-blue.svg\"|src=\"_static/doi-10.1016_j.bpj.2015.08.015-blue.svg\"|g" -i debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/index.html
make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.10.3'
   dh_sphinxdoc -O--buildsystem=pybuild -Npython-mdtraj-doc
dh_sphinxdoc: warning: Sphinx documentation not found
   dh_installchangelogs -O--buildsystem=pybuild
	install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc
	install -p -m0644 debian/.debhelper/generated/python-mdtraj-doc/dh_installchangelogs.dch.trimmed debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/changelog.Debian
	install -m0755 -d debian/python3-mdtraj/usr/share/doc/python3-mdtraj
	install -p -m0644 debian/.debhelper/generated/python3-mdtraj/dh_installchangelogs.dch.trimmed debian/python3-mdtraj/usr/share/doc/python3-mdtraj/changelog.Debian
   dh_installexamples -O--buildsystem=pybuild
dh_installexamples: warning: Cannot auto-detect main package for python-mdtraj-doc.  If the default is wrong, please use --doc-main-package
	install -m0755 -d debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/1vii_3frames.pdb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/ala2.h5 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/atom-selection.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/centroids.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/clustering.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/data debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/hbonds.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/iterload.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/native-contact.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/nmr.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/principal-components.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/ramachandran-plot.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/rmsd-benchmark.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/rmsd-drift.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/simulation-with-openmm.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/solvent-accessible-surface-area.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/test_examples.py debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
	cp --reflink=auto -a ./examples/two-pass-clustering.ipynb debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/examples
   dh_installman -O--buildsystem=pybuild
	install -m0755 -d debian/python3-mdtraj/usr/share/man/man1/
	install -p -m0644 ./debian/mdconvert-mdtraj.1 debian/python3-mdtraj/usr/share/man/man1/mdconvert-mdtraj.1
	install -m0755 -d debian/python3-mdtraj/usr/share/man/man1/
	install -p -m0644 ./debian/mdinspect.1 debian/python3-mdtraj/usr/share/man/man1/mdinspect.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/python3-mdtraj/usr/share/man/man1/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: 6.20250108
D: dh_python3 dh_python3:181: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild']
D: dh_python3 dh_python3:182: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=['--buildsystem=pybuild'])
D: dh_python3 dh_python3:183: supported Python versions: 3.12,3.13 (default=3.13)
D: dh_python3 debhelper:166: skipping package python-mdtraj-doc (missing ${python3:Depends} in Depends/Recommends)
D: dh_python3 debhelper:174: source=mdtraj, binary packages=['python3-mdtraj']
D: dh_python3 dh_python3:205: processing package python3-mdtraj...
D: dh_python3 fs:50: moving files from debian/python3-mdtraj/usr/lib/python3.12/dist-packages to debian/python3-mdtraj/usr/lib/python3/dist-packages/
D: dh_python3 fs:50: moving files from debian/python3-mdtraj/usr/lib/python3.13/dist-packages to debian/python3-mdtraj/usr/lib/python3/dist-packages/
D: dh_python3 fs:338: package python3-mdtraj details = {'requires.txt': {'debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.10.3.egg-info/requires.txt'}, 'egg-info': {'debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj-1.10.3.egg-info/PKG-INFO'}, 'dist-info': set(), 'nsp.txt': set(), 'shebangs': {/usr/bin/python3, /usr/bin/python3}, 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': {Version('3.12'), Version('3.13')}, 'ext_no_version': set()}
D: dh_python3 depends:103: generating dependencies for package python3-mdtraj
D: dh_python3 pydist:175: trying to find dependency for netCDF4 (python=None)
D: dh_python3 pydist:209: dependency: module seems to be installed
D: dh_python3 pydist:284: dependency: included in build-deps
D: dh_python3 pydist:175: trying to find dependency for numpy<3,>=1.25.0 (python=None)
D: dh_python3 pydist:209: dependency: module seems to be installed
D: dh_python3 pydist:284: dependency: included in build-deps
D: dh_python3 pydist:175: trying to find dependency for packaging (python=None)
D: dh_python3 pydist:209: dependency: module seems to be installed
D: dh_python3 pydist:284: dependency: included in build-deps
D: dh_python3 pydist:175: trying to find dependency for pyparsing (python=None)
D: dh_python3 pydist:209: dependency: module seems to be installed
D: dh_python3 pydist:284: dependency: included in build-deps
D: dh_python3 pydist:175: trying to find dependency for scipy (python=None)
D: dh_python3 pydist:209: dependency: module seems to be installed
D: dh_python3 pydist:284: dependency: included in build-deps
D: dh_python3 depends:253: D={'python3:any', 'python3-scipy', 'python3-pyparsing', 'python3-packaging', 'python3-numpy', 'python3 (>= 3.12~)', 'python3 (<< 3.14)', 'python3-netcdf4'}; R=[]; S=[]; E=[], B=[]; RT=[]
	rm -f debian/python-mdtraj-doc.debhelper.log
   debian/rules execute_after_dh_python3
make[1]: Entering directory '/build/reproducible-path/mdtraj-1.10.3'
dh_numpy3
	mv debian/python3-mdtraj.substvars.new debian/python3-mdtraj.substvars
	mv debian/python-mdtraj-doc.substvars.new debian/python-mdtraj-doc.substvars
# setup.py builds the static lib libtheobald.a for each python version
# but dh_python3 can't tell the difference between the different builds,
# since py3.11 compiles libtheobald.o with -fwrapv, where py3.12 uses -fno-strict-overflow
# So clean up manually (assume the binary difference is not an issue)
rm -f debian/python3-mdtraj/usr/lib/python3.*/dist-packages/mdtraj/core/lib/libtheobald.a
for d in debian/python3-mdtraj/usr/lib/python3.*/dist-packages/mdtraj/core/lib; do if [-d $d]; then rmdir -p --ignore-fail-on-non-empty $d; fi; done
/bin/sh: 1: [-d: not found
make[1]: Leaving directory '/build/reproducible-path/mdtraj-1.10.3'
   dh_installsystemduser -O--buildsystem=pybuild
   dh_perl -O--buildsystem=pybuild
   dh_link -O--buildsystem=pybuild
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css
	ln -s ../../../../../sphinx_rtd_theme/static/css/theme.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/theme.css
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css
	ln -s ../../../../../sphinx_rtd_theme/static/css/badge_only.css debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/css/badge_only.css
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff2
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff2
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.woff debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.woff
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.ttf
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.ttf
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.svg
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.svg debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.svg
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.eot
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/fontawesome-webfont.eot debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/fontawesome-webfont.eot
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.ttf
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.ttf
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Italic.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.ttf
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-BoldItalic.ttf debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-BoldItalic.ttf
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Bold.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/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/RobotoSlab-Bold.woff2
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/RobotoSlab-Bold.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/RobotoSlab-Bold.woff2
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.woff2
	ln -s ../../../../../sphinx_rtd_theme/static/fonts/Lato-Regular.woff2 debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-Regular.woff2
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/fonts/Lato-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-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/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/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/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/language_data.js
	ln -s ../../../../javascript/sphinxdoc/1.0/language_data.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/language_data.js
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js
	ln -s ../../../../javascript/sphinxdoc/1.0/doctools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/doctools.js
	rm -f debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/searchtools.js
	ln -s ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/searchtools.js
   dh_strip_nondeterminism -O--buildsystem=pybuild
	Using 1739273589 as canonical time
	Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_native-contact_6_0.png using File::StripNondeterminism::handlers::png
	Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_hbonds_9_1.png using File::StripNondeterminism::handlers::png
	Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/file.png using File::StripNondeterminism::handlers::png
	Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_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_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_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_clustering_11_0.png using File::StripNondeterminism::handlers::png
	Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_static/plus.png using File::StripNondeterminism::handlers::png
	Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_pca_9_0.png using File::StripNondeterminism::handlers::png
	Normalizing debian/python-mdtraj-doc/usr/share/doc/python-mdtraj-doc/html/_images/notebook-examples_pca_12_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/_static/mdtraj_logo-small.png using File::StripNondeterminism::handlers::png
   dh_compress -O--buildsystem=pybuild
	cd debian/python-mdtraj-doc
	cd debian/python3-mdtraj
	chmod a-x usr/share/doc/python3-mdtraj/changelog.Debian usr/share/man/man1/mdconvert-mdtraj.1 usr/share/man/man1/mdinspect.1
	chmod a-x usr/share/doc/python-mdtraj-doc/changelog.Debian usr/share/doc/python-mdtraj-doc/html/_static/example-trajectoryview-data.json usr/share/doc/python-mdtraj-doc/html/_static/mdtraj_logo.xcf usr/share/doc/python-mdtraj-doc/html/notebook-examples/atom-selection.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/clustering.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/hbonds.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/iterload.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/native-contact.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/openmm.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/pca.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/ramachandran-plot.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/rmsd-benchmark.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/rmsd-drift.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/solvent-accessible-surface-area.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/two-pass-clustering.ipynb
	gzip -9nf usr/share/doc/python3-mdtraj/changelog.Debian usr/share/man/man1/mdconvert-mdtraj.1 usr/share/man/man1/mdinspect.1
	gzip -9nf usr/share/doc/python-mdtraj-doc/changelog.Debian usr/share/doc/python-mdtraj-doc/html/_static/example-trajectoryview-data.json usr/share/doc/python-mdtraj-doc/html/_static/mdtraj_logo.xcf usr/share/doc/python-mdtraj-doc/html/notebook-examples/atom-selection.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/clustering.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/hbonds.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/iterload.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/native-contact.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/openmm.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/pca.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/ramachandran-plot.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/rmsd-benchmark.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/rmsd-drift.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/solvent-accessible-surface-area.ipynb usr/share/doc/python-mdtraj-doc/html/notebook-examples/two-pass-clustering.ipynb
	cd '/build/reproducible-path/mdtraj-1.10.3'
	cd '/build/reproducible-path/mdtraj-1.10.3'
   dh_fixperms -O--buildsystem=pybuild
	find debian/python3-mdtraj ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/python-mdtraj-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/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 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 d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	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 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/python3-mdtraj -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/python3-mdtraj/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
	find debian/python3-mdtraj/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
   dh_missing -O--buildsystem=pybuild
   dh_dwz -a -O--buildsystem=pybuild
	install -m0755 -d debian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-linux-gnu
	dwz -mdebian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-linux-gnu/python3-mdtraj.debug -M/usr/lib/debug/.dwz/aarch64-linux-gnu/python3-mdtraj.debug -- debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so
	objcopy --compress-debug-sections debian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-linux-gnu/python3-mdtraj.debug
	chmod 0644 -- debian/python3-mdtraj/usr/lib/debug/.dwz/aarch64-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/1f
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/1f/d844929cffcb3aaf8b98910c2b549f4ddd3412.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/1f/d844929cffcb3aaf8b98910c2b549f4ddd3412.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/1f/d844929cffcb3aaf8b98910c2b549f4ddd3412.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a9
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a9/d711ce8fd6562b4b2cd64aa30bc668208e09d1.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a9/d711ce8fd6562b4b2cd64aa30bc668208e09d1.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a9/d711ce8fd6562b4b2cd64aa30bc668208e09d1.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/2c
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/2c/6e9fb95a64bc1878a3162daf724cc337b296d9.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/2c/6e9fb95a64bc1878a3162daf724cc337b296d9.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/2c/6e9fb95a64bc1878a3162daf724cc337b296d9.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/2e
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/2e/37e12e251519e11d7305555bfe3484a60a0b11.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/2e/37e12e251519e11d7305555bfe3484a60a0b11.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/2e/37e12e251519e11d7305555bfe3484a60a0b11.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/61
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/61/e5d9b85439a158dbe1a41711f329966c092c2c.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/61/e5d9b85439a158dbe1a41711f329966c092c2c.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/61/e5d9b85439a158dbe1a41711f329966c092c2c.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/18
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/18/013191355b7a7e4bacf2d5285b9760c3b77cce.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/18/013191355b7a7e4bacf2d5285b9760c3b77cce.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/18/013191355b7a7e4bacf2d5285b9760c3b77cce.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/1b
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/1b/479427c74295dcafb212fc53927bea051021e3.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/1b/479427c74295dcafb212fc53927bea051021e3.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/1b/479427c74295dcafb212fc53927bea051021e3.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a1
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a1/0ff124bf6add939373aa074a0c9fa4a43cd7eb.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a1/0ff124bf6add939373aa074a0c9fa4a43cd7eb.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/a1/0ff124bf6add939373aa074a0c9fa4a43cd7eb.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/fa
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/fa/8daa1ba86795cd161c10bb44b87fe57fc300ea.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/fa/8daa1ba86795cd161c10bb44b87fe57fc300ea.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/fa/8daa1ba86795cd161c10bb44b87fe57fc300ea.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6f
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6f/67af01e0870aa4de7ee5eb3e1e4384fd4029ff.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6f/67af01e0870aa4de7ee5eb3e1e4384fd4029ff.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/6f/67af01e0870aa4de7ee5eb3e1e4384fd4029ff.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/91
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/91/c51e365b59757fa99363fdf816e7cb84ba15c2.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/91/c51e365b59757fa99363fdf816e7cb84ba15c2.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/91/c51e365b59757fa99363fdf816e7cb84ba15c2.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4f
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4f/cd95fb781c2c2cc40594f40a730623edadd534.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4f/cd95fb781c2c2cc40594f40a730623edadd534.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/4f/cd95fb781c2c2cc40594f40a730623edadd534.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/60
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/60/e18d7aee6d1b8fbc4a25bba06cae3293e002f6.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/60/e18d7aee6d1b8fbc4a25bba06cae3293e002f6.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/60/e18d7aee6d1b8fbc4a25bba06cae3293e002f6.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/33
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/33/d6cc1211b74f960234c81b57949779cba88bb5.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/33/d6cc1211b74f960234c81b57949779cba88bb5.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/33/d6cc1211b74f960234c81b57949779cba88bb5.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/5e
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/5e/6b5bca7434d511600b184d79f4833ec5dd84e7.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/5e/6b5bca7434d511600b184d79f4833ec5dd84e7.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/5e/6b5bca7434d511600b184d79f4833ec5dd84e7.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/cb
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/cb/6c7d811af2bbe2191755fdf2ea6b29d25b6c05.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/cb/6c7d811af2bbe2191755fdf2ea6b29d25b6c05.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/cb/6c7d811af2bbe2191755fdf2ea6b29d25b6c05.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/24
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/24/19603f5de9b2402c19622ed0d2797123e31096.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/24/19603f5de9b2402c19622ed0d2797123e31096.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/24/19603f5de9b2402c19622ed0d2797123e31096.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/55
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/55/68b9b95ba40b9d533eb050eb36388492a1774f.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/55/68b9b95ba40b9d533eb050eb36388492a1774f.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/55/68b9b95ba40b9d533eb050eb36388492a1774f.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/12
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/12/74786013583b3d1a292b4547fd6bb6bf4b19ec.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/12/74786013583b3d1a292b4547fd6bb6bf4b19ec.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/12/74786013583b3d1a292b4547fd6bb6bf4b19ec.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e8
	objcopy --only-keep-debug --compress-debug-sections debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e8/7d0f4604bd431796eff71c45e45406943dc6ed.debug
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e8/7d0f4604bd431796eff71c45e45406943dc6ed.debug
	strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so
	objcopy --add-gnu-debuglink debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.build-id/e8/7d0f4604bd431796eff71c45e45406943dc6ed.debug debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-aarch64-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/aarch64-linux-gnu debian/.debhelper/python3-mdtraj/dbgsym-root/usr/lib/debug/.dwz
	rm -fr debian/python3-mdtraj/usr/lib/debug/.dwz
	rmdir -p --ignore-fail-on-non-empty debian/python3-mdtraj/usr/lib/debug
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/usr/share/doc
	ln -s python3-mdtraj debian/.debhelper/python3-mdtraj/dbgsym-root/usr/share/doc/python3-mdtraj-dbgsym
	install -m0755 -d debian/.debhelper/python3-mdtraj
   dh_makeshlibs -a -O--buildsystem=pybuild
	rm -f debian/python3-mdtraj/DEBIAN/shlibs
   dh_shlibdeps -a -O--buildsystem=pybuild
	install -m0755 -d debian/python3-mdtraj/DEBIAN
	dpkg-shlibdeps -Tdebian/python3-mdtraj.substvars debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_rmsd.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/_lprmsd.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dtr.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/xtc.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/trr.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/formats/dcd.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighbors.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/_geometry.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-312-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/neighborlist.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-313-aarch64-linux-gnu.so debian/python3-mdtraj/usr/lib/python3/dist-packages/mdtraj/geometry/drid.cpython-312-aarch64-linux-gnu.so
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
   dh_installdeb -O--buildsystem=pybuild
	install -m0755 -d debian/python3-mdtraj/DEBIAN
	printf '#!/bin/sh\nset -e\n' > debian/python3-mdtraj/DEBIAN/postinst
	cat debian/python3-mdtraj.postinst.debhelper >> debian/python3-mdtraj/DEBIAN/postinst
	chmod 0755 -- debian/python3-mdtraj/DEBIAN/postinst
	printf '#!/bin/sh\nset -e\n' > debian/python3-mdtraj/DEBIAN/prerm
	cat debian/python3-mdtraj.prerm.debhelper >> debian/python3-mdtraj/DEBIAN/prerm
	chmod 0755 -- debian/python3-mdtraj/DEBIAN/prerm
	install -m0755 -d debian/python-mdtraj-doc/DEBIAN
   dh_gencontrol -O--buildsystem=pybuild
	install -m0755 -d debian/python3-mdtraj/DEBIAN
	echo misc:Depends= >> debian/python3-mdtraj.substvars
	echo misc:Pre-Depends= >> debian/python3-mdtraj.substvars
	install -m0755 -d debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN
	dpkg-gencontrol -ppython3-mdtraj -ldebian/changelog -Tdebian/python3-mdtraj.substvars -cdebian/control -Pdebian/.debhelper/python3-mdtraj/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=python3-mdtraj-dbgsym "-DDepends=python3-mdtraj (= \${binary:Version})" "-DDescription=debug symbols for python3-mdtraj" "-DBuild-Ids=1274786013583b3d1a292b4547fd6bb6bf4b19ec 18013191355b7a7e4bacf2d5285b9760c3b77cce 1b479427c74295dcafb212fc53927bea051021e3 1fd844929cffcb3aaf8b98910c2b549f4ddd3412 2419603f5de9b2402c19622ed0d2797123e31096 2c6e9fb95a64bc1878a3162daf724cc337b296d9 2e37e12e251519e11d7305555bfe3484a60a0b11 33d6cc1211b74f960234c81b57949779cba88bb5 4fcd95fb781c2c2cc40594f40a730623edadd534 5568b9b95ba40b9d533eb050eb36388492a1774f 5e6b5bca7434d511600b184d79f4833ec5dd84e7 60e18d7aee6d1b8fbc4a25bba06cae3293e002f6 61e5d9b85439a158dbe1a41711f329966c092c2c 6f67af01e0870aa4de7ee5eb3e1e4384fd4029ff 91c51e365b59757fa99363fdf816e7cb84ba15c2 a10ff124bf6add939373aa074a0c9fa4a43cd7eb a9d711ce8fd6562b4b2cd64aa30bc668208e09d1 cb6c7d811af2bbe2191755fdf2ea6b29d25b6c05 e87d0f4604bd431796eff71c45e45406943dc6ed fa8daa1ba86795cd161c10bb44b87fe57fc300ea" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
	install -m0755 -d debian/python-mdtraj-doc/DEBIAN
	echo misc:Depends= >> debian/python-mdtraj-doc.substvars
	echo misc:Pre-Depends= >> debian/python-mdtraj-doc.substvars
	dpkg-gencontrol -ppython-mdtraj-doc -ldebian/changelog -Tdebian/python-mdtraj-doc.substvars -cdebian/control -Pdebian/python-mdtraj-doc
dpkg-gencontrol: warning: package python-mdtraj-doc: substitution variable ${python3:Depends} unused, but is defined
dpkg-gencontrol: warning: package python-mdtraj-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined
	chmod 0644 -- debian/.debhelper/python3-mdtraj/dbgsym-root/DEBIAN/control
	dpkg-gencontrol -ppython3-mdtraj -ldebian/changelog -Tdebian/python3-mdtraj.substvars -cdebian/control -Pdebian/python3-mdtraj
	chmod 0644 -- debian/python-mdtraj-doc/DEBIAN/control
	chmod 0644 -- debian/python3-mdtraj/DEBIAN/control
   dh_md5sums -O--buildsystem=pybuild
	install -m0755 -d debian/python3-mdtraj/DEBIAN
	cd debian/python3-mdtraj >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	install -m0755 -d debian/python-mdtraj-doc/DEBIAN
	cd debian/python-mdtraj-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/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/python3-mdtraj ..
	dpkg-deb --root-owner-group --build debian/python-mdtraj-doc ..
	dpkg-deb --root-owner-group --build debian/.debhelper/python3-mdtraj/dbgsym-root ..
dpkg-deb: building package 'python3-mdtraj-dbgsym' in '../python3-mdtraj-dbgsym_1.10.3-2_arm64.deb'.
dpkg-deb: building package 'python-mdtraj-doc' in '../python-mdtraj-doc_1.10.3-2_all.deb'.
dpkg-deb: building package 'python3-mdtraj' in '../python3-mdtraj_1.10.3-2_arm64.deb'.
 dpkg-genbuildinfo --build=binary -O../mdtraj_1.10.3-2_arm64.buildinfo
 dpkg-genchanges --build=binary -O../mdtraj_1.10.3-2_arm64.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/1325680 and its subdirectories
I: Current time: Fri Mar 20 02:17:51 -12 2026
I: pbuilder-time-stamp: 1774016271
Sat Feb 15 07:54:54 UTC 2025  I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net.
Sat Feb 15 07:54:54 UTC 2025  I: Preparing to do remote build '2' on codethink04-arm64.debian.net.
Sat Feb 15 08:17:15 UTC 2025  I: Deleting $TMPDIR on codethink04-arm64.debian.net.
Sat Feb 15 08:17:16 UTC 2025  I: mdtraj_1.10.3-2_arm64.changes:
Format: 1.8
Date: Tue, 11 Feb 2025 12:33:09 +0100
Source: mdtraj
Binary: python-mdtraj-doc python3-mdtraj python3-mdtraj-dbgsym
Architecture: all arm64
Version: 1.10.3-2
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Changed-By: Drew Parsons <dparsons@debian.org>
Description:
 python-mdtraj-doc - Read, write and analyze MD trajectories in Python (documentation)
 python3-mdtraj - Read, write and analyze MD trajectories in Python
Changes:
 mdtraj (1.10.3-2) unstable; urgency=medium
 .
   * move pandoc to Build-Depends-Indep (for doc build)
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 8f8a48e30a0d5cbcacf62fdfdff5403d1b0642f0 1324592 python3-mdtraj_1.10.3-2_arm64.deb
Checksums-Sha256:
 c957b277c0a8506dd30511c29022ca64aa155be49991a4b13b0994ca45a5e2b0 14162 mdtraj_1.10.3-2_arm64.buildinfo
 a8bcc3f62836e43fb2dbf0c61972519460f72806f752dfce8f0aaca2d39fd86e 1869916 python-mdtraj-doc_1.10.3-2_all.deb
 cd5656c1d6d3d5f927a17e696c0c1f25532bb3e9a906c3d11b72978235f5bfa0 10754216 python3-mdtraj-dbgsym_1.10.3-2_arm64.deb
 00f3450d1aa286957ce010478bd377863aa621868cf0099609dae849897e6389 1324592 python3-mdtraj_1.10.3-2_arm64.deb
Files:
 fcf3a1627a96d1035a0002df0f029eaf 14162 python optional mdtraj_1.10.3-2_arm64.buildinfo
 3938d0dd0ed50484408b899c0013b0aa 1869916 doc optional python-mdtraj-doc_1.10.3-2_all.deb
 d87313073ef2888cf92ff773d4509470 10754216 debug optional python3-mdtraj-dbgsym_1.10.3-2_arm64.deb
 8575dd8f847618229b875b603b6052e3 1324592 python optional python3-mdtraj_1.10.3-2_arm64.deb
Sat Feb 15 08:17:17 UTC 2025  I: diffoscope 288 will be used to compare the two builds:
Running as unit: rb-diffoscope-arm64_1-60357.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.7tctVdzV/mdtraj_1.10.3-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.7tctVdzV/mdtraj_1.10.3-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.7tctVdzV/mdtraj_1.10.3-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.7tctVdzV/b1/mdtraj_1.10.3-2_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.7tctVdzV/b2/mdtraj_1.10.3-2_arm64.changes

## command (total time: 0.000s)
       0.000s      1 call     cmp (internal)

## has_same_content_as (total time: 0.000s)
       0.000s      1 call     diffoscope.comparators.binary.FilesystemFile

## main (total time: 0.004s)
       0.004s      2 calls    outputs
       0.000s      1 call     cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 228ms
CPU time consumed: 229ms
Sat Feb 15 08:17:28 UTC 2025  I: diffoscope 288 found no differences in the changes files, and a .buildinfo file also exists.
Sat Feb 15 08:17:28 UTC 2025  I: mdtraj from trixie built successfully and reproducibly on arm64.
Sat Feb 15 08:17:29 UTC 2025  I: Submitting .buildinfo files to external archives:
Sat Feb 15 08:17:29 UTC 2025  I: Submitting 16K	b1/mdtraj_1.10.3-2_arm64.buildinfo.asc
Sat Feb 15 08:17:30 UTC 2025  I: Submitting 16K	b2/mdtraj_1.10.3-2_arm64.buildinfo.asc
Sat Feb 15 08:17:31 UTC 2025  I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sat Feb 15 08:17:31 UTC 2025  I: Done submitting .buildinfo files.
Sat Feb 15 08:17:31 UTC 2025  I: Removing signed mdtraj_1.10.3-2_arm64.buildinfo.asc files:
removed './b1/mdtraj_1.10.3-2_arm64.buildinfo.asc'
removed './b2/mdtraj_1.10.3-2_arm64.buildinfo.asc'